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The path towards prediction: An exploration of the evolutionary dynamics of the yeast polarity network

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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Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance

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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Enabling yeast replication in extreme cold and heat

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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Beyond Saccharomyces pastorianus for modern lager brews: Exploring non-cerevisiae Saccharomyces hybrids with heterotic maltotriose consumption and novel aroma profile

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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Synthetic Genomics From a Yeast Perspective

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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Droplet microfluidics for bioprocess engineering

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

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Engineering of vitamin and cofactor synthesis in yeasts

Perli, T. (author)

The increase in world population together with an unsustainable and fossil fuel-based economy are at the root of the significant increase in the average global temperature since the pre-industrial era. Switching to a more sustainable and circular bio-based economy is one of the main pillars included in the Paris agreement aimed at reducing green...

doctoral thesis 2021

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Fed-Batch Droplet Nanobioreactor for Controlled Growth of Cyberlindnera (Pichia) jadinii: A Proof-Of-Concept Demonstration

Totlani, K. (author), Wang, Yen Chieh (author), Bisschops, Maxime (author), de Riese, Thorben (author), Kreutzer, M.T. (author), van Gulik, W.M. (author), van Steijn, V. (author)

A key bottleneck in bioprocess development is that state-of-the-art tools used for screening of cells and optimization of cultivation conditions do not represent the conditions enforced at industrial scale. At industrial scale, cell growth is strictly controlled (“fed-batch”) to optimize the metabolites produced by the cells. In contrast,...

journal article 2021

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Origin of Lactose Fermentation in Kluyveromyces lactis by Interspecies Transfer of a Neo-functionalized Gene Cluster during Domestication

Varela, Javier A. (author), Puricelli, Martina (author), Ortiz Merino, R.A. (author), Giacomobono, Romina (author), Braun-Galleani, Stephanie (author), Wolfe, Kenneth H. (author), Morrissey, John P. (author)

Humans have used yeasts to make cheese and kefir for millennia, but the ability to ferment the milk sugar lactose is found in only a few yeast species, of which the foremost is Kluyveromyces lactis [1]. Two genes, LAC12 (lactose permease) and LAC4 (lactase), are sufficient for lactose uptake and hydrolysis to glucose and galactose [2]. Here,...

journal article 2019

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Physiological responses of Saccharomyces cerevisiae to industrially relevant conditions: Slow growth, low pH, and high CO₂ levels

Hakkaart, X.D.V. (author), Liu, Y. (author), Hulst, Mandy (author), el Masoudi, Anissa (author), Peuscher, Eveline (author), Pronk, J.T. (author), van Gulik, W.M. (author), Daran-Lapujade, P.A.S. (author)

Engineered strains of Saccharomyces cerevisiae are used for industrial production of succinic acid. Optimal process conditions for dicarboxylic-acid yield and recovery include slow growth, low pH, and high CO₂. To quantify and understand how these process parameters affect yeast physiology, this study investigates individual and...

journal article 2019

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Laboratory evolution for forced glucose-xylose co-consumption enables identification of mutations that improve mixed-sugar fermentation by xylose-fermenting Saccharomyces cerevisiae

Papapetridis, I. (author), Verhoeven, M.D. (author), Wiersma, S.J. (author), Goudriaan, M. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)

Simultaneous fermentation of glucose and xylose can contribute to improved productivity and robustness of yeast-based processes for bioethanol production from lignocellulosic hydrolysates. This study explores a novel laboratory evolution strategy for identifying mutations that contribute to simultaneous utilisation of these sugars in batch...

journal article 2018

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Laboratory evolution of a glucose-phosphorylation-deficient, arabinose-fermenting S. cerevisiae strain reveals mutations in GAL2 that enable glucose-insensitive l-arabinose uptake

Verhoeven, M.D. (author), Bracher, J.M. (author), Nijland, Jeroen G. (author), Bouwknegt, J. (author), Daran, J.G. (author), Driessen, Arnold J.M. (author)

Cas9-assisted genome editing was used to construct an engineered glucose-phosphorylation-negative S. cerevisiae strain, expressing the Lactobacillus plantaruml-arabinose pathway and the Penicillium chrysogenum transporter PcAraT. This strain, which showed a growth rate of 0.26 h−1 on l-arabinose in aerobic batch cultures, was subsequently...

journal article 2018

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Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D

Salazar, A.N. (author), Gorter de Vries, A.R. (author), van den Broek, M.A. (author), Wijsman, M. (author), de la Torre, P. (author), Brickwedde, A. (author), Brouwers, N. (author), Daran, J.G. (author), Abeel, T.E.P.M.F. (author)

The haploid Saccharomyces cerevisiae strain CEN.PK113–7D is a popular model system for metabolic engineering and systems biology research. Current genome assemblies are based on short-read sequencing data scaffolded based on homology to strain S288C. However, these assemblies contain large sequence gaps, particularly in subtelomeric regions, and...

journal article 2017

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Molecular responses of Saccharomyces cerevisiae to near-zero growth rates

Bisschops, M.M.M. (author)

doctoral thesis 2016

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Analysis of the hybrid genomes of brewing yeasts

Bolat, I. (author)

One of the best guarded secrets of brewers is represented by the brewing yeast employed in beer fermentation, due to its profound impact upon the specific flavour profile of the final product. The current research tackles the genome diversity of lager brewing strains as well as their impact on important phenotypic traits. Furthermore, the...

doctoral thesis 2016

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Growth-rate dependency of de novo resveratrol production in chemostat cultures of an engineered Saccharomyces cerevisiae strain

Vos, T. (author), De la Torre Cortes, P. (author), Van Gulik, W.M. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)

Introduction: Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints...

journal article 2015

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Reducing the genetic complexity of glycolysis in Saccharomyces cerevisiae

Solis Escalante, D. (author)

Glycolysis, a biochemical pathway that oxidizes glucose to pyruvate, is at the core of sugar metabolism in Saccharomyces cerevisiae (bakers’ yeast). Glycolysis is not only a catabolic route involved in energy conservation, but also provides building blocks for anabolism. From an applied perspective, several glycolytic intermediates are key...

doctoral thesis 2015

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Replacement of the Saccharomyces cerevisiae acetyl-CoA synthetases by alternative pathways for cytosolic acetyl-CoA synthesis

Kozak, B.U. (author), Van Rossum, H.M. (author), Benjamin, K.R. (author), Wu, L. (author), Daran, J.G. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author)

Cytosolic acetyl-coenzyme A is a precursor for many biotechnologically relevant compounds produced by Saccharomyces cerevisiae. In this yeast, cytosolic acetyl-CoA synthesis and growth strictly depend on expression of either the Acs1 or Acs2 isoenzyme of acetyl-CoA synthetase (ACS). Since hydrolysis of ATP to AMP and pyrophosphate in the ACS...

journal article 2013

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Towards fermentation of galacturonic acid-containing feedstocks with Saccharomyces cerevisiae

Huisjes, E.H. (author)

The ambition to reduce our current dependence on fossil transportation fuels has driven renewed interest in bioethanol. Pectin-rich feedstocks like sugar beet pulp and citrus peel, which are currently sold as cattle feed, are promising raw materials for the production of bioethanol. This thesis explores the challenges related to the fermentation...

doctoral thesis 2013

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Metabolic engineering of free-energy (ATP) conserving reactions in Saccharomyces cerevisiae

De Kok, S. (author)

Metabolic engineering – the improvement of cellular activities by manipulation of enzymatic, transport and regulatory functions of the cell – has enabled the industrial production of a wide variety of biological molecules from renewable resources. Microbial production of fuels and chemicals thereby provides an alternative to oil-based production...

doctoral thesis 2012