Hetong Yang

Viruses as self-assembled nanocontainers for encapsulation of functional cargoes

Viruses naturally exhibit an incredible variety of sophisticated nanostructures, which makes them ideal biological building blocks for nanoengineered material research. By mimicking their spontaneous assembly process, tremendous advances have been made towards utilizing virus and virus-like particles (VLPs) as protein cages, scaffolds, and templates for nanomaterials in the last few years. This review outlines recent progress in the field of bionanotechnology in which viruses are introduced to encapsulate various functional cargoes in a precise and controlled fashion. The encapsulation mechanisms are summarized into three main strategies: electrostatic interaction, chemical conjugation, and covalent attachment by genetic manipulation. The combination with chemical modification and genetic engineering heralds a brilliant future for fabrication of functional nanomaterials. These well-defined architectures will find attractive applications in biosensing, drug delivery, enzyme confinement, light-harvesting system, and pharmaceutical therapy.

Surface modification of cowpea chlorotic mottle virus capsids via a copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction and their adhesion behavior with HeLa cells

A copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction was exploited for the surface modification of cowpea chlorotic mottle virus (CCMV). The exposed carboxyl residues of the CCMV capsids were modified with an alkyne and then further modified with an azide, using a triazole connection in the presence of CuSO4, tris(2-carboxyethyl)phosphine hydrochloride (TCEP), and a bathocuproin disulfonic acid disodium salt (BCDS). Fluorogenic coumarin was successfully grafted onto the CCMV capsids and monitored by fast protein liquid chromatography (FPLC) and UV-irradiated SDS-PAGE. An oligo-ethylene glycol (OEG) short chain and an Arg-Gly-Asp (RGD) peptide were also connected to the CCMV capsids via the CuAAC reaction. Size-exclusion FPLC, transmission electron microscopy (TEM), and dynamic light scattering (DLS) analyses confirmed the modification and integrity of the viral capsids. Interestingly, OEG-CCMV displayed a unique phenomenon of connected bridges with the intact capsids crosslinked to each other. Coumarin-CCMV, OEG-CCMV, and RGD-CCMV were absorbed onto APTES slides for cell binding with HeLa cells. The opposite adhesion behavior of OEG-CCMV and RGD-CCMV indicated the inhibition effect of OEG and the promotion effect of RGD for cell attachment. This provides a generalized method for chemical modification of the surface of virus capsids with multivalent ligands, which demonstrates the potential applications in bioimaging, tissue engineering, and drug delivery.

Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, P.R. China

BackgroundSoil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. An enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. In the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation.MethodsAtrazine-degrading bacteria were isolated by direct plating on a specially developed SM agar. The atrazine degradation genes trzN and atzABC were detected by multiplex PCR. The diversity of atrazine degraders was characterized by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) genotyping followed by 16S rRNA gene phylogenetic analysis. The occurrence of atrazine-degrading bacteria was also assessed by conventional PCR targeting trzN and atzABC in soil DNA.ResultsA total of 116 atrazine-degrading isolates were recovered from bulk and rhizosphere soils sampled near an atrazine factory and from geographically distant maize fields. Fifteen genotypes were distinguished among 56 industrial isolates, with 13 of them representing eight phylogenetic groups of the genus Arthrobacter. The remaining two were closely related to Pseudomonas alcaliphila and Gulosibacter molinativorax and constituted major components of the atrazine-degrading community in the most heavily contaminated industrial plantless soil. All isolates from the adjacent sites inhabited by cogon grass or common reed were various Arthrobacter spp. with a strong prevalence of A. aurescens group. Only three genotypes were distinguished among 60 agricultural strains. Genetically similar Arthrobacter ureafaciens bacteria which occurred as minor inhabitants of cogon grass roots in the industrial soil were ubiquitous and predominant atrazine degraders in the maize rhizosphere. The other two genotypes represented two distant Nocardioides spp. that were specific to their geographic origins.ConclusionsDirect plating on SM agar enabled rapid isolation of atrazine-degrading bacteria and analysis of their natural diversity in soil. The results obtained provided evidence that contaminated soils harbored communities of genetically distinct bacteria capable of individually degrading and utilizing atrazine. The community structures of culturable atrazine degraders were habitat-specific. Bacteria belonging to the genus Arthrobacter were the predominant degraders of atrazine in the plant rhizosphere.

Colonization of plant roots and enhanced atrazine degradation by a strain of Arthrobacter ureafaciens

Our previous research found that culturable atrazine degraders associated with maize roots were dominated by genetically similar strains of Arthrobacter ureafaciens, suggesting their rhizosphere competence. The present study aimed to assess the root-colonizing capacity of strain A. ureafaciens DnL1-1 and to evaluate consequent root-associated degradation of atrazine. A soil-sand assay and pot experiments provided evidence that A. ureafaciens DnL1-1 competitively colonized roots of maize, wheat, and alfalfa following seed inoculation. Atrazine was not absolutely required but promoted colonization of plant roots by the bacterium. In association with plants, A. ureafaciens DnL1-1 enhanced the degradation of atrazine and strongly reduced accumulation of its dealkylated metabolites. Our results show that after low-level inoculation of seeds, the bacterium A. ureafaciens DnL1-1 can establish root populations sufficient for the rapid degradation of atrazine in soil that makes it a promising bioremediation agent which can be easily applied to large areas of polluted soil. Application of the root-colonizing, atrazine-degrading Arthrobacter bacteria as seed inoculants may be a reliable remediation strategy for soils contaminated with chlorinated s-triazines and their degradation products.

Draft Genome Sequence of Stenotrophomonas maltophilia Strain B418, a Promising Agent for Biocontrol of Plant Pathogens and Root-Knot Nematode

ABSTRACT Stenotrophomonas maltophilia strain B418 was isolated from a barley rhizosphere in China. This bacterium exhibits broad-spectrum inhibitory activities against plant pathogens and root-knot nematode along with growth-promoting effects. Here, we present the draft genome sequence of S. maltophilia B418.

Trichoderma cyanodichotomus sp. nov., a new soil-inhabiting species with a potential for biological control

During a biodiversity survey of Trichoderma (Ascomycota, Hypocreales, Hypocreaceae) in coastal and lake wetlands of China, a new species, Trichoderma cyanodichotomus, was isolated from Dongting Lake wetland of Hunan province. The strain TW21990-1 was characterized as having two types of conidia and producing a distinct blue-green pigment on potato dextrose agar and cornmeal dextrose agar. The taxonomic position was analyzed using three molecular markers, internal transcribed spacer rDNA, translation elongation factor 1-alpha, and RNA polymerase II subunit B, revealing less than 95.0% homology with all known Trichoderma species. The combined phylogenetic tree further identified T. cyanodichotomus as an independent subgroup belonging to Section Pachybasium, with no close relatives. In vitro antagonistic activity by dual-culture assay exhibited broad inhibition against various plant pathogens, including Botryosphaeria dothidea, Pythium aphanidermatum, Rhizoctonia solani, and Verticillium dahliae. In addition, TW21990-1 demonstrated moderate hydrolase activity of cellulase, chitinase, β-1,3-glucanase, and protease, which might be involved in mycoparasitism. Greenhouse experiments showed strong biocontrol effects against tomato damping-off incited by P. aphanidermatum, together with increased seedling height and weight gain. The identification of T. cyanodichotomus will provide useful information for sufficient utilization of fungal resources.

Fungal and mushroom hydrophobins: A review

Hydrophobins are surface active proteins that are produced by filamentous fungi including mushrooms. Their ability to self-assemble into an amphipathic membrane at any hydrophilic–hydrophobic interface is most intriguing. These small secreted proteins comprise of eight conserved cysteine residues which form four disulfide bridges and an extraordinary hydrophobic patch. Hydrophobins play critical roles in fungal (and/or mushrooms) growth as structural components and in the interaction of fungi and mushrooms with the environment. The biophysical and biochemical properties of the isolated proteins are remarkable, such as strong adhesion, high surface activity and the formation of various self-assembled structures. With the increasing demands of hydrophobins from fungi and mushroom sources, production and purification in large scale is under challenge. Various applications, ranging from food industries, cosmetics, nanotechnology, biosensors and electrodes, to biomaterials and pharmaceuticals are emerging and a bright future is foreseen.

Targeted cowpea chlorotic mottle virus-based nanoparticles with tumor-homing peptide F3 for photothermal therapy

Our aim was to devise targeted drug delivery systems using genetically modified cowpea chlorotic mottle virus (CCMV) capsids by fusion expression with tumorhoming peptide F3 for efficient delivery of therapeutic substances into tumor cells. The RNA-binding domain at the N terminus (amino acid residues 1–25) of CCMV capsid protein (CP) was selectively deleted, and F3 was inserted for the expression in Pichia pastoris. After chromatographic purification, F3-CCMV capsids were obtained via selfassembly of the F3-CP fusion protein and then analyzed by transmission electron microscopy and dynamic light scattering analysis, which revealed spherical nanoparticles (NPs) ca. 18 nm in diameter with regular monodispersity. Near-infrared fluorescent dye IR780 iodide, which has been applied for cancer imaging, photodynamic therapy, and photothermal therapy, was encapsulated in F3-CCMV NPs. The resultant F3-CCMV-IR780 NPs showed excellent molecular targeting to nucleolin receptor overexpressed on the surface of MCF-7 tumor cells. Furthermore, the in vitro cellular uptake and cell viability assay proved a photothermal effect by a single dose of near-infrared laser irradiation. The present system may offer a programmable nanoscaffoldbased drug delivery system vehicle for fabrication of promising therapeutic substances for cancer therapy.