Biology subjects

YANG, Q.

Publications and source records attributed to YANG, Q..

4 recordsLinked to original sources

bioRxiv2026

Isolation, extraction, and physicochemical characterization of exosome-like nanovesicles from ginseng adventitious roots in tissue culture

This study aimed to establish a method for isolating exosome-like nanovesicles from ginseng adventitious roots and their culture supernatant, to investigate the effects of methyl jasmonate (MeJA) induction on vesicle yield and composition, and to provide experimental evidence for the scalable production of ginseng-derived exosome-like nanovesicles. Exosome-like nanovesicles were isolated from ginseng adventitious roots and culture supernatant using low-speed centrifugation combined with stirred-cell ultrafiltration. Physicochemical characterization was performed using transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), Zeta potential analysis, and Q-ToF LC-MS lipidomics. Ginseng adventitious roots were treated with 200 M MeJA to evaluate changes in vesicle particle concentration, total protein, total saponins, and miRNA expression before and after induction. Paraffin section fluorescence staining was used to observe the distribution of vesicle-related signals in adventitious root tissues. Exosome-like nanovesicles with typical bilayer membrane structures were isolated from both ginseng adventitious roots and culture supernatant.The particle size ranged from 77.333 to 171.733 nm, and the particle concentration ranged from 2.1E+8 to 7.6E+10 /mL. The vesicles contained lipid components including glycerides, phospholipids, and sphingolipids. Induction with 200 M MeJA increased vesicle particle concentration and total protein content, significantly upregulated the total saponin level in vesicles derived from adventitious roots, and altered the miRNA expression pattern of the vesicles. Tissue section fluorescence observation showed overlap between vacuolar markers and membrane vesicle dye signals. Low-speed centrifugation combined with ultrafiltration can effectively prepare ginseng-derived exosome-like nanovesicles. MeJA induction can regulate vesicle yield and active components, providing foundational data for the scalable process development of such vesicles.

plant biology↗

bioRxiv2025

Tryptophan Chemistry Driven by a Widespread Cytochrome P422 Enzyme Family

Tryptophan serves as a versatile biosynthetic precursor across living organisms. While heme-binding proteins (HBPs) mediate key reactions in tryptophan transformation, the full diversity of HBPs remains largely unexplored. Here, we developed the novel Cofactor-Integrative Structural Inspector (CISSspector) to systematically identify HBPs in the extensive extant microbial genomic sequence database, which revealed several uncharacterized HBP families. We experimentally characterized one of the most prominent families, the cytochrome P422 (formerly DUF6875) family, distributed throughout the prokaryotes and eukaryotes. Strikingly, we discovered that this enzyme family orchestrates four chemically distinct and biochemically unprecedented transformations, with regioselectivity, including N1-, C6-, and C7-hydroxylations and intramolecular C-S bond formations. Notably, the discovery of enzymes capable of Trp N1- and C7-hydroxylation addresses a long-standing gap in the natural enzyme arsenal. Structural analysis of the representative cytochrome P422 enzyme Mc170 revealed a structurally unique HBP fold in which conserved residues form a substrate "clamp" that positions the tryptophan indole ring for selective modification. Our work unveils a hidden enzymatic repertoire of HBPs, expands the known landscape of tryptophan metabolism, and establishes an artificial intelligence-augmented framework for discovering cryptic enzymes with broad implications for synthetic biology and natural product discovery.

biochemistry↗

bioRxiv2023

Metagenomic Analysis Reveals the Transfer of Antibiotic Resistance from Manure-Fertilized Soil to Carrot Microbiome

Crops grown in manure-fertilized soil are more likely to be contaminated with antibiotic resistance genes (ARGs) than when grown in unmanured soil, and therefore more likely to represent a route of ARG exposure to consumers. Existing studies scarcely focused on the residual ARGs on the carrot peel growing in the manured soil after the careful washing. In the present study, residual microbiome and resistome on the carrots surface (Daucus carota subsp. sativus) at harvest after careful washing was investigated to reveal the impact of manure fertilization. Residual surface bacteria were recovered from the peel, and total bacterial DNA was extracted for the high-throughput sequencing-based metagenomic analysis. Despite the overall unaltered level of alpha diversity in both soil and carrot peel samples, manuring increased the resistome in soil significantly, but not on the carrot peel. The largely overlapped resistome detected on carrots grown with and without manuring, plus the pattern revealed by source tracking analysis indicated a soil-source of ARGs on carrots, whereas the beta-lactamases CTX-M-84, OXY-4, and CTX-M-122 only detected in the manured soil and on the carrot peel harvested from manured soil indicated that beta-lactamases appear to be transferred from manure to the carrot. The evident impact of soil resistome and community on carrot peel microbiome, plus the limited level of plasmid and integron mediated ARGs transfer suggested the main ARGs transfer pathway from manured soil to carrot peel was via the colonization of rhizosphere soil microbes. To further elucidate the ARG propagation within the soil-carrot system, a network was constructed to explore the pattern of nine types of concurrent ARGs genotypes carried by ten different host populations, emphasizing that the residual antibiotic resistances transfer via raw carrot represents a risk to human health even after extensive washing.

microbiology↗

bioRxiv2021

Crucial Roles of Carotenoids as Bacterial Endogenous Defense System for Bacterial Radioresistance of Deinococcus radiodurans

BackgroundThe central dogma of radiation biology is that the cytotoxic and mutagenic effects of radiation are principally the result of biological macromolecules (DNA, RNA, polysaccharides, proteins and lipids) damage caused during the course of irradiation. Previous studies on the radioresistance of the extremely radiation-resistant red-carotenoid-pigmented bacterium Deinococcus radiodurans have been focused on DNA repair system. However, relative little is known about the biochemical basis of the extraordinary recovery capacity of D. radiodurans for ionizing radiation and can include hundreds of DNA double-strand breaks. Methodology/Principal FindingsHere we identified a novel carotenoid in D. radiodurans as ((all-E)-1-hydroxy-3,4-didehydro-1,2,2,3-quahydro-{beta},{psi}-carotene-4-one-1) and characterized the intracellular distribution of carotenoids. Following exposure to ionizing radiation, the wild-type parent of D. radiodurans survived much higher compared with radiation-sensitive colorless mutants screened by 60Co irradiation and by knockout of crtB or crtI genes for the carotenoid biosynthesis. Electron paramagnetic resonance spectroscopy analysis showed that two carotenoid can effectively scavenge radicals including superoxide anion (O2.-) and hydroxyl radical (.OH). Consistent results showing the substantial antioxidant abilities of the two carotenoids were obtained by UV-induction of bacteriophage {lambda} method in vivo, and the detectable reaction potentials of two carotenoids with nitric oxide (NO) evaluated by ultraviolet-visible near-infrared ray (UV/vis/NIR) spectra assay. Conclusions/SignificanceOur findings support the idea that the degree of bacterial radioresistance of D. radiodurans is partly related to the levels of carotenoids in the cells. Carotenoids, as an important member of the structural and non-structural components of the cells, are endogenous scavengers of reactive oxygen species and can effectively quench radicals generated during irradiation. The current work suggests that carotenoids play a previously unrecognized protection role in the endogenous defense System (EDS) that facilitates the recovery from radiation injury. And we propose a complete model to elucidate the mechanisms of extreme radioresistance in this remarkable bacterium.

microbiology↗