A5023101249- Microbial Natural Products and Biosynthesis
- Genomics and Phylogenetic Studies
- Biochemical and Molecular Research
- RNA and protein synthesis mechanisms
- Microbial bioremediation and biosurfactants
- Chemical Synthesis and Analysis
- Wastewater Treatment and Nitrogen Removal
- Marine Sponges and Natural Products
- Metabolomics and Mass Spectrometry Studies
- Microbial Metabolic Engineering and Bioproduction
- Plant Disease Resistance and Genetics
- Carbohydrate Chemistry and Synthesis
- Microbial Metabolism and Applications
- Gut microbiota and health
- Plant biochemistry and biosynthesis
- Protist diversity and phylogeny
- Polyamine Metabolism and Applications
- Biological Stains and Phytochemicals
- Enzyme Catalysis and Immobilization
- Synthesis and Catalytic Reactions
- Epigenetics and DNA Methylation
- Metal-Catalyzed Oxygenation Mechanisms
- Actinomycetales infections and treatment
- Metalloenzymes and iron-sulfur proteins
- Tannin, Tannase and Anticancer Activities
Shaanxi University of Chinese Medicine
2025
The Ohio State University
2016-2024
Florida State University
2019-2024
University of Illinois Urbana-Champaign
2011-2019
University of California, Davis
2006-2014
University of Illinois System
2011
University of Minnesota
2010
Significance The discovery of natural products, an important source human medicines, is critical for the development new therapeutics against health threats, including cancer and multidrug-resistant pathogens. Yet, in recent years, industrial pharmaceuticals from products has been stymied due to a variety reasons, repeated previously known compounds. Here, we demonstrate large-scale genomics as one potential solution this problem by mining collection 10,000 actinomycetes novel phosphonic...
Abstract microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging curated database of >60,000 monocultures, users can known and unknown MS/MS spectra link them to their respective producers via fragmentation patterns. Identification microbe-derived metabolites relative without priori knowledge will vastly enhance the understanding microorganisms’ role ecology human health.
Abstract A strain of Vibrio sp. isolated from marine sediments produced large quantities bright red pigments that could be used to dye many fibers including wool, nylon, acrylics, and silk. Characterization the by electrospray ionization mass spectrometry (ESI‐MS) nuclear magnetic resonance (NMR) revealed three prodiginine‐like structures with nonpolar characteristics low molecular mass. UV‐visible spectra major constituent in methanol solution showed absorbance at λ max 530 nm wavelength....
For more than half a century the pharmaceutical industry has sifted through natural products produced by microbes, uncovering new scaffolds and fashioning them into broad range of vital drugs. We sought strategy to reinvigorate discovery with distinctive structures using bacterial genome sequencing combined metabolomics. By correlating genetic content from 178 actinomycete genomes mass spectrometry-enabled analyses their exported metabolomes, we paired secondary metabolites biosynthetic gene...
In phylogenetic analyses of the genus Streptomyces using 16S rRNA gene sequences, albus subsp . NRRL B-1811 T forms a cluster with five other species having identical or nearly sequences. Moreover, morphological and physiological characteristics these species, including almquistii B-1685 , flocculus B-2465 gibsonii B-1335 rangoonensis B-12378 are quite similar. This is particular taxonomic interest because type The related strains were subjected to multilocus sequence analysis (MLSA)...
Fosfomycin is a wide-spectrum antibiotic that used clinically to treat acute cystitis in the United States. The compound produced by several strains of streptomycetes and pseudomonads. We sequenced biosynthetic gene cluster responsible for fosfomycin production Pseudomonas syringae PB-5123. Surprisingly, pathway this organism very different from Streptomyces fradiae wedmorensis. pathways share first last steps, involving conversion phosphoenolpyruvate phosphonopyruvate (PnPy)...
Methylphosphonate synthase (MPnS) produces methylphosphonate, a metabolic precursor to methane in the upper ocean. Here, we determine 2.35-angstrom resolution structure of MPnS and discover that it has an unusual 2-histidine-1-glutamine iron-coordinating triad. We further solve related enzyme, hydroxyethylphosphonate dioxygenase from Streptomyces albus (SaHEPD), find displays same motif. SaHEPD can be converted into by mutation glutamine-adjacent residues, identifying molecular requirements...
As microbial genome sequencing becomes more widespread, the capacity of microorganisms to produce an immense number metabolites has come into better view. Utilizing a metabolite/gene cluster correlation platform, biosynthetic origins new family natural products, rimosamides, were discovered. The rimosamides identified in Streptomyces rimosus and associated with their NRPS/PKS-type gene based upon high frequency co-occurrence across 179 strains actinobacteria. This also led discovery related...
Natural products (NPs) are a rich source of medicines, but traditional discovery methods often unsuccessful due to high rates rediscovery. Genetic approaches for NP promising, progress has been slow the difficulty identifying unique biosynthetic gene clusters (BGCs) and poor expression. We previously developed metabologenomics method, which combines genomic metabolomic data discover new NPs their BGCs. Here, we utilize in combination with molecular networking novel class NPs, tyrobetaines:...
ABSTRACT Nitrobenzene 1,2-dioxygenase from Comamonas sp. strain JS765 catalyzes the initial reaction in nitrobenzene degradation, forming catechol and nitrite. The enzyme also oxidizes aromatic rings of mono- dinitrotoluenes at nitro-substituted carbon, but basis for this specificity is not understood. In study, site-directed mutagenesis was used to modify active site dioxygenase, contribution specific residues controlling substrate performance evaluated. activities six mutant enzymes...
Abstract Natural product discovery has been boosted by genome mining approaches, but compound purification is often still challenging. We report an enzymatic strategy for “stable isotope labeling of phosphonates in extract” (SILPE) that facilitates their purification. used the phosphonate methyltransferase DhpI involved dehydrophos biosynthesis to methylate a variety natural products crude spent medium with mixture labeled and unlabeled S ‐adenosyl methionine. Mass‐guided fractionation then...
Actinobacteria such as streptomycetes are renowned for their ability to produce bioactive natural products including nonribosomal peptides (NRPs) and polyketides (PKs). The advent of genome sequencing has revealed an even larger genetic repertoire secondary metabolism with most the small molecule these gene clusters still unknown. Here, we employed a "protein-first" method called PrISM (Proteomic Investigation Secondary Metabolism) screen 26 unsequenced actinomycetes using mass...
Phosphonic acid natural products have potent inhibitory activities that led to their application as antibiotics. Recent studies uncovered large collections of gene clusters encoding for unknown phosphonic acids across microbial genomes. However, our limited understanding metabolism presents a significant challenge toward accurately informing the discovery new bioactive compounds directly from sequence information alone. Here, we use genome mining identify family conserved branch point...
Different Bacillus species have successfully been used as biopesticides against a broad range of plant pathogens. Among these, tequilensis EA-CB0015 has shown to efficiently control Black sigatoka disease in banana plants, presumably by mechanisms adaptation that involve modifying the phyllosphere environment. Here, we report complete genome strain EA-CB0015, its precise taxonomic identity, and determined key genetic features may contribute effective biocontrol We found B. harbors singular 4...
Introduction This study aims to identify the therapeutic targets and regulatory mechanisms of antitumor drug gallic acid (GA) in cervical cancer (CC). Methods HeLa cells were treated with GA subjected RNA-sequencing using DNBSEQ platform. By combining results Gene Expression Omnibus (GEO) Cancer Genome Atlas (TCGA) analysis RNA-seq, differentially expressed genes (DEGs), including those upregulated downregulated CC compared normal cervix GEO TCGA database, while reversed after treatment GA,...
Bacteria that assimilate synthetic nitroarene compounds represent unique evolutionary models, as their metabolic pathways are in the process of adaptation and optimization for consumption these toxic chemicals. We used Acidovorax sp. strain JS42, which is capable growth on nitrobenzene 2-nitrotoluene, experiments to examine how a degradation pathway evolves when its host challenged with direct selective pressure non-native substrates. Although same enzyme initiates 2-nitrotoluene also...
Phosphonate natural products have a history of successful application in medicine and biotechnology due to their ability inhibit essential cellular pathways. This has inspired efforts discover phosphonate by prioritizing microbial strains whose genomes encode uncharacterized biosynthetic gene clusters (BGCs). Thus, success genome mining is dependent on establishing the fundamental principles underlying biosynthesis inhibitory chemical moieties facilitate accurate prediction BGCs...
Many toxic man-made compounds have been introduced into the environment, and bacterial strains that are able to grow on them ideal model systems for studying evolution of metabolic pathways regulatory systems. Acidovorax sp. strain JS42 is unique in its ability use 2-nitrotoluene as a sole carbon, nitrogen, energy source growth. The LysR-type transcriptional regulator NtdR activates expression degradation genes not only when nitroaromatic present, but also presence wide range aromatic acids...