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Kingma, E. (author)All living systems possess the ability to evolve. This ability has allowed life to adopt a large diversity of shapes, colors, sizes and lifestyles. However, despite being a fundamental property of life, our knowledge of what makes living systems evolvable is limited. The fact that evolution can be sometimes be hopelessly unpredictable while in...doctoral thesis 2023
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Koster, C.C. (author)Building synthetic cells is extremely interesting from a fundamental perspective, as the ability to rationally build viable, dividing, and self-maintaining cells provides knowledge on the minimal requirements to sustain life. This should enhance our understanding about which biological parts are minimally required for a cell to live, and how...doctoral thesis 2023
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den Ridder, M.J. (author)Mass spectrometry-based cellular proteomics has taken a prominent role in many fields of research, including life sciences, biotechnology and microbial ecology. Still, advanced mass spectrometry-based proteomics methods are not routinely applied to microbes. The cell factory and model organism Saccharomyces cerevisiae, for example, is very well...doctoral thesis 2023
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den Ridder, M.J. (author), van den Brandeler, Wiebeke (author), Altiner, Meryem (author), Daran-Lapujade, P.A.S. (author), Pabst, Martin (author)The yeast Saccharomyces cerevisiae is a widely-used eukaryotic model organism and a promising cell factory for industry. However, despite decades of research, the regulation of its metabolism is not yet fully understood, and its complexity represents a major challenge for engineering and optimizing biosynthetic routes. Recent studies have...journal article 2023
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Koster, C.C. (author), Kleefeldt, Askar A. (author), van den Broek, M.A. (author), Luttik, M.A.H. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)Mitochondria fulfil many essential roles and have their own genome, which is expressed as polycistronic transcripts that undergo co- or posttranscriptional processing and splicing. Due to the inherent complexity and limited technical accessibility of the mitochondrial transcriptome, fundamental questions regarding mitochondrial gene...journal article 2023
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Glazenburg, M.M. (author), Laan, L. (author)Cellular life exhibits order and complexity, which typically increase over the course of evolution. Cell polarization is a well-studied example of an ordering process that breaks the internal symmetry of a cell by establishing a preferential axis. Like many cellular processes, polarization is driven by self-organization, meaning that the...review 2023
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Daalman, W.K. (author), Sweep, E. (author), Laan, L. (author)Accurate phenotype prediction based on genetic information has numerous societal applications, such as crop design or cellular factories. Epistasis, when biological components interact, complicates modelling phenotypes from genotypes. Here we show an approach to mitigate this complication for polarity establishment in budding yeast, where...journal article 2023
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Maire, T.T.H. (author)While life is present everywhere on earth, each individual species can only grow and proliferate in a specific set of conditions. Moreover due to inherent fluctuation of the environment, individual organisms are often periodically confronted to stressful conditions that prohibit growth, reproduction and increase mortality. One of the most common...doctoral thesis 2022
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Laman Trip, J.D.S. (author)Open questions are whether life can be enabled in uninhabitable environments, and whether there is a limit to howmuch one can tune the speed of proliferation. Answering such questions has broad implications. It may reveal whether we can live in unforeseen habitats, whether we can slow down aging, and whether there are limits to lifespan. In this...doctoral thesis 2022
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Lip, K.Y.F. (author)Saccharomyces yeasts are common workhorses for the production of alcoholic beverage and bio-ethanol. In these production processes, temperature is one of the predominant factors determining the operational costs of the industrial fermentation processes and the quality of the products (alcoholic beverage) because it influences the functioning of...doctoral thesis 2022
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Gyurchev, Nikola Y. (author), Coral-Medina, Ángela (author), Weening, S.M. (author), Almayouf, Salwa (author), Kuijpers, Niels G.A. (author), Nevoigt, Elke (author), Louis, Edward J. (author)Non-domesticated, wild Saccharomyces yeasts have promising characteristics for beer diversification, particularly when used in the generation of de novo interspecific hybrids. A major motivation for the current work was the question whether attractive novel Saccharomyces interspecific hybrids can be created for the production of exotic lager...journal article 2022
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de Valk, S.C. (author), Bouwmeester, Susan E. (author), de Hulster, A.F. (author), Mans, R. (author)Background: In the yeast Saccharomyces cerevisiae, which is widely applied for industrial bioethanol production, uptake of hexoses is mediated by transporters with a facilitated diffusion mechanism. In anaerobic cultures, a higher ethanol yield can be achieved when transport of hexoses is proton-coupled, because of the lower net ATP yield of...journal article 2022
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Genetic bases for the metabolism of the DMS precursor S-methylmethionine by Saccharomyces cerevisiaeEder, Matthias (author), Sanchez, Isabelle (author), Camarasa, Carole (author), Daran, J.G. (author), Legras, Jean Luc (author), Dequin, Sylvie (author)Dimethyl sulfide (DMS) is a sulfur containing volatile that enhances general fruity aroma and imparts aromatic notes in wine. The most important precursor of DMS is S-methylmethionine (SMM), which is synthesized by grapes and can be metabolized by the yeast S. cerevisiae during wine fermentation. Precursor molecules left after fermentation...journal article 2022
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den Ridder, M.J. (author), Knibbe, E. (author), van den Brandeler, Wiebeke (author), Daran-Lapujade, P.A.S. (author), Pabst, Martin (author)The importance of obtaining comprehensive and accurate information from cellular proteomics experiments asks for a systematic investigation of sample preparation protocols. In particular when working with unicellular organisms with strong cell walls, such as found in the model organism and cell factory Saccharomyces cerevisiae. Here, we...journal article 2022
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Koster, C.C. (author), Postma, E.D. (author), Knibbe, E. (author), Cleij, C.V. (author), Daran-Lapujade, P.A.S. (author)Synthetic Genomics focuses on the construction of rationally designed chromosomes and genomes and offers novel approaches to study biology and to construct synthetic cell factories. Currently, progress in Synthetic Genomics is hindered by the inability to synthesize DNA molecules longer than a few hundred base pairs, while the size of the...review 2022
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van Aalst, A.C.A. (author), Mans, R. (author), Pronk, J.T. (author)Background: Saccharomyces cerevisiae is intensively used for industrial ethanol production. Its native fermentation pathway enables a maximum product yield of 2 mol of ethanol per mole of glucose. Based on conservation laws, supply of additional electrons could support even higher ethanol yields. However, this option is disallowed by the...journal article 2022
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Minden, Steven (author), Aniolek, Maria (author), Sarkizi Shams Hajian, Christopher (author), Teleki, Attila (author), Zerrer, Tobias (author), Delvigne, Frank (author), van Gulik, W.M. (author), Deshmukh, Amit (author), Noorman, H.J. (author), Takors, Ralf (author)Carbon limitation is a common feeding strategy in bioprocesses to enable an efficient microbiological conversion of a substrate to a product. However, industrial settings inherently promote mixing insufficiencies, creating zones of famine conditions. Cells frequently traveling through such regions repeatedly experience substrate shortages and...journal article 2022
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Boonekamp, F.J. (author), Knibbe, E. (author), Vieira Lara, M.A. (author), Wijsman, M. (author), Luttik, M.A.H. (author), van Eunen, Karen (author), den Ridder, M.J. (author), Pabst, Martin (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)Although transplantation of single genes in yeast plays a key role in elucidating gene functionality in metazoans, technical challenges hamper humanization of full pathways and processes. Empowered by advances in synthetic biology, this study demonstrates the feasibility and implementation of full humanization of glycolysis in yeast. Single...journal article 2022
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Malubhoy, Zahabiya (author), Bahia, Frederico Mendonça (author), de Valk, Sophie Claire (author), de Hulster, A.F. (author), Rendulić, Toni (author), Ortiz, Juan Paulo Ragas (author), Xiberras, Joeline (author), Klein, Mathias (author), Mans, R. (author), Nevoigt, Elke (author)Background: The microbial production of succinic acid (SA) from renewable carbon sources via the reverse TCA (rTCA) pathway is a process potentially accompanied by net-fixation of carbon dioxide (CO<sub>2</sub>). Among reduced carbon sources, glycerol is particularly attractive since it allows a nearly twofold higher CO<sub>2</sub>-fixation...journal article 2022
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Totlani, K. (author)A crucial challenge during the initial stages of bioprocess development is that tools used to screen microorganisms and optimize cultivation conditions do not represent the environment imposed at industrial scale. Inside an industrial-scale bioreactor, microorganisms are often cultivated under fed-batch conditions, where nutrients are supplied...doctoral thesis 2021