Biophysical characterization of a designed TMV coat protein mutant, R46G, that elicits a moderate hypersensitivity response in Nicotiana sylvestris

Interfacially Bridging Covalent Network Yields Hyperstable and Ultralong Virus-Based Fibers for Engineering Functional Materials

We present a strategy of interfacially bridging covalent network within tobacco mosaic virus (TMV) virus-like particles (VLPs). We arranged T103C cysteine to laterally conjugate adjacent subunits. In the axis direction, we set A74C mutation and systematically investigated candidate from E50C to P54C as the other thiol function site, for forming longitudinal disulfide bond chains. Significantly, the T103C-TMV-E50C-A74C shows the highest robustness in assembly capability and structural stability with the largest length, for TMV VLP to date. The fibers with lengths from several to a dozen of micrometers even survive under pH 13. The robust nature of this TMV VLP allows for reducer-free synthesis of excellent electrocatalysts for application in harshly alkaline hydrogen evolution.

Tracing the Lineage of Two Traits Associated with the Coat Protein of the Tombusviridae: Silencing Suppression and HR Elicitation in Nicotiana Species

In this paper we have characterized the lineage of two traits associated with the coat proteins (CPs) of the tombusvirids: Silencing suppression and HR elicitation in Nicotiana species. We considered that the tombusvirid CPs might collectively be considered an effector, with the CP of each CP-encoding species comprising a structural variant within the family. Thus, a phylogenetic analysis of the CP could provide insight into the evolution of a pathogen effector. The phylogeny of the CP of tombusvirids indicated that CP representatives of the family could be divided into four clades. In two separate clades the CP triggered a hypersensitive response (HR) in Nicotiana species of section Alatae but did not have silencing suppressor activity. In a third clade the CP had a silencing suppressor activity but did not have the capacity to trigger HR in Nicotiana species. In the fourth clade, the CP did not carry either function. Our analysis illustrates how structural changes that likely occurred in the CP effector of progenitors of the current genera led to either silencing suppressor activity, HR elicitation in select Nicotiana species, or neither trait.

The coat protein of Alternanthera mosaic virus is the elicitor of a temperature-sensitive systemic necrosis in Nicotiana benthamiana, and interacts with a host boron transporter protein

Different isolates of Alternanthera mosaic virus (AltMV; Potexvirus), including four infectious clones derived from AltMV-SP, induce distinct systemic symptoms in Nicotiana benthamiana. Virus accumulation was enhanced at 15 °C compared to 25 °C; severe clone AltMV 3-7 induced systemic necrosis (SN) and plant death at 15 °C. No interaction with potexvirus resistance gene Rx was detected, although SN was ablated by silencing of SGT1, as for other cases of potexvirus-induced necrosis. Substitution of AltMV 3-7 coat protein (CPSP) with that from AltMV-Po (CP(Po)) eliminated SN at 15 °C, and ameliorated symptoms in Alternanthera dentata and soybean. Substitution of only two residues from CP(Po) [either MN(13,14)ID or LA(76,77)IS] efficiently ablated SN in N. benthamiana. CPSP but not CP(Po) interacted with Arabidopsis boron transporter protein AtBOR1 by yeast two-hybrid assay; N. benthamiana homolog NbBOR1 interacted more strongly with CPSP than CP(Po) in bimolecular fluorescence complementation, and may affect recognition of CP as an elicitor of SN.

Structure-function relationship between the tobamovirus TMV-Cg coat protein and the HR-like response

The tobamovirus TMV-Cg induces an HR-like response in Nicotiana tabacum cv. Xanthi nn sensitive plants lacking the N or N' resistance genes. This response has been characterized by the appearance of necrotic lesions in the inoculated leaf and viral systemic spread, although the defence pathways are activated in the plant. A previous study demonstrated that the coat protein (CP) of TMV-Cg (CPCg) was the elicitor of this HR-like response. We examined the influence of four specific amino acid substitutions on the structure of CPCg, as well as on the development of the host response. To gain insights into the structural implications of these substitutions, a set of molecular dynamic experiments was performed using comparative models of wild-type and mutant CPCg as well as the CP of the U1 strain of TMV (CPU1), which is not recognized by the plants. A P21L mutation produces severe changes in the three-dimensional structure of CPCg and is more unstable when this subunit is laterally associated in silico. This result may explain the observed incapacity of this mutant to assemble virions. Two other CPCg mutations (R46G and S54K) overcome recognition by the plant and do not induce an HR-like response. A double CPCg mutant P21L-S54K recovered its capacity to form virions and to induce an HR-like response. Our results suggest that the structural integrity of the CP proteins is important for triggering the HR-like response.

Hydrodynamic modeling: the solution conformation of macromolecules and their complexes

Hydrodynamic bead modeling (HBM) is the representation of a macromolecule by an assembly of spheres (or beads) for which measurable hydrodynamic (and related) parameters are then computed in order to understand better the macromolecular solution conformation. An example-based account is given of the main stages in HBM of rigid macromolecules, namely: model construction, model visualization, accounting for hydration, and hydrodynamic calculations. Different types of models are appropriate for different macromolecules, according to their composition, to what is known about the molecule or according to the types of experimental data that the model should reproduce. Accordingly, the construction of models based on atomic coordinates as well as much lower resolution data (e.g., electron microscopy images) is described. Similarly, several programs for hydrodynamic calculations are summarized, some generating the most basic set of solution parameters (e.g., sedimentation and translational diffusion coefficients, intrinsic viscosity, radius of gyration, and Stokes radius) while others extend to data determined by nuclear magnetic resonance, fluorescence anisotropy, and electric birefringence methods. An insight into the topic of hydrodynamic hydration is given, together with some practical suggestions for its satisfactory treatment in the modeling context. All programs reviewed are freely available.

Two Amino Acid Substitutions in the Coat Protein of Pepper mild mottle virus Are Responsible for Overcoming the L(4) Gene-Mediated Resistance in Capsicum spp

ABSTRACT The Capsicum spp. L genes (L(1) to L(4)) confer resistance to tobamoviruses. Currently, the L(4) gene from Capsicum chacoense is the most effective resistance gene and has been used widely in breeding programs in Japan which have developed new resistant cultivars against Pepper mild mottle virus (PMMoV). However, in 2004, mild mosaic symptoms began appearing on the leaves of commercial pepper plants in the field which possessed the L(4) resistance gene. Serological and biological assays on Capsicum spp. identified the causal virus strain as a previously unreported pathotype, P(1,2,3,4). PMMoV sequence analysis of the virus and site-directed mutagenesis using a PMMoV-J of the P(1,2) pathotype revealed that two amino acid substitutions in the coat protein, Gln to Arg at position 46 and Gly to Lys at position 85, were responsible for overcoming the L(4) resistance gene.

Sedimentation velocity analysis of heterogeneous protein-protein interactions: sedimentation coefficient distributions c(s) and asymptotic boundary profiles from Gilbert-Jenkins theory

Interacting proteins in rapid association equilibrium exhibit coupled migration under the influence of an external force. In sedimentation, two-component systems can exhibit bimodal boundaries, consisting of the undisturbed sedimentation of a fraction of the population of one component, and the coupled sedimentation of a mixture of both free and complex species in the reaction boundary. For the theoretical limit of diffusion-free sedimentation after infinite time, the shapes of the reaction boundaries and the sedimentation velocity gradients have been predicted by Gilbert and Jenkins. We compare these asymptotic gradients with sedimentation coefficient distributions, c(s), extracted from experimental sedimentation profiles by direct modeling with superpositions of Lamm equation solutions. The overall shapes are qualitatively consistent and the amplitudes and weight-average s-values of the different boundary components are quantitatively in good agreement. We propose that the concentration dependence of the area and weight-average s-value of the c(s) peaks can be modeled by isotherms based on Gilbert-Jenkins theory, providing a robust approach to exploit the bimodal structure of the reaction boundary for the analysis of experimental data. This can significantly improve the estimates for the determination of binding constants and hydrodynamic parameters of the complexes.

Spinning with Dave: David Yphantis's contributions to ultracentrifugation

For nearly 50 years David Yphantis has helped advance analytical ultracentrifugation, promoted rigor in the thermodynamic analysis of biochemical data and encouraged students and colleagues to look for the deepest possible understanding of science. This article, written by five of Dave's students, presents some of the impressions he has made over the years.

Tobacco mosaic virus assembly and disassembly: determinants in pathogenicity and resistance

The structural proteins of plant viruses have evolved to self-associate into complex macromolecules that are centrally involved in virus biology. In this review, the structural and biophysical properties of the Tobacco mosaic virus (TMV) coat protein (CP) are addressed in relation to its role in host resistance and disease development. TMV CP affects the display of several specific virus and host responses, including cross-protection, systemic virus movement, hypersensitive disease resistance, and symptom development. Studies indicate that the three-dimensional structure of CP is critical to the control of these responses, either directly through specific structural motifs or indirectly via alterations in CP assembly. Thus, both the structure and assembly of the TMV CP function as determinants in the induction of disease and resistance responses.

A method for directly fitting the time derivative of sedimentation velocity data and an alternative algorithm for calculating sedimentation coefficient distribution functions

The time-derivative method for deriving the sedimentation coefficient distribution, g(s*), from sedimentation velocity data that was developed by Walter Stafford has many advantages and is now widely used. By fitting Gaussian functions to the g(s*) distribution both sedimentation and diffusion coefficients (and therefore molecular masses) for individual species can be obtained. However, some of the approximations used in these procedures limit the accuracy of the results. An alternative approach is proposed in which the dc/dt data are fitted rather than g(s*). This new approach gives improved accuracy, extends the range to sedimentation coefficients below 1 S, and enhances resolution of multiple species. For both approaches the peaks from individual species are broadened when the data cover too wide a time span, and this effect is explored and quantified. An alternative algorithm for calculating ĝ(s*) from the dc/dt curves is presented and discussed. Rather than first averaging the dc/dt data for individual scan pairs and then calculating ĝ(s*) from that average, the ĝ(s*) distributions are calculated for every scan pair and then subsequently averaged. This alternative procedure yields smaller error bars for g(s*) and somewhat greater accuracy for fitted hydrodynamic properties when the time span becomes large.

Analytical ultracentrifugation as a contemporary biomolecular research tool

Analytical ultracentrifugation has again become a widely used biomolecular research technique for determining sample purity, characterizing assembly and disassembly mechanisms of biomolecular complexes, determining subunit stoichiometries, detecting and characterizing macromolecular conformational changes, and measuring equilibrium constants and thermodynamic parameters for self- and hetero-associating systems. Concomitant with the availability of modern instrumentation is a strong need for biomedical scientists to become acquainted with the fundamental principles of analytical ultracentrifugation and the new data analysis methodologies that have greatly transformed this technique as it exists today.