A5053787660- Fungal and yeast genetics research
- Fermentation and Sensory Analysis
- Evolution and Genetic Dynamics
- CRISPR and Genetic Engineering
- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Biofuel production and bioconversion
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Insect behavior and control techniques
- Plant and animal studies
- Protein Kinase Regulation and GTPase Signaling
- Nutrition, Genetics, and Disease
- Metabolism, Diabetes, and Cancer
- DNA Repair Mechanisms
- Amino Acid Enzymes and Metabolism
- Single-cell and spatial transcriptomics
- Steroid Chemistry and Biochemistry
- Horticultural and Viticultural Research
- Ubiquitin and proteasome pathways
- Cancer, Hypoxia, and Metabolism
- Genomics and Phylogenetic Studies
- Polyamine Metabolism and Applications
- Biochemical Analysis and Sensing Techniques
KU Leuven
2014-2024
VIB-KU Leuven Center for Microbiology
2012-2024
VIB-KU Leuven Center for Cancer Biology
2012-2023
Vlaams Instituut voor Biotechnologie
2009-2017
Universitat Pompeu Fabra
2015
Centre for Genomic Regulation
2015
Institució Catalana de Recerca i Estudis Avançats
2015
Ghent University Hospital
2012
Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping fate of duplicated genes remain heavily debated because molecular processes and forces involved difficult reconstruct. Here, we study a large family fungal glucosidase that underwent several duplication events. We reconstruct all key ancestral enzymes show very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars....
Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution isogenic yeast populations different initial ploidy study adaptation increasing ethanol. Whole-genome sequencing more than 30 evolved over 100 adapted clones isolated throughout two-year experiment revealed how a interplay de novo single nucleotide mutations, copy...
While specific mutations allow organisms to adapt stressful environments, most changes in an organism's DNA negatively impact fitness. The mutation rate is therefore strictly regulated and often considered a slowly-evolving parameter. In contrast, we demonstrate unexpected flexibility cellular rates as response selective pressure. We show that hypermutation independently evolves when different Escherichia coli cultures high ethanol stress. Furthermore, hypermutator states are transitory...
Abstract Loss of gene function is common throughout evolution, even though it often leads to reduced fitness. In this study, we systematically evaluated how an organism adapts after deleting genes that are important for growth under oxidative stress. By evolving, sequencing, and phenotyping over 200 yeast lineages, found loss can enhance organism’s capacity evolve adapt. Although led immediate decrease in fitness, many mutants rapidly acquired suppressor mutations restored Depending on the...
Abstract The emergence of new genes throughout evolution requires rewiring and extension regulatory networks. However, the molecular details how transcriptional regulation gene copies evolves remain largely unexplored. Here we show duplication a transcription factor allowed two independent circuits. Interestingly, ancestral was promiscuous could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds type...
Current methods for single-cell RNA sequencing (scRNA-seq) of yeast cells do not match the throughput and relative simplicity state-of-the-art techniques that are available mammalian cells. In this study, we report how 10x Genomics’ droplet-based technology can be modified to allow analysis The protocol, which is based on in-droplet spheroplasting cells, yields an order-of-magnitude higher in comparison existing methods. After extensive validation method, demonstrate its use by studying...
Abstract Ethanol is a ubiquitous environmental stressor that toxic to all lifeforms. Here, we use the model eukaryote Saccharomyces cerevisiae show exposure sublethal ethanol concentrations causes DNA replication stress and an increased mutation rate. Specifically, find slows down affects localization of Mrc1, conserved protein helps stabilize replisome. In addition, also results in recruitment error-prone polymerases fork. Interestingly, preventing this through mutagenesis PCNA/Pol30...
When grown on solid substrates, different microorganisms often form colonies with very specific morphologies. Whereas the pioneers of microbiology used colony morphology to discriminate between species and strains, phenomenon has not received much attention recently. In this study, we use a genome-wide assay in model yeast Saccharomyces cerevisiae identify all genes that affect morphology. We show several major signalling cascades, including MAPK, TORC, SNF1 RIM101 pathways play role,...
Pkh1, -2, and -3 are the yeast orthologs of mammalian 3-phosphoinositide-dependent protein kinase-1 (PDK1). Although essential for viability, their functioning remains poorly understood. Sch9, kinase B and/or S6K ortholog, has been identified as one targets. We now have shown that in vitro interaction Pkh1 Sch9 depends on hydrophobic PDK1-interacting fragment pocket requires complementary motif Sch9. demonstrated phosphorylates both vivo its PDK1 site this phosphorylation is a wild type cell...
For yeast cells, tolerance to high levels of ethanol is vital both in their natural environment and industrially relevant conditions. We recently genotyped experimentally evolved strains adapted identified mutations linked tolerance. In this study, by integrating genomic sequencing data with quantitative proteomics profiles from six (data set identifier PXD006631) construction protein interaction networks, we elucidate exactly how the genotype phenotype are related at molecular level. Our...
Scientific Report16 October 2012Open Access Functional divergence of gene duplicates through ectopic recombination Joaquin F Christiaens Department Microbial and Molecular Systems, Centre Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, B-3001 Leuven (Heverlee), Belgium VIB Laboratory Systems Biology, Search for more papers by this author Sebastiaan E Van Mulders Malting Brewing Science, Faculty Bioscience Engineering, Jorge Duitama Chris A Brown Arts Sciences Center Harvard...
Abstract Beer would not exist without microbes. During fermentation, yeast cells convert cereal‐derived sugars into ethanol and CO 2 . Yeast also produces a wide array of aroma compounds that influence beer taste aroma. The complex interaction between all these results in each having its own distinctive palette. This article contains protocols needed to brew standard lab environment focuses on the use brewing. More specifically, it provides for propagation, brewing calculations and, course,...