Solubilization and stabilization of bacteriophage MS2 in organic solvents

Application of bacteriophages in biopolymer-based functional food packaging films

Recently, food spoilage caused by pathogens has been increasing. Therefore, applying control strategies is essential. Bacteriophages can potentially reduce this problem due to their host specificity, ability to inhibit bacterial growth, and extend the shelf life of food. When bacteriophages are applied directly to food, their antibacterial activity is lost. In this regard, bacteriophage-loaded biopolymers offer an excellent option to improve food safety by extending their shelf life. Applying bacteriophages in food preservation requires comprehensive and structured information on their isolation, culturing, storage, and encapsulation in biopolymers for active food packaging applications. This review focuses on using bacteriophages in food packaging and preservation. It discusses the methods for phage application on food, their use for polymer formulation and functionalization, and their effect in enhancing food matrix properties to obtain maximum antibacterial activity in food model systems.

Use of whey protein as a natural polymer for the encapsulation of plant biocontrol bacteria: A review

Climate changes, drought, the salinity of water and soil, the emergence of new breeds of pests and pathogens, the industrialization of countries, and environmental contamination are among the factors limiting the production of agricultural products. The use of chemicals (in the form of fertilizers, pesticides and fungicides) to enhance products against biotic and abiotic stresses has limitations. To eliminate the effects of agricultural chemicals, synthetic agrochemicals should be replaced with natural substances and useful microorganisms. To be more effective and efficient, plant biocontrol bacteria need a coating layer around themselves to protect them from adverse conditions. Whey protein, a valuable by-product of the cheese industry, is one of the important natural polymers. Due to its high protein content, safety, and biodegradability, whey can have many applications in agriculture and encapsulation of bacteria to resist pests and plant diseases. This compound is a rich source of amino acids that can activate plant defense systems and defense enzymes. Considering the amazing potentialities of formulation whey protein, this review attends to the efficiency of whey protein as coating layers on fruit and vegetables and in the packaging system to increase the shelf life of agricultural products against phytopathogens.

Single-Point Mutations in Qβ Virus-like Particles Change Binding to Cells

Virus-like particles (VLPs) constitute large, polyvalent platforms onto which a wide variety of functional units can be grafted. Their use in biological settings often depends on their specific binding to cells or receptors of interest; this can be compromised by excessive nonspecific association with other cells. We found that lysine residues mediate such nonspecific interactions, presumably by virtue of protonation and interaction with anionic membrane lipid headgroups and/or complementary residues of cell surface proteins and polysaccharides. Chemical acylation of surface-exposed amines of the Qβ VLP led to a significant reduction in the association of particles with mammalian cells. Single-point mutations of particular lysine residues to either glutamine, glutamic acid, tryptophan, or phenylalanine were mostly well-tolerated and formed intact capsids, but the introduction of double and triple mutants was far less forgiving. Introduction of glutamic acid at position 13 (K13E) led to a dramatic increase in cellular binding, whereas removal of the lysine at position 46 (K46Q) led to an equally striking reduction. Several plasma membrane components were found to specifically interact with the Qβ capsid irrespective of surface charge. These results suggest that specific cellular interactions are engaged or obviated by such mutations and provide us with more "benign" particles to which can be added binding functionality for targeted delivery applications.

Development of immunoassays with high sensitivity for detecting imidacloprid in environment and agro-products using phage-borne peptides

Imidacloprid is the most widely used neonicotinoid insecticide and has been reported to pose a threat to ecological security and human health. Therefore, simple-to-operate and highly sensitive methods for the detection of trace levels of imidacloprid are necessary. Here, we isolated two phage-borne peptides that compete with imidacloprid to bind the monoclonal antibody (mAb) 3D11 from phage display peptide libraries. A phage-enzyme-linked immunosorbent assay (P-ELISA) and two phage time-resolved fluoroimmunoassays (P-TRFIAs) for the detection of imidacloprid were developed using the phage-borne peptides as substitutes for chemically synthesized antigens. After systematic optimization, the half-maximum inhibition concentrations (IC₅₀) of the P-ELISA, P-TRFIA-1, and P-TRFIA-2 were 0.067 ng mL^-1, 0.085 ng mL^-1, and 0.056 ng mL^-1, respectively. Based on their IC₅₀ values, the sensitivities of the P-ELISA and P-TRFIAs were more than four times greater than those of previous immunoassays. Additionally, the immunoassays showed satisfactory recovery in the detection of spiked samples and good correlation with high performance liquid chromatography (HPLC) for the detection of samples containing incurred residues.

The use of biological seed coatings based on bacteriophages and polymers against Clavibacter michiganensis subsp. nebraskensis in maize seeds

Biological control of bacteria with bacteriophages is a viable alternative to antibiotics. To be successful, biological control bacteriophages must be stable when exposed to the environment. Stabilization can be achieved through incorporation of bacteriophages into polymers and stabilizers that will be coated onto the seed. For this study, bacteriophages against Clavibacter michiganensis subsp. nebraskensis (Cmn), the causal agent of Goss's wilt, were incorporated into polyvinyl polymers with alcohol, ether and pyrrolidone functional groups and coated onto maize (Zea mays L.) seeds. The objectives of this study were to evaluate polymers and stabilizers that can protect Clavibacter michiganensis subsp. nebraskensis (CN8) bacteriophages against dehydration during storage. Bacteriophages stability when coated on seed depended on the glass transition temperature (Tg), functional groups of the polymer, and the presence of stabilizers such as sugars and proteins. Polyvinyl alcohol (PVOH) provided the greatest stability for CN8 bacteriophages on seed when coatings did not contain a stabilizer. A possible reason for the greater stability of this coating is having a glass transition temperature (Tg) very close to ambient temperature. PVOH combined with whey protein isolate (WPI) maintained CN8 bacteriophage activity in storage for four months at 26 °C and seven months at 10 °C. This coating also significantly reduced bacterial loads in seedlings grown from contaminated seeds, without affecting seed germination. Bacteriophage-polymer coatings which are stable during drying and storage, and are compatible with biological systems, not only provide an alternative to traditional antibiotics in agriculture, but also provide options for food, environmental and medical applications.

Monitoring the Disassembly of Virus-like Particles by 19F-NMR

Virus-like particles (VLPs) are stable protein cages derived from virus coats. They have been used extensively as biomolecular platforms, e.g., nanocarriers or vaccines, but a convenient in situ technique is lacking for tracking functional status. Here, we present a simple way to monitor disassembly of 19F-labeled VLPs derived from bacteriophage Qβ by 19F NMR. Analysis of resonances, under a range of conditions, allowed determination not only of the particle as fully assembled but also as disassembled, as well as detection of a degraded state upon digestion by cells. This in turn allowed mutational redesign of disassembly and testing in both bacterial and mammalian systems as a strategy for the creation of putative, targeted-VLP delivery systems.

Bioengineered protein-based nanocage for drug delivery

Nature, in its wonders, presents and assembles the most intricate and delicate protein structures and this remarkable phenomenon occurs in all kingdom and phyla of life. Of these proteins, cage-like multimeric proteins provide spatial control to biological processes and also compartmentalizes compounds that may be toxic or unstable and avoids their contact with the environment. Protein-based nanocages are of particular interest because of their potential applicability as drug delivery carriers and their perfect and complex symmetry and ideal physical properties, which have stimulated researchers to engineer, modify or mimic these qualities. This article reviews various existing types of protein-based nanocages that are used for therapeutic purposes, and outlines their drug-loading mechanisms and bioengineering strategies via genetic and chemical functionalization. Through a critical evaluation of recent advances in protein nanocage-based drug delivery in vitro and in vivo, an outlook for de novo and in silico nanocage design, and also protein-based nanocage preclinical and future clinical applications will be presented.

Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses

Laser-induced all-atom nonequilibrium molecular dynamics simulation of virus dissociation.

Photonics and plasmonics go viral: self-assembly of hierarchical metamaterials

Sizing and shaping of mesoscale architectures with nanoscale features is a key opportunity to produce the next generation of higher-performing products and at the same time unveil completely new phenomena. This review article discusses recent advances in the design of novel photonic and plasmonic structures using a biology-inspired design. The proteinaceous capsids from viruses have long been discovered as platform technologies enabling unique applications in nanotechnology, materials, bioengineering, and medicine. In the context of materials applications, the highly organized structures formed by viral capsid proteins provide a 3D scaffold for the precise placement of plasmon and gain materials. Based on their highly symmetrical structures, virus-based nanoparticles have a high propensity to self-assemble into higher-order crystalline structures, yielding hierarchical hybrid materials. Recent advances in the field have led to the development of virus-based light harvesting systems, plasmonic structures for application in high-performance metamaterials, binary nanoparticle lattices, and liquid crystalline arrays for sensing or display technologies. There is still much that could be explored in this area, and we foresee that this is only the beginning of great technological advances in virus-based materials for plasmonics and photonics applications.

Polymeric systems incorporating plant viral nanoparticles for tailored release of therapeutics

Therapeutic polylactide (PLA) nanofibrous matrices are fabricated by incorporating plant viral nanoparticles (PVNs) infused with fluorescent agents ethidium bromide (EtBr) and rhodamine (Rho), and cancer therapeutic doxorubicin (Dox). The native virus, Red clover necrotic mosaic virus (RCNMV), reversibly opens and closes upon exposure to the appropriate environmental stimuli. Infusing RCNMV with small molecules allows the incorporation of PVN(Active) into fibrous matrices via two methods: direct processing by in situ electrospinning of a polymer and PVNs solution or immersion of the matrix into a viral nanoparticle solution. Five organic solvents commonly in-use for electrospinning are evaluated for potential negative impact on RCNMV stability. In addition, leakage of rhodamine from the corresponding PVN(Rho) upon solvent exposure is determined. Incorporation of the PVN into the matrices are evaluated via transmission electron, scanning electron and fluorescent microscopies. Finally, the percent cumulative release of doxorubicin from both PLA nanofibers and PLA and polyethylene oxide (PEO) hybrid nanofibers demonstrate tailored release due to the incorporation of PVN(Dox) as compared to the control nanofibers with free Dox. Preliminary kinetic analysis results suggest a two-phase release profile with the first phase following a hindered Fickian transport mechanism for the release of Dox for the polymer-embedded PVNs. In contrast, the nanofiber matrices that incorporate PVNs through the immersion processing method followed a pseudo-first order kinetic transport mechanism.

Liquid viruses by nanoscale engineering of capsid surfaces

Surface engineering of plant virus capsids via cationization (1) and stoichiometric coupling of a polymer surfactant coronal layer (2) produces a highly concentrated, solvent-free liquid virus at 28 °C. These ionic bionanoconstructs are viscoelastic, retain plant infectivity and can be dispersed in a range of organic solvents for aerosol delivery.

Engineered mutations change the structure and stability of a virus-like particle

The single-coat protein (CP) of bacteriophage Qβ self-assembles into T = 3 icosahedral virus-like particles (VLPs), of interest for a wide range of applications. These VLPs are very stable, but identification of the specific molecular determinants of this stability is lacking. To investigate these determinants along with manipulations that confer more capabilities to our VLP material, we manipulated the CP primary structure to test the importance of various putative stabilizing interactions. Optimization of a procedure to incorporate fused CP subunits allowed for good control over the average number of covalent dimers in each VLP. We confirmed that the disulfide linkages are the most important stabilizing elements for the capsid and that acidic conditions significantly enhance the resistance of VLPs to thermal degradation. Interdimer interactions were found to be less important for VLP assembly than intradimer interactions. Finally, a single point mutation in the CP resulted in a population of smaller VLPs in three distinct structural forms.

Inactivation of aerosolized Bacillus atrophaeus (BG) endospores and MS2 viruses by combustion of reactive materials

Accidental release of biological agents from a bioweapon facility may contaminate large areas, possibly causing disastrous environmental consequences. To address this issue, novel halogen-containing reactive materials are being designed with the added capability to inactivate viable airborne microorganisms. This study determined the efficiency of combustion products of such materials to inactivate aerosolized bacteria and viruses. Spores of Bacillus atrophaeus and MS2 viruses dispersed in dry air were exposed for subsecond time intervals to hydrocarbon flames seeded with different reactive powders so that bioaerosol particles interacted with the combustion products in a controlled high-temperature environment. The experiments were designed to quantify differences in the biocidal effects of different reactive material powders including Al and Mg, a B•Ti nanocomposite, an 8Al•MoO(3) nanothermite, and a novel Al•I(2) nanocomposite. Compared to pure hydrocarbon flame, powder-seeded flame (with no iodine) produced about an order of magnitude greater inactivation of bacterial spores. The iodine-containing material increased the spore inactivation by additional 2 orders of magnitude. The aerosolized MS2 viruses (generally not as stress-resistant as spores) were fully inactivated when exposed to combustion of either the iodinated or noniodinated powders. Overall, the study suggests a great biocidal potential of combustion products generated by novel iodine-containing nanocomposite materials.

Virus-based nanocarriers for drug delivery

New nanocarrier platforms based on natural biological building blocks offer great promises in revolutionalizing medicine. The usage of specific protein cage structures: virus-like particles (VLPs) for drug packaging and targetted delivery is summarized here. Versatile chemical and genetic modifications on the outer surfaces and inner cavities of VLPs facilitate the preparation of new materials that could meet the biocompatibility, solubility and high uptake efficiency requirements for drug delivery. A full evaluation on the toxicity, bio-distribution and immunology of these materials are envisaged to boost their application potentials.

Antiviral properties of polymeric aziridine- and biguanide-modified core-shell magnetic nanoparticles

Polycationic superparamagnetic nanoparticles (∼150-250 nm) were evaluated as virucidal agents. The particles possess a core-shell structure, with cores consisting of magnetite clusters and shells of functional silica covalently bound to poly(hexamethylene biguanide) (PHMBG), polyethyleneimine (PEI), or PEI terminated with aziridine moieties. Aziridine was conjugated to the PEI shell through cationic ring-opening polymerization. The nanometric core-shell particles functionalized with biguanide or aziridine moieties are able to bind and inactivate bacteriophage MS2, herpes simplex virus HSV-1, nonenveloped infectious pancreatic necrosis virus (IPNV), and enveloped viral hemorrhagic septicaemia virus (VHSV). The virus-particle complexes can be efficiently removed from the aqueous milieu by simple magnetocollection.

Bacteriophages and viruses as a support for organic synthesis and combinatorial chemistry

Display of polypeptide on the coat proteins of bacteriophages and viruses is a powerful tool for selection and amplification of libraries of great diversity. Chemical diversity of these libraries, however, is limited to libraries made of natural amino acid side chains. Bacteriophages and viruses can be modified chemically; peptide libraries presented on phage thus can be functionalized to yield moieties that cannot be encoded genetically. In this review, we summarize the possibilities for using bacteriophage and viral particles as support for the synthesis of diverse chemically modified peptide libraries. This review critically summarizes the key chemical considerations for on-phage syntheses such as selection of reactions compatible with protein of phage, modification of phage "support" that renders it more suitable for reactions, and characterization of reaction efficiency.

Simulated sunlight action spectra for inactivation of MS2 and PRD1 bacteriophages in clear water

Action spectra for simulated sunlight were measured in clear water for two viruses: PRD1, a double-stranded DNA bacteriophage, and MS2, a single-stranded RNA bacteriophage. Viruses were diluted into phosphate buffered saline (20 mM PBS, pH 7.5) and exposed for 22 h to simulated sunlight either directly or through one of six glass filters with 50% cutoff wavelengths ranging from 280 to 350 nm. Virus survival was measured using the double agar layer plaque method. Both UVA (320-400 nm) and UVB (280-320 nm) light were found to contribute to PRD1 inactivation, while only UVB inactivated MS2. A computational model was developed for interpreting these action spectra with 3-nm resolution. Using these methods, we provide detailed estimates of the sensitivity of MS2 and PRD1 to photoinactivation from 285 to 345 nm. The resulting sensitivity coefficients can be combined with solar spectra to estimate inactivation rates in clear water under different sunlight conditions. This approach will be useful for modeling the inactivation of viruses and other microorganisms in sunlit natural and engineered systems.

Surface functionalization of virus-like particles by direct conjugation using azide-alkyne click chemistry

We present a cell-free protein synthesis (CFPS) platform and a one-step, direct conjugation scheme for producing virus-like particle (VLP) assemblies that display multiple ligands including proteins, nucleic acids, and other molecules. Using a global methionine replacement approach, we produced bacteriophage MS2 and bacteriophage Qβ VLPs with surface-exposed methionine analogues (azidohomoalanine and homopropargylglycine) containing azide and alkyne side chains. CFPS enabled the production of VLPs with yields of ~ 300 μg/mL and with 85% incorporation of methionine analogues without requiring a methionine auxotrophic production host. We then directly conjugated azide- and alkyne-containing proteins (including an antibody fragment and the granulocyte-macrophage colony stimulating factor, or GM-CSF), nucleic acids and poly(ethylene glycol) chains to the VLP surface using Cu(I) catalyzed click chemistry. The GM-CSF protein, after conjugation to VLPs, was shown to partially retain its ability to stimulate the proliferation of cells. Conjugation of GM-CSF to VLPs resulted in a 3-5-fold reduction in its bioactivity. The direct attachment scheme facilitated conjugation of three different ligands to the VLPs in a single step, and enabled control of the relative ratios and surface abundance of the attached species. This platform can be used for the production of novel VLP bioconjugates for use as drug delivery vehicles, diagnostics, and vaccines.

Dramatic thermal stability of virus-polymer conjugates in hydrophobic solvents

We have developed a method for integrating the self-assembling tobacco mosaic virus capsid into hydrophobic solvents and hydrophobic polymers. The capsid was modified at tyrosine residues to display an array of linear poly(ethylene glycol) chains, allowing it to be transferred into chloroform. In a subsequent step, the capsids could be transferred to a variety of hydrophobic solvents, including benzyl alcohol, o-dichlorobenzene, and diglyme. The thermal stability of the material against denaturation increased from 70 °C in water to at least 160 °C in hydrophobic solvents. With a view toward material fabrication, the polymer-coated TMV rods were also incorporated into solid polystyrene and thermally cast at 110 °C. Overall, this process significantly expands the range of processing conditions for TMV-based materials, with the goal of incorporating these templated nanoscale systems into conductive polymer matrices.

Effects of ionic strength on bacteriophage MS2 behavior and their implications for the assessment of virus retention by ultrafiltration membranes

Bacteriophage MS2 is widely used as a surrogate to estimate pathogenic virus elimination by membrane filtration processes used in water treatment. Given that this water technology may be conducted with different types of waters, we focused on investigating the effects of ionic strength on MS2 behavior. For this, MS2 was analyzed while suspended in solutions of various ionic strengths, first in a batch experiment and second during membrane ultrafiltration, and quantified using (i) quantitative reverse transcriptase PCR (qRT-PCR), which detects the total number of viral genomes, (ii) qRT-PCR without the RNA extraction step, which reflects only particles with a broken capsid (free RNA), and (iii) the PFU method, which detects only infectious viruses. At the beginning of the batch experiments using solutions containing small amounts of salts, losses of MS2 infectivity (90%) and broken particles (20%) were observed; these proportions did not change during filtration. In contrast, in high-ionic-strength solutions, bacteriophage kept its biological activity under static conditions, but it quickly lost its infectivity during the filtration process. Increasing the ionic strength decreased both the inactivation and the capsid breakup in the feed suspension and increased the loss of infectivity in the filtration retentate, while the numbers of MS2 genomes were identical in both experiments. In conclusion, the effects of ionic strength on MS2 behavior may significantly distort the results of membrane filtration processes, and therefore, the combination of classical and molecular methods used here is useful for an effective validation of the retention efficiency of ultrafiltration membranes.

Virus engineering: functionalization and stabilization

Chemically and/or genetically engineered viruses, viral capsids and viral-like particles carry the promise of important and diverse applications in biomedicine, biotechnology and nanotechnology. Potential uses include new vaccines, vectors for gene therapy and targeted drug delivery, contrast agents for molecular imaging and building blocks for the construction of nanostructured materials and electronic nanodevices. For many of the contemplated applications, the improvement of the physical stability of viral particles may be critical to adequately meet the demanding physicochemical conditions they may encounter during production, storage and/or medical or industrial use. The first part of this review attempts to provide an updated general overview of the fast-moving, interdisciplinary virus engineering field; the second part focuses specifically on the modification of the physical stability of viral particles by protein engineering, an emerging subject that has not been reviewed before.

Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration

Background

Thermostable enzymes from thermophilic microorganisms are playing more and more important roles in molecular biology R&D and industrial applications. However, over-production of recombinant soluble proteins from thermophilic microorganisms in mesophilic hosts (e.g. E. coli) remains challenging sometimes.

Results

An open reading frame TM0438 from a hyperthermophilic bacterium Thermotoga maritima putatively encoding 6-phosphogluconate dehydrogenase (6PGDH) was cloned and expressed in E. coli. The purified protein was confirmed to have 6PGDH activity with a molecular mass of 53 kDa. The k_cat of this enzyme was 325 s^-1 and the K_m values for 6-phosphogluconate, NADP⁺, and NAD⁺ were 11, 10 and 380 μM, respectively, at 80°C. This enzyme had half-life times of 48 and 140 h at 90 and 80°C, respectively. Through numerous approaches including expression vectors, hosts, cultivation conditions, inducers, and codon-optimization of the 6pgdh gene, the soluble 6PGDH expression levels were enhanced to ~250 mg per liter of culture by more than 500-fold. The recombinant 6PGDH accounted for >30% of total E. coli cellular proteins when lactose was used as a low-cost inducer. In addition, this enzyme coupled with glucose-6-phosphate dehydrogenase for the first time was demonstrated to generate two moles of NADPH per mole of glucose-6-phosphate.

Conclusion

We have achieved a more than 500-fold improvement in the expression of soluble T. maritima 6PGDH in E. coli, characterized its basic biochemical properties, and demonstrated its applicability for NADPH regeneration by a new enzyme cocktail. The methodology for over-expression and simple purification of this thermostable protein would be useful for the production of other thermostable proteins in E. coli.