Mutational analyses of the putative calcium binding site and hinge of the turnip crinkle virus coat protein

Calcium signaling: an emerging player in plant antiviral defense

Calcium is a universal messenger in different kingdoms of living organisms and regulates most physiological processes, including defense against pathogens. The threat of viral infections in humans has become very clear in recent years, and this has triggered detailed research into all aspects of host-virus interactions, including the suppression of calcium signaling in infected cells. At the same time, however, the threat of plant viral infections is underestimated in society, and research in the field of calcium signaling during plant viral infections is scarce. Here we highlight an emerging role of calcium signaling for antiviral protection in plants, in parallel with the known evidence from studies of animal cells. Obtaining more knowledge in this domain might open up new perspectives for future crop protection and the improvement of food security.

The Red clover necrotic mosaic virus capsid protein N-terminal lysine-rich motif is a determinant of symptomatology and virion accumulation

The interaction between viral capsid protein (CP) and its cognate viral RNA modulates many steps in the virus infection cycle, such as replication, translation and assembly. The N-terminal 50 amino acids of the Red clover necrotic mosaic virus (RCNMV) CP are rich in basic residues (especially lysine) and are essential for the core functions of the CP, namely RNA binding and virion assembly. To further elucidate additional biological roles for these basic residues, a series of alanine substitution mutations was introduced into infectious clones of RCNMV RNA-1 and assayed for symptomatology, virion formation and systemic infection. Infectivity assays conducted in Nicotiana benthamiana revealed that all nine alanine substitution mutants (ASMs) were competent for systemic infection. Two ASMs (K4A and K7A/K8A) induced severe symptoms and delayed the systemic spread of viral genomes when compared with wild-type RCNMV. However, these ASMs were still competent for virion formation. Three other ASMs (K25A, K33A and K38A) displayed milder symptoms and significant reductions in virion accumulation when compared with wild-type RCNMV, but retained the ability to spread systemically. Evidence from these last three ASMs, as well as a CP null mutant, showed that RCNMV is able to move systemically in N. benthamiana as a nonvirion form. These observations reaffirm the necessity of the N-terminal lysine-rich residues of the RCNMV CP for efficient virion accumulation. They also reveal additional roles for the CP in the modulation of host symptomatology, independent of its role in virion assembly and the rate of systemic viral movement in N. benthamiana.

Viral calciomics: interplays between Ca2+ and virus

Ca²⁺ is one of the most universal and versatile signaling molecules and is involved in almost every aspect of cellular processes. Viruses are adept at utilizing the universal Ca²⁺ signal to create a tailored cellular environment that meets their own demands. This review summarizes most of the known mechanisms by which viruses perturb Ca²⁺ homeostasis and utilize Ca²⁺ and cellular Ca²⁺-binding proteins to their benefit in their replication cycles. Ca²⁺ plays important roles in virion structure formation, virus entry, viral gene expression, posttranslational processing of viral proteins and virion maturation and release. As part of the review, we introduce an algorithm to identify linear “EF-hand” Ca²⁺-binding motifs which resulted in the prediction of a total of 93 previously unrecognized Ca²⁺-binding motifs in virus proteins. Many of these proteins are nonstructural proteins, a class of proteins among which Ca²⁺ interactions had not been formerly appreciated. The presence of linear Ca²⁺-binding motifs in viral proteins enlarges the spectrum of Ca²⁺–virus interplay and expands the total scenario of viral calciomics.

On-virus construction of polyvalent glycan ligands for cell-surface receptors

Glycans arrayed on the exterior of virus particles were used as substrates for glycosyltransferase reactions to build di- and trisaccharides from the virus surface. The resulting particles exhibited tight and specific associations with cognate receptors on beads and cells, in one example defeating in cis cell-surface interactions in a manner characteristic of polyvalent binding. Combined with the ability of viruses to provide structurally well-defined attachment points, the methodology provides a convenient and powerful way to prepare complex carbohydrate ligands for clustered receptors.

Synthesis and structure of a triptycene-based nanosized molecular cage

A triptycene-based nanosized molecular cage was designed and efficiently synthesized by Eglington-Glaser coupling reaction, and its structure was determined by NMR, MS spectrometry and X-ray analysis. Moreover, it was found that the cage molecules could pack into a microporous structure in the solid state and 1,3,5-trimethylbenzene molecules were located in the channels.

Fluorescent signal amplification of carbocyanine dyes using engineered viral nanoparticles

We report enhancement in the fluorescent signal of the carbocyanine dye Cy5 by using an engineered virus as a scaffold to attach >40 Cy5 reporter molecules at fixed locations on the viral capsid. Although cyanine dye loading is often accompanied by fluorescence quenching, our results demonstrate that organized spatial distribution of Cy5 reporter molecules on the capsid obviates this commonly encountered problem. In addition, we observe energy transfer from the virus to adducted dye molecules, resulting in a highly fluorescent viral nanoparticle. We have used this enhanced fluorescence for the detection of DNA-DNA hybridization. When compared with the most often used detection methods in a microarray-based genotyping assay for Vibrio cholerae O139, these viral nanoparticles markedly increased assay sensitivity, thus demonstrating their applicability for existing DNA microarray protocols.

Physical Controls on Directed Virus Assembly at Nanoscale Chemical Templates

Viruses are attractive building blocks for nanoscale heterostructures, but little is understood about the physical principles governing their directed assembly. In situ force microscopy was used to investigate organization of Cowpea Mosaic Virus engineered to bind specifically and reversibly at nanoscale chemical templates with sub-30 nm features. Morphological evolution and assembly kinetics were measured as virus flux and inter-viral potential were varied. The resulting morphologies were similar to those of atomic-scale epitaxial systems, but the underlying thermodynamics was analogous to that of colloidal systems in confined geometries. The 1D templates biased the location of initial cluster formation, introduced asymmetric sticking probabilities, and drove 1D and 2D condensation at sub-critical volume fractions. The growth kinetics followed a t(1/2) law controlled by the slow diffusion of viruses. The ability of poly(ethylene glycol) (PEG) to induce the lateral expansion of virus clusters away from the 1D templates suggests a significant role for weak interactions.

Cowpea mosaic virus for material fabrication: addressable carboxylate groups on a programmable nanoscaffold

For the first time, decoration of surface-exposed carboxylate groups on Cowpea mosaic virus particles is reported, thus increasing the number and types of addressable surface groups on this nanoscaffold. First, the addressabilty of carboxylates was demonstrated using a carboxylate-selective fluorescent dye, N-cyclohexyl-N'-(4-(dimethylamino)naphthyl)carbodiimide. Second, it was shown that the virions can be decorated with approximately 180 redox active, methyl(aminopropyl)viologen moieties by coupling to the surface carboxylates. The display of multiple redox centers on the virus particle surface may lead to the development of novel electron-transfer mediators in redox catalysis, to biosensors, and to nanoelectronic devices such as molecular batteries.

Face-Driven Corner-Linked Octahedral Nanocages: M6L8 Cages Formed by C3-Symmetric Triangular Facial Ligands Linked via C4-Symmetric Square Tetratopic PdII Ions at Truncated Octahedron Corners

The face-driven corner-linked truncated octahedral nanocages, [Pd6L8]12+ (1, L1 = N,N',N' '-tris(3-pyridinyl)-1,3,5-benzenetricarboxamide; 2, L2 = N,N',N' '-tris(4-pyridinylmethyl)-1,3,5-benzenetricarboxamide), were prepared with eight C3-symmetric tridentate ligands and six square planar tetratopic palladium(II) ions. The combination of the nitrogen donor atom at a approximately 120 degrees kink position of the carboxamido pyridinyl group and the tilted pyridyl versus the facial plane of the ligands can provide the needed curvature for the formation of octahedral cages. The nitrogen atoms can coordinate to the square planar palladium(II) ions to form kinks with approximately 120 degrees angles at the C4-symmetric square planar corners of the truncated octahedron. Depending on the conformation of the ligand, L1, two different truncated octahedral cages of around 2.4 nm in diameters were formed. The major form of 1 with syn-conformational ligands has a cavity volume of approximately 1600 A3. The cage has 12 ports (3.4 x 3.5 A2) at all edges of the octahedron. The minor form of cage 1 with anti-conformational ligands has a slightly increased cavity volume ( approximately 1900 A3) and port size (3.3 x 8.0 A2). The insertion of a methylene group in L2 has not only increased the cavity volume of 2 to approximately 2200 A3 but also enlarged the port size to 4.1 x 8.0 A2. However, an atomic force microscopy (AFM) study of cage 2 showed that the cages had a height of 1.8 +/- 0.1 nm. This value is about 30% smaller than the calculated size of 2.6 nm from the crystal structure. This tip-induced decrease in height in cage 2 suggests the nonrigidity of cage 2.

Virus crystals as nanocomposite scaffolds

The generation of long-range three-dimensional nanoscopic patterns is a major goal in materials chemistry. Here we report a strategy for creating such systems using virus crystals as scaffolds which can be infiltrated with metal specifically palladium and platinum. The inorganic component effectively packs within the porous macromolecular crystal architecture, providing a route for patterning these materials on the nanometer length scale. To verify the quality of the metal infiltration, SEM-EDX was used to determine the homogeneous distribution of metal across the crystal, and TEM was used to confirm that the metal was confined within the porous structure of the crystal.

A virus-based nanoblock with tunable electrostatic properties

Five different "HIS tag" mutants of cowpea mosaic virus were made by genetically introducing six contiguous histidine residues at various locations on the virus capsid. The mutant particles showed differential affinity for binding nickel, and their electrostatic properties could be controlled as a function of the protonation state of the exposed histidine sequence. The specific addressability of the HIS tag was corroborated by the selective modification of the histidine sequence with nanogold cross-linked to the Ni-NTA moiety.

Role of metal ion-mediated interactions in the assembly and stability of Sesbania mosaic virus T=3 and T=1 capsids

Sesbania mosaic virus (SeMV) capsids are stabilized by RNA-protein, protein-protein and calcium-mediated protein-protein interactions. The removal of calcium has been proposed to be a prerequisite for the disassembly of the virus. The crystal structure of native T=3 SeMV capsid revealed that residues D146 and D149 from one subunit and Y205, N267 and N268 of the neighboring subunit form the calcium-binding site (CBS). The CBS environment is found to be identical even in the recombinant CP-NDelta65 T=1 capsids. Here, we have addressed the role of calcium and the residues involved in calcium co-ordination in the assembly and stability of T=3 and T=1 capsids by mutational analysis. Deletion of N267 and N268 did not affect T=3 or T=1 assembly, although the capsids were devoid of calcium, suggesting that assembly does not require calcium ions. However, the stability of the capsids was reduced drastically. Site-directed mutagenesis revealed that either a single mutation (D149N) or a double mutation (D146N-D149N) of SeMV coat protein affected drastically both the assembly and stability of T=3 capsids. On the other hand, the D146N-D149N mutation in CP-NDelta65 did not affect the assembly of T=1 capsid, although their stability was reduced considerably. Since the major difference between the T=3 and T=1 capsids is the absence of the N-terminal arginine-rich motif (N-ARM) and the beta-annulus from the subunits forming the T=1 capsids, it is possible that D149 initiates the N-ARM-RNA interactions that lead to the formation of the beta-annulus, which is essential for T=3 capsid assembly.

Chemical Conjugation of Heterologous Proteins on the Surface of Cowpea Mosaic Virus

Genetic economy leads to symmetric distributions of chemically identical subunits in icosaherdal and helical viruses. Modification of the subunit genes of a variety of viruses has permitted the display of polypeptides on both the infectious virions and virus particles made in expression systems. Icosahedral chimeric particles of this type often display novel properties resulting in high local concentrations of the insert. Here we report an extension of this concept in which entire proteins were chemically cross-linked to lysine and cysteine residues genetically engineered on the coat protein of icosahedral Cowpea mosaic virus particles. Three exogenous proteins, the LRR domain of internalin B, the T4 lysozyme, and the Intron 8 gene product of the of the HER2 tyrosine kinase receptor were derivatized with appropriate bifunctional cross-linkers and conjugated to the virus capsid. Characterization of these particles demonstrated that (1) virtually 100% occupancy of the 60 sites was achieved; (2) biological activity (either enzyme or binding specificity) of the attached protein was preserved; (3) in one case (LRR-internalin B) the attached protein conformed with the icosahedral symmetry to the extent that a reconstruction of the derivatized particles displayed added density with a shape consistent with the X-ray structure of the attached protein. Strategies demonstrated here allow virus particle targeting to specific cell types and the use of an icosahedral virus as a platform for structure determination of small proteins at moderate resolution.

Hybrid virus-polymer materials. 1. Synthesis and properties of PEG-decorated cowpea mosaic virus

Cowpea mosaic virus was derivatized with poly(ethylene glycol) to give well-controlled loadings of polymer on the outer surface of the coat protein assembly. The resulting conjugates displayed altered densities and immunogenicities, consistent with the known chemical and biological properties of PEG. These studies make CPMV potentially useful as a tailored vehicle for drug delivery.

Blue fluorescent antibodies as reporters of steric accessibility in virus conjugates

Nonenveloped viruses provide the chemist with large, preassembled polyvalent protein scaffolds for modification. These structures are typically porous to small molecules but not to large ones. The solution-phase structures and reactivities of such assemblies may be substantially different than indicated by X-ray crystal structures. Here, the attachment of organic compounds to either the inside or outside surface of the cowpea mosaic virus (CPMV) coat protein was verified with an indicating antibody-antigen interaction. Antibody binding was subsequently blocked by the installation of poly(ethylene glycol) chains. These results typify the type of site-specific control that is available with CPMV and related virus building blocks.

Covariation in the capsid protein of hibiscus chlorotic ringspot virus induced by serial passaging in a host that restricts movement leads to avirulence in its systemic host

Hibiscus chlorotic ringspot virus (HCRSV) from naturally infected Hibiscus rosa-sinensis L. loses virulence in its experimental systemic host Hibiscus cannabinus L. (kenaf) after serial passages in a local lesion host Chenopodium quinoa. Here we report the genetic changes responsible for the loss of virulence at the molecular level. A remarkable covariation of eight site-specific amino acids was found in the HCRSV capsid protein (CP) after serial passages in C. quinoa: Val(49)-->Ile, Ile(95)-->Val, Lys(270)-->Arg, Gly(272)-->Asp, Tyr(274)-->His, Ala(311)-->Asp, Asp(334)-->Ala, and Ala(335)-->Thr. Covariation of at least three of the eight amino acids, Val(49), Ile(95), and Lys(270), caused the virus to become avirulent in kenaf. Interestingly, the nature of the covariation was consistent and reproducible at each serial passage. These data indicate that the nonsynonymous substitutions of amino acids in the HCRSV CP after serial passages in C. quinoa are not likely to be random events but may be due to host-associated positive selection or accelerated genetic drift. The observed interdependence among the three amino acids leading to avirulence in kenaf may have implications for structural or functional relationships in this virus-host interaction.

Stability of rice yellow mottle virus and cellular compartmentalization during the infection process in Oryza sativa (L.)

Rice yellow mottle virus (RYMV) is icosahedral in morphology and known to swell in vitro, but the biological function of swollen particles remains unknown. Anion-exchange chromatography was used to identify three markedly stable forms of RYMV particles from infected plants: (1) an unstable swollen form lacking Ca2+ and dependent upon basic pH; (2) a more stable transitional form lacking Ca2+ but dependent upon acidic pH; and (3) a pH-independent, stable, compact form containing Ca2+. Particle stability increased over the time course of infection in rice plants: transitional and swollen forms were abundant during early infection (2 weeks postinfection), whereas compact forms increased during later stages of infection. Electron microscopy of infected tissue revealed virus particles in vacuoles of xylem parenchyma and mesophyll cells early in the time course of infection and suggested that vacuoles and other vesicles were the major storage compartments for virus particles. We propose a model in which virus maturation is associated with the virus accumulation in vacuoles. In this acidic compartment, virus particles may bind Ca2+ to produce a highly stable, compact form of the virus. The localization of subcellular RYMV isoforms in infected cells and the corresponding biological properties of the virus are discussed.

Symptom induction by Cowpea chlorotic mottle virus on Vigna unguiculata is determined by amino acid residue 151 in the coat protein

The type strain of Cowpea chlorotic mottle virus (CCMV-T) produces a bright chlorosis in cowpea (Vigna unguiculata cv. California Blackeye). The attenuated variant (CCMV-M) induces mild green mottle symptoms that were previously mapped to RNA 3. Restriction fragment exchanges between RNA 3 cDNA clones of CCMV-T and CCMV-M that generate infectious transcripts and site-directed mutagenesis indicated that the codon encoding amino acid residue 151 of the coat protein determines the symptom phenotypes of CCMV-T and CCMV-M. Amino acid 151 is within an alpha-helical structure required for calcium ion binding and virus particle stability. No differences in virion stability or accumulation were detected between CCMV-T and CCMV-M. Mutational analysis suggested that the amino acid at position 151 and not the nucleotide sequence induce the symptom phenotype. Thus, it is likely that subtle influences by amino acid residue 151 in coat protein-host interactions result in chlorotic and mild green mottle symptoms.

The membrane M protein carboxy terminus binds to transmissible gastroenteritis coronavirus core and contributes to core stability

The architecture of transmissible gastroenteritis coronavirus includes three different structural levels, the envelope, an internal core, and the nucleocapsid that is released when the core is disrupted. Starting from purified virions, core structures have been reproducibly isolated as independent entities. The cores were stabilized at basic pH and by the presence of divalent cations, with Mg(2+) ions more effectively contributing to core stability. Core structures showed high resistance to different concentrations of detergents, reducing agents, and urea and low concentrations of monovalent ions (<200 mM). Cores were composed of the nucleoprotein, RNA, and the C domain of the membrane (M) protein. At high salt concentrations (200 to 300 mM), the M protein was no longer associated with the nucleocapsid, which resulted in destruction of the core structure. A specific ionic interaction between the M protein carboxy terminus and the nucleocapsid was demonstrated using three complementary approaches: (i) a binding assay performed between a collection of M protein amino acid substitution or deletion mutants and purified nucleocapsids that led to the identification of a 16-amino-acid (aa) domain (aa 237 to 252) as being responsible for binding the M protein to the nucleocapsid; (ii) the specific inhibition of this binding by monoclonal antibodies (MAbs) binding to a carboxy-terminal M protein domain close to the indicated peptide but not by MAbs specific for the M protein amino terminus; and (iii) a 26-residue peptide, including the predicted sequence (aa 237 to 252), which specifically inhibited the binding. Direct binding of the M protein to the nucleoprotein was predicted, since degradation of the exposed RNA by RNase treatment did not affect the binding. It is proposed that the M protein is embedded within the virus membrane and that the C region, exposed to the interior face of the virion in a population of these molecules, interacts with the nucleocapsid to which it is anchored, forming the core. Only the C region of the M protein is part of the core.

Cell-to-cell movement of potato virus X involves distinct functions of the coat protein

Complementation of movement-deficient potato virus X (PVX) coat protein (CP) mutants, namely PVX.CP-Xho lacking the 18 C-terminal amino acid residues and PVX.DeltaCP lacking the entire CP gene, was studied by transient co-expression with heterologous proteins. These data demonstrated that the potyvirus CPs and both the major and minor CPs of beet yellows closterovirus could complement cell-to-cell movement of PVX.CP-Xho but not PVX.DeltaCP. These data also indicated that the C-terminally truncated PVX CP lacked a movement function which could be provided in trans by the CPs of other filamentous viruses, whereas another movement determinant specified by some region outside the most C-terminal part of the PVX CP could not be complemented either by potyvirus or closterovirus CPs. Surprisingly, the CP of spherical cocksfoot mottle sobemovirus rescued all of the PVX CP movement functions, complementing the spread of PVX.CP-Xho and, to a lesser extent, PVX.DeltaCP. Both these mutants were also rescued by the tobacco mosaic virus (TMV) movement protein (MP). To shed light on the movement function of PVX CP, attempts were made to complement PVX.CP-Xho by a series of TMV MP mutants. An internal deletion abolished complementation, suggesting that the internal region of TMV MP, which includes a number of overlapping functional domains important for cell-to-cell transport, provides an activity complementing movement determinant(s) specified by the C-terminal region of PVX CP.

The multifunctional capsid proteins of plant RNA viruses

This article summarizes studies of viral coat (capsid) proteins (CPs) of RNA plant viruses. In addition, we discuss and seek to interpret the knowledge accumulated to data. CPs are named for their primary function; to encapsidate viral genomic nucleic acids. However, encapsidation is only one feature of an extremely diverse array of structural, functional, and ecological roles played during viral infection and spread. Herein, we consider the evolution of viral CPs and their multitude of interactions with factors encoded by the virus, host plant, or viral vector (biological transmission agent) that influence the infection and epidemiological facets of plant disease. In addition, applications of today's understanding of CPs in the protection of crops from viral infection and use in the manufacture of valuable compounds are considered.