A5076983738- Microbial Natural Products and Biosynthesis
- Microbial Metabolic Engineering and Bioproduction
- Microbial Metabolism and Applications
- Fungal Biology and Applications
- Genomics and Phylogenetic Studies
- Plant Pathogens and Fungal Diseases
- Plant biochemistry and biosynthesis
- Quantum Information and Cryptography
- Mycorrhizal Fungi and Plant Interactions
- Bioinformatics and Genomic Networks
- Fermentation and Sensory Analysis
- Plant-Microbe Interactions and Immunity
- Fungal and yeast genetics research
- Random lasers and scattering media
- Lichen and fungal ecology
- Antifungal resistance and susceptibility
- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
- Quantum and electron transport phenomena
- Mycotoxins in Agriculture and Food
- Mechanical and Optical Resonators
- Enzyme Production and Characterization
- Probiotics and Fermented Foods
- Genetic diversity and population structure
- Plant Disease Resistance and Genetics
Wageningen University & Research
2018-2025
Westerdijk Fungal Biodiversity Institute
2018-2023
Institute for Scientific and Technological Research
2006-2010
Abstract Fueled by the explosion of (meta)genomic data, genome mining specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played central role through analysis Biosynthetic Gene Clusters (BGCs). Thousands candidate BGCs from microbial genomes been identified stored in public databases. Interpreting function novelty predicted requires comparison with well-documented set known...
Abstract With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role the discovery novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these are often organised into gene clusters (BGCs). In 2015, we defined Minimum Information about Biosynthetic Gene cluster (MIBiG): standardised format describes minimally required information to...
Abstract Specialized or secondary metabolites are small molecules of biological origin, often showing potent activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis these natural products is governed by sets co-regulated physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs a standardized machine-readable way, Minimum Information Biosynthetic Gene cluster (MIBiG) data standard repository was initiated...
Abstract Genome mining has become a key technology to explore and exploit natural product diversity through the identification analysis of biosynthetic gene clusters (BGCs). Initially, this was performed on single-genome basis; currently, process is being scaled up large-scale pan-genomes entire genera, complete strain collections metagenomic datasets from which thousands bacterial genomes can be extracted at once. However, no bioinformatic framework currently available for effective size...
Type III polyketide synthases (PKSs) produce secondary metabolites with diverse biological activities, including antimicrobials. While they have been extensively studied in plants and bacteria, only a handful of type PKSs from fungi has characterized the last 15 years. The exploitation fungal to novel bioactive compounds requires understanding diversity these enzymes, as well their biosynthetic pathways. Here, phylogenetic reconciliation analyses 522 1,193 genomes revealed complex...
To date little is known about the genetic background that drives production and diversification of secondary metabolites in Hypoxylaceae . With recent availability high-quality genome sequences for 13 representative species one relative ( Xylaria hypoxylon ) we attempted to survey diversity biosynthetic pathways these organisms investigate their true potential as metabolite producers. Manual search strategies based on accumulated knowledge biosynthesis fungi enabled us identify 783 across 14...
<title>Abstract</title> <bold>Background</bold>: The increasing demand for novel drug leads requires bioprospecting non-model taxa. Comparative genomics and correlative omics are a fast efficient method linking bioactive but genetically orphan natural products to their biosynthetic gene clusters (BGCs) identifying potentially leads. Here we implement these approaches the first systematic comparison of BGC diversity in lichen-forming fungi (LFF, comprising 20% known fungi), prolific...
Natural products, also known as specialized or secondary metabolites, show extraordinary chemical diversity and potent biological activities. Their biosynthesis usually first encompasses scaffold generation, followed by additional tailoring maturation steps, leading to the mature compound. The latter steps are often performed accessory enzymes maturases. While knowledge about reaction substrate specificities of these is essential for natural product biosynthesis, it scattered in literature,...
Xylindein is a blue-green pigment produced by the fungi Chlorociboria aeruginascens and aeruginosa. Its stunning color optoelectronic properties make xylindein valuable for textiles as natural semiconductor material. However, producing from culture broths remains challenging because of slow growth species poor solubility in organic solvents. An alternative production route obtaining pure heterologous expression biosynthetic genes. Here, we resequenced genome C. aeruginosa, subsequent mining...
Cinnamic acid is an aromatic compound commonly found in plants and functions as a central intermediate lignin synthesis. Filamentous fungi are able to degrade cinnamic through multiple metabolic pathways. One of the best studied pathways non-oxidative decarboxylation styrene. In Aspergillus niger, enzymes decarboxylase (CdcA, formally ferulic decarboxylase) flavin prenyltransferase (PadA) catalyze together sorbic acid. The corresponding genes, cdcA padA, clustered genome with putative...
Biopesticides are an attractive biotechnological alternative to conventional pesticides for soil-borne plant diseases. A screening strategy with over 100 actinomycetes bacteria isolated from diverse rhizosphere soils uncovered the Streptomyces rochei strain JK1 as a potent inhibitor of oomycete growth. The culture filtrates inhibited growth in plate assays and could suppress two major oomycete-caused diseases caused by Pythium myriotylum Phytophthora sojae. macrolide secondary metabolite...
Candida vulturna is a new member of the haemulonii species complex that recently received much attention as it includes emerging multidrug-resistant pathogen auris. Here, we describe high-quality genome sequence C. type strain CBS 14366T to cover all genomes pathogenic members.
Fungi have provided us with life-changing small bioactive molecules, the best-known examples being first broad-spectrum antibiotic penicillin, immunosuppressive cyclosporine, and cholesterol-lowering statins. Since 1980s, exploration of chemical diversity in nature has been highly reduced.
Non-ribosomal peptide synthetases (NRPSs) and NRPS-like enzymes are abundant in microbes as they involved the production of primary secondary metabolites. In contrast to well-studied NRPSs, known produce non-ribosomal peptides, exhibit more diverse activities their evolutionary relationships unclear. Here, we present first in-depth phylogenetic analysis fungal A domains from functionally characterized pathways, found NRPSs. This study clearly differentiated amino acid reductases, including...
We present an application of the genetic algorithmic computational method to optimization concurrence measure entanglement for cases one dimensional chains, as well square and triangular lattices in a simple tight-binding approach which hopping electrons is much stronger than phonon dissipation.
Chlorociboria aeruginascens DSM 107184 is a wood-decomposing ascomycetous fungus known to produce the bluish-green dimeric naphthoquinone derivate xylindein. Here, we present first draft genome sequence, which contains 588 contigs with total length of 33.1 Mb. Altogether, 8,648 protein-coding genes were predicted.
In this paper, we study the numerical optimization of nearest-neighbor concurrence bipartite one- and two-dimensional lattices, as well non-bipartite lattices. These systems are described in framework a tight-binding Hamiltonian while was performed using genetic algorithms. Our results show that optimized lattice structures is considerably higher than non-optimized systems. case one-dimensional chains, increases dramatically when system begins to dimerize, i.e., it undergoes structural phase...
Fungal plant pathogens constantly evolve and deploy novel peptide metabolite effectors to break down resistance adapt new host plants. The blast fungal pathogen Pyricularia oryzae is a single species subdivided into multiple host-specific lineages. This specialization likely due secreted effectors, including effectors. Here, we mined 68 genomes of P. , belonging six lineages, identify secondary (SM) biosynthetic gene clusters (BGCs) associated with specialization. A similarity network...
Abstract Fungal plant pathogens constantly evolve and deploy novel peptide metabolite effectors to break down resistance adapt new host plants. The blast fungal pathogen Pyricularia oryzae is a single species subdivided into multiple host-specific lineages that have evolved through gain and/or loss of virulence effector related genes chromosomal rearrangement. Here, we mined 68 genomes P. , belonging six lineages, identify secondary (SM) biosynthetic gene clusters (BGCs) likely associated...