A5083255554- Microbial Natural Products and Biosynthesis
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Plant biochemistry and biosynthesis
- Enzyme Structure and Function
- Legume Nitrogen Fixing Symbiosis
- Microbial Community Ecology and Physiology
- Biochemical and Molecular Research
- RNA and protein synthesis mechanisms
- Botany and Geology in Latin America and Caribbean
- Protein Structure and Dynamics
- Enzyme Production and Characterization
- Fungal Biology and Applications
- Enzyme Catalysis and Immobilization
- Bacterial Genetics and Biotechnology
- Microbial Metabolism and Applications
- Insect symbiosis and bacterial influences
- Salmonella and Campylobacter epidemiology
- Marine Sponges and Natural Products
- Vibrio bacteria research studies
- Gut microbiota and health
- Photosynthetic Processes and Mechanisms
- Plant-Microbe Interactions and Immunity
- Biochemical and biochemical processes
- Bioinformatics and Genomic Networks
Leiden University
2022-2025
Instituto Politécnico Nacional
2015-2024
Center for Research and Advanced Studies of the National Polytechnic Institute
2015-2024
National Biodiversity Institute
2017
Instituto Tecnológico Superior de Irapuato
2017
Instituto Nacional de Cancerología
2011
University of Warwick
2003-2011
Universidad Nacional Autónoma de México
2007
Howard Hughes Medical Institute
2006
Salk Institute for Biological Studies
2006
A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded biosynthetic gene clusters. Information about these clusters, is currently dispersed throughout the literature, making it difficult exploit. To facilitate consistent systematic deposition retrieval data on we propose Minimum a Biosynthetic Gene cluster (MIBiG) standard.
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...
Desferrioxamines are a structurally related family of tris-hydroxamate siderophores that form strong hexadentate complexes with ferric iron. Desferrioxamine B has been used clinically for the treatment iron overload in man. We have unambiguously identified desferrioxamine E as major siderophore produced by Streptomyces coelicolor M145 and cluster four genes (desA−D) directs biosynthesis this model actinomycete. On basis comparative sequence analysis proteins encoded these genes, we propose...
Natural products from microbes have provided humans with beneficial antibiotics for millennia. However, a decline in the pace of antibiotic discovery exerts pressure on human health as resistance spreads, challenge that may better faced by unveiling chemical diversity produced microbes. Current microbial genome mining approaches revitalized research into antibiotics, but empirical nature these methods limits space is explored. Here, we address problem finding novel pathways incorporating...
The complete genome sequence of the original isolate model actinomycete Streptomyces lividans 66, also referred to as 1326, was deciphered after a combination next-generation sequencing platforms and hybrid assembly pipeline. Comparative analysis genomes S. 66 closely related strains, including coelicolor M145 TK24, used identify strain-specific genes. genetic diversity identified included large genomic island with mosaic structure, present in but not strain TK24. Sequence analyses showed...
Polyketide synthases (PKSs) are involved in the biosynthesis of many important natural products. In bacteria, type III PKSs typically catalyze iterative decarboxylation and condensation reactions malonyl-CoA building blocks polyhydroxyaromatic Here it is shown that Gcs, a PKS encoded by sco7221 ORF bacterium Streptomyces coelicolor, required for germicidin family 3,6-dialkyl-4-hydroxypyran-2-one Evidence consistent with Gcs-catalyzed elongation specific β-ketoacyl-ACP products fatty acid...
Siderophore-mediated iron acquisition has been well studied in many bacterial pathogens because it contributes to virulence. In contrast, siderophore-mediated by saprophytic bacteria received relatively little attention. The independent identification of the des and cch gene clusters that direct production tris -hydroxamate ferric iron-chelators desferrioxamine E coelichelin, respectively, which could potentially act as siderophores saprophyte Streptomyces coelicolor A3(2), recently...
Desferrioxamines are hydroxamate siderophores widely conserved in both aquatic and soil-dwelling Actinobacteria. While the genetic enzymatic bases of siderophore biosynthesis their transport model families this phylum well understood, evolutionary studies lacking. Here, we perform a comprehensive desferrioxamine-centric (des genes) phylogenomic analysis, which includes genomes six novel strains isolated from an iron phosphorous depleted oasis Chihuahuan desert Mexico. Our analyses reveal...
Cycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate bacterial sub-communities isolated from coralloid roots of species Dioon (Zamiaceae) sampled their natural habitats. We employed sub-community co-culture experimental strategy reveal both predominant rare bacteria, which were characterized using phylogenomics detailed metabolic...
Folates are tripartite molecules comprising pterin, para-aminobenzoate (PABA), and glutamate moieties, which essential cofactors involved in DNA amino acid synthesis. The obligately intracellular Chlamydia species have lost several biosynthetic pathways for nutrients they can obtain from their host but retained the capacity to synthesize folate. In most bacteria, synthesis of pterin moiety folate requires FolEQBK enzymes, while PABA is carried out by PabABC enzymes. Bioinformatic analyses...
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...
Cycads are among the few plants that have developed specialized roots to host nitrogen-fixing bacteria. We describe bacterial diversity of coralloid from seven Dioon species and their surrounding rhizosphere soil. Using 16S rRNA gene amplicon sequencing, we found all inhabited by a broad groups, including cyanobacteria Rhizobiales most abundant groups. The composition endophytes similar in six Mexican evaluated, suggesting recent divergence populations and/or plant-driven restrictions...
Calculations predict that testing of 5 000-10 000 molecules and >1 billion US dollars (£0.8 billion, £1=$1.2) are required for one single drug to come the market. A solution this problem is establish more efficient protocols reduce high rate re-isolation continuous rediscovery natural products during early stages development process. The study 'rare actinobacteria' has emerged as a possible approach increasing discovery leads from sources. Here, we define simple genomic metric, defined...
The expansion of the genetic repertoire an organism by gene duplication or horizontal transfer (HGT) can aid adaptation.
Cardiolipin (CL) is an anionic membrane lipid present in bacteria, plants, and animals, but absent from archaea. It generally thought that bacteria use enzyme belonging to the phospholipase D superfamily as cardiolipin synthase (Cls) catalyzing a reversible phosphatidyl group transfer one phosphatidylglycerol (PG) molecule another PG form CL glycerol. In contrast, eukaryotes Cls of CDP-alcohol phosphatidyltransferase uses cytidine diphosphate-diacylglycerol (CDP-DAG) donor group, which...
Despite the prominent role of horizontal gene transfer (HGT) in shaping bacterial metabolism, little is known about impact HGT on evolution enzyme function. Specifically, what influence a recently acquired function an existing gene? For example, certain members genus Corynebacterium have horizontally whole l-tryptophan biosynthetic operon, whereas closely related actinobacteria, for Mycobacterium, trpF missing. In performed by dual-substrate (βα)8 phosphoribosyl isomerase (priA gene) also...