A5087000945- Microbial Metabolic Engineering and Bioproduction
- Fungal and yeast genetics research
- Biofuel production and bioconversion
- Fermentation and Sensory Analysis
- Enzyme Catalysis and Immobilization
- Enzyme Structure and Function
- Biochemical Acid Research Studies
- Viral Infectious Diseases and Gene Expression in Insects
- Amino Acid Enzymes and Metabolism
- Fungal Biology and Applications
- Microbial metabolism and enzyme function
- Enzyme Production and Characterization
- Probiotics and Fermented Foods
- Biochemical and Molecular Research
- RNA and protein synthesis mechanisms
- Microbial Natural Products and Biosynthesis
- Plant biochemistry and biosynthesis
- CRISPR and Genetic Engineering
- Polyamine Metabolism and Applications
- Biotin and Related Studies
- Metal Extraction and Bioleaching
- Microbial Metabolites in Food Biotechnology
- Metabolism and Genetic Disorders
- Plant Gene Expression Analysis
- Plant nutrient uptake and metabolism
Delft University of Technology
2015-2024
Wageningen University & Research
2021
Cancer Genomics Centre
2007-2015
Universidade Estadual de Campinas (UNICAMP)
2015
Centre for Medical Systems Biology
2014
Cardiff University
2008
Czech Academy of Sciences, Institute of Biotechnology
1998
Leiden University
1986-1987
University of Groningen
1987
Graduate School Experimental Plant Sciences
1972
Penicillins and derived β-lactam antibiotics are essential in healthcare. To gain more insight into penicillin synthesis van den Berg colleagues sequence analyze the genome transcriptome of filamentous fungus Penicillium chrysogenum. Industrial production with chrysogenum is based on an unprecedented effort microbial strain improvement. synthesis, we sequenced 32.19 Mb P. Wisconsin54-1255 identified numerous genes responsible for key steps production. DNA microarrays were used to compare...
A variety of techniques for strain engineering in Saccharomyces cerevisiae have recently been developed. However, especially when multiple genetic manipulations are required, construction is still a time-consuming process. This study describes new CRISPR/Cas9-based approaches easy, fast yeast and explores their potential simultaneous introduction modifications. An open-source tool (http://yeastriction.tnw.tudelft.nl) presented identification suitable Cas9 target sites S. strains....
After an extensive selection procedure, Saccharomyces cerevisiae strains that express the xylose isomerase gene from fungus Piromyces sp. E2 can grow anaerobically on with a mu(max) of 0.03 h(-1). In order to investigate whether reactions downstream control rate consumption, we overexpressed structural genes for all enzymes involved in conversion xylulose glycolytic intermediates, xylose-isomerase-expressing S. strain. The were xylulokinase (EC 2.7.1.17), ribulose 5-phosphate 5.3.1.6),...
ABSTRACT Malic acid is a potential biomass-derivable “building block” for chemical synthesis. Since wild-type Saccharomyces cerevisiae strains produce only low levels of malate, metabolic engineering required to achieve efficient malate production with this yeast. A promising pathway from glucose proceeds via carboxylation pyruvate, followed by reduction oxaloacetate malate. This redox- and ATP-neutral, CO 2 -fixing has theoretical maximum yield mol (mol glucose) −1 . previously engineered...
Abstract Background Flavonoids comprise a large family of secondary plant metabolic intermediates that exhibit wide variety antioxidant and human health-related properties. Plant production flavonoids is limited by the low productivity complexity recovered flavonoids. Thus to overcome these limitations, engineering specific pathway in microbial systems have been envisaged produce high quantity single molecules. Result Saccharomyces cerevisiae was engineered key intermediate flavonoid,...
We have recently reported about a Saccharomyces cerevisiae strain that, in addition to the Piromyces XylA xylose isomerase gene, overexpresses native genes for conversion of xylulose glycolytic intermediates. This engineered (RWB 217) exhibited unprecedentedly high specific growth rates and ethanol production under anaerobic conditions with as sole carbon source. However, when RWB 217 was grown on glucose–xylose mixtures, diauxic pattern observed relatively slow consumption second phase....
Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry academia. We sequenced, assembled, annotated analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) differences genome organization compared to the reference strain S. S288C were analyzed. In addition a few large deletions duplications, nearly 3000 indels identified CEN.PK113-7D relative S288C. These overrepresented genes whose functions are...
Evidence is presented that xylose metabolism in the anaerobic cellulolytic fungus Piromyces sp. E2 proceeds via a isomerase rather than reductase/xylitol-dehydrogenase pathway found xylose-metabolising yeasts. The XylA gene encoding was functionally expressed Saccharomyces cerevisiae. Heterologous activities cell extracts, assayed at 30 degrees C, were 0.3-1.1 micromol min(-1) (mg protein)(-1), with Km for of 20 mM. engineered S. cerevisiae strain grew very slowly on xylose. It co-consumed...
Profiles of genome-wide transcriptional events for a given environmental condition can be importance in the diagnosis poorly defined environments. To identify clusters genes constituting such diagnostic profiles, we characterized specific responses Saccharomyces cerevisiaeto growth limitation by carbon, nitrogen, phosphorus, or sulfur. Microarray experiments were performed using cells growing steady-state conditions chemostat cultures at same dilution rate. This enabled us to study effects...
ABSTRACT The specific growth rate is a key control parameter in the industrial production of baker’s yeast. Nevertheless, quantitative data describing its effect on fermentative capacity are not available from literature. In this study, physiology and an Saccharomyces cerevisiae strain aerobic, glucose-limited chemostat cultures was investigated. At rates (dilution rates, D ) below 0.28 h −1 , glucose metabolism fully respiratory. Above dilution rate, respirofermentative set in, with ethanol...
In <i>Saccharomyces cerevisiae</i>, the<i>NDI1</i> gene encodes a mitochondrial NADH dehydrogenase, the catalytic side of which projects to matrix inner membrane. addition this dehydrogenase,<i>S. cerevisiae</i> exhibits another NADH-dehydrogenase activity, oxidizes at cytosolic To investigate whether open reading frames<i>YMR145c/NDE1</i> and <i>YDL 085w/NDE2,</i> exhibit sequence similarity with <i>NDI1</i>, encode latter enzyme, NADH-dependent respiration was assayed in wild-type <i>S....
In contrast to batch cultivation, chemostat cultivation allows the identification of carbon source responses without interference by carbon-catabolite repression, accumulation toxic products, and differences in specific growth rate. This study focuses on yeast Saccharomyces cerevisiae, grown aerobic, carbon-limited cultures. Genome-wide transcript levels vivo fluxes were compared for two sugars, glucose maltose, C2-compounds, ethanol acetate. previous reports cultures, few genes (180 genes)...
When xylose metabolism in yeasts proceeds exclusively via NADPH-specific reductase and NAD-specific xylitol dehydrogenase, anaerobic conversion of the pentose to ethanol is intrinsically impossible. has a dual specificity for both NADPH NADH, alcoholic fermentation feasible but requires formation large amounts polyols (e.g., xylitol) maintain closed redox balance. As result, yield on will be sub-optimal. This paper demonstrates that ethanol, without substantial by-product formation, possible...
ABSTRACT The yeast Saccharomyces cerevisiae is unique among eukaryotes in exhibiting fast growth both the presence and complete absence of oxygen. Genome-wide transcriptional adaptation to aerobiosis anaerobiosis was studied assays using DNA microarrays. This technique combined with chemostat cultivation, which allows controlled variation a single parameter under defined conditions at fixed specific rate. Of 6,171 open reading frames investigated, 5,738 (93%) yielded detectable transcript...
Abstract The heterotrophic marine alga Crypthecodinium cohnii is known to produce docosahexaenoic acid (DHA), a polyunsaturated fatty with food and pharmaceutical applications, during batch cultivation on complex media containing sea salt, yeast extract, glucose. In the present study, fed‐batch was studied as an alternative fermentation strategy for DHA production. Glucose acetic were compared carbon sources. For both substrates, feed rate adapted maximum specific consumption of C. cohnii....
Metabolic fluxes may be regulated "hierarchically," e.g., by changes of gene expression that adjust enzyme capacities (V(max)) and/or "metabolically" interactions enzymes with substrates, products, or allosteric effectors. In the present study, a method is developed to dissect hierarchical regulation into contributions transcription, translation, protein degradation, and posttranslational modification. The was applied through individual glycolytic when yeast Saccharomyces cerevisiae...