Novel Inter-Subunit Contacts in Barley Stripe Mosaic Virus Revealed by Cryo-Electron Microscopy

Electroless Deposition of Noble Metals on Rod-Shape Plant Viruses in Various Aqueous Metal Precursor Solutions

The challenge of synthesizing noble metal nanostructures sustainably has encouraged researchers to explore biological routes for nanostructure production, such as biotemplating. Plant viruses with rod-shape morphology, such as tobacco mosaic virus (TMV) and barley stripe mosaic virus (BSMV), offer promising biotemplates to produce metal nanorods. TMV and BSMV can be incubated in aqueous metal precursor solutions to mineralize metals on the coat proteins (CPs) of the viruses. Previous studies have primarily examined palladium (Pd) mineralization on TMV and BSMV using Na2PdCl4 as the Pd precursor. There is limited scientific literature on the effect of using alternative Pd precursor solutions besides Na2PdCl4 such as K2PdCl4 and PdCl2 to mineralize Pd on TMV and BSMV. Past attempts at mineralizing other noble metals such as platinum (Pt) and gold (Au) required an initial layer of Pd to be deposited on the TMV and BSMV biotemplates. In this study, we aimed to expand the understanding of using alternative Pd precursor solutions to mineralize Pd on TMV and BSMV. Additionally, the deposition of Pt and Au onto TMV and BSMV without the need for an initial Pd mineralization layer was achieved using alternative Pt and Au precursors, including K2PtCl4 and AuCl3, respectively. Pd, Pt, and Au were successfully deposited on TMV and BSMV by incubation in aqueous solutions of Na2PdCl4, K2PdCl4, PdCl2, K2PtCl4, and AuCl3. Kinetic studies were also conducted using ultraviolet-visible (UV-vis) spectroscopy to examine the rates at which Pd, Pt, and Au precursor ions were reduced during the mineralization process, mimicking their adsorption onto TMV and BSMV CPs. BSMV adsorbed noble metal precursor ions faster than TMV as determined by UV-vis spectroscopy. While palladium nanorods (PdNRs) offer high electrical conductivity desirable for electronic applications, Pd-coated TMV and BSMV may face limitations due to their organic cores, potentially compromising conductivity. To address this, one approach is to convert the organic core into conductive amorphous carbon through thermal annealing. In this study, in situ transmission electron microscopy was utilized to thermally anneal Pd-TMV2Cys, thereby transforming them into PdNRs with amorphous carbon cores.

Zn2+-dependent association of cysteine-rich protein with virion orchestrates morphogenesis of rod-shaped viruses

The majority of rod-shaped and some filamentous plant viruses encode a cysteine-rich protein (CRP) that functions in viral virulence; however, the roles of these CRPs in viral infection remain largely unknown. Here, we used barley stripe mosaic virus (BSMV) as a model to investigate the essential role of its CRP in virus morphogenesis. The CRP protein γb directly interacts with BSMV coat protein (CP), the mutations either on the His-85 site in γb predicted to generate a potential CCCH motif or on the His-13 site in CP exposed to the surface of the virions abolish the zinc-binding activity and their interaction. Immunogold-labeling assays show that γb binds to the surface of rod-shaped BSMV virions in a Zn2+-dependent manner, which enhances the RNA binding activity of CP and facilitates virion assembly and stability, suggesting that the Zn2+-dependent physical association of γb with the virion is crucial for BSMV morphogenesis. Intriguingly, the tightly binding of diverse CRPs to their rod-shaped virions is a general feature employed by the members in the families Virgaviridae (excluding the genus Tobamovirus) and Benyviridae. Together, these results reveal a hitherto unknown role of CRPs in the assembly and stability of virus particles, and expand our understanding of the molecular mechanism underlying virus morphogenesis.

Structural Insights into Plant Viruses Revealed by Small-Angle X-ray Scattering and Atomic Force Microscopy

The structural study of plant viruses is of great importance to reduce the damage caused by these agricultural pathogens and to support their biotechnological applications. Nowadays, X-ray crystallography, NMR spectroscopy and cryo-electron microscopy are well accepted methods to obtain the 3D protein structure with the best resolution. However, for large and complex supramolecular structures such as plant viruses, especially flexible filamentous ones, there are a number of technical limitations to resolving their native structure in solution. In addition, they do not allow us to obtain structural information about dynamics and interactions with physiological partners. For these purposes, small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM) are well established. In this review, we have outlined the main principles of these two methods and demonstrated their advantages for structural studies of plant viruses of different shapes with relatively high spatial resolution. In addition, we have demonstrated the ability of AFM to obtain information on the mechanical properties of the virus particles that are inaccessible to other experimental techniques. We believe that these under-appreciated approaches, especially when used in combination, are valuable tools for studying a wide variety of helical plant viruses, many of which cannot be resolved by classical structural methods.

From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y

The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.

Determining Macromolecular Structures Using Cryo-Electron Microscopy

Structural insights into macromolecular and protein complexes provide key clues about the molecular basis of the function. Cryogenic electron microscopy (cryo-EM) has emerged as a powerful structural biology method for studying protein and macromolecular structures at high resolution in both native and near-native states. Despite the ability to get detailed structural insights into the processes underlying protein function using cryo-EM, there has been hesitancy amongst plant biologists to apply the method for biomolecular interaction studies. This is largely evident from the relatively fewer structural depositions of proteins and protein complexes from plant origin in electron microscopy databank. Even though the progress has been slow, cryo-EM has significantly contributed to our understanding of the molecular biology processes underlying photosynthesis, energy transfer in plants, besides viruses infecting plants. This chapter introduces sample preparation for both negative-staining electron microscopy (NSEM) and cryo-EM for plant proteins and macromolecular complexes and data analysis using single particle analysis for beginners.

Changes in the Structure of Potato Virus A Virions after Limited in situ Proteolysis According to Tritium Labeling Data and Computer Simulation

Coat proteins (CP) of the potato virus A virions (PVA) contain partially disordered N-terminal domains, which are necessary for performing vital functions of the virus. Comparative analysis of the structures of coat proteins (CPs) in the intact PVA virions and in the virus particles lacking N-terminal 32 amino acids (PVAΔ32) was carried out in this work based on the tritium planigraphy data. Using atomic-resolution structure of the potato virus Y potyvirus (PVY) protein, which is a homolog of the CP PVA, the available CP surfaces in the PVY virion were calculated and the areas of intersubunit/interhelix contacts were determined. For this purpose, the approach of Lee and Richards [Lee, B., and Richards, F. M. (1971) J. Mol. Biol., 55, 379-400] was used. Comparison of incorporation profiles of the tritium label in the intact and trypsin-degraded PVAΔ32 revealed position of the ΔN-peptide shielding the surface domain (a.a. 66-73, 141-146) and the interhelix zone (a.a. 161-175) of the PVA CP. Presence of the channels/cavities was found in the virion, which turned out to be partially permeable to tritium atoms. Upon removal of the ΔN-peptide, decrease in the label incorporation within the virion (a.a. 184-200) was also observed, indicating possible structural transition leading to the virion compactization. Based on the obtained data, we can conclude that part of the surface ΔN-peptide is inserted between the coils of the virion helix thus increasing the helix pitch and providing greater flexibility of the virion, which is important for intercellular transport of the viruses in the plants.

Engineering Alkaline-Stable Barley Stripe Mosaic Virus-Like Particles for Efficient Surface Modification

Viruses and virus-like particles are powerful templates for materials synthesis because of their capacity for precise protein engineering and diverse surface functionalization. We recently developed a recombinant bacterial expression system for the production of barley stripe mosaic virus-like particles (BSMV VLPs). However, the applicability of this biotemplate was limited by low stability in alkaline conditions and a lack of chemical handles for ligand attachment. Here, we identify and validate novel residues in the BSMV Caspar carboxylate clusters that mediate virion disassembly through repulsive interactions at high pH. Point mutations of these residues to create attractive interactions that increase rod length ~2 fold, with an average rod length of 91 nm under alkaline conditions. To enable diverse chemical surface functionalization, we also introduce reactive lysine residues at the C-terminus of BSMV coat protein, which is presented on the VLP surface. Chemical conjugation reactions with this lysine proceed more quickly under alkaline conditions. Thus, our alkaline-stable VLP mutants are more suitable for rapid surface functionalization of long nanorods. This work validates novel residues involved in BSMV VLP assembly and demonstrates the feasibility of chemical functionalization of BSMV VLPs for the first time, enabling novel biomedical and chemical applications.

Surface Functionalization of Rod-Shaped Viral Particles for Biomedical Applications

While synthetic nanoparticles play a very important role in modern medicine, concerns regarding toxicity, sustainability, stability, and dispersity are drawing increasing attention to naturally derived alternatives. Rod-shaped plant viruses and virus-like particles (VLPs) are biological nanoparticles with powerful advantages such as biocompatibility, tunable size and aspect ratio, monodispersity, and multivalency. These properties facilitate controlled biodistribution and tissue targeting for powerful applications in medicine. Ongoing research efforts focus on functionalizing or otherwise engineering these structures for a myriad of applications, including vaccines, imaging, and drug delivery. These include chemical and biological strategies for conjugation to small molecule chemical dyes, drugs, metals, polymers, peptides, proteins, carbohydrates, and nucleic acids. Many strategies are available and vary greatly in efficiency, modularity, selectivity, and simplicity. This review provides a comprehensive summary of VLP functionalization approaches while highlighting biomedically relevant examples. Limitations of current strategies and opportunities for further advancement will also be discussed.

Supramolecular assembly of protein building blocks: from folding to function

Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.

Engineering Tobacco Mosaic Virus and Its Virus-Like-Particles for Synthesis of Biotemplated Nanomaterials

Biomolecules are increasingly attractive templates for the synthesis of functional nanomaterials. Chief among them is the plant tobacco mosaic virus (TMV) due to its high aspect ratio, narrow size distribution, diverse biochemical functionalities presented on the surface, and compatibility with a number of chemical conjugations. These properties are also easily manipulated by genetic modification to enable the synthesis of a range of metallic and non-metallic nanomaterials for diverse applications. This article reviews the characteristics of TMV and related viruses, and their virus-like particle (VLP) derivatives, and how these may be manipulated to extend their use and function. A focus of recent efforts has been on greater understanding and control of the self-assembly processes that drive biotemplate formation. How these features have been exploited in engineering applications such as, sensing, catalysis, and energy storage are briefly outlined. While control of VLP surface features is well-established, fewer tools exist to control VLP self-assembly, which limits efforts to control template uniformity and synthesis of certain templated nanomaterials. However, emerging advances in synthetic biology, machine learning, and other fields promise to accelerate efforts to control template uniformity and nanomaterial synthesis enabling more widescale industrial use of VLP-based biotemplates.

Structural basis for the multitasking nature of the potato virus Y coat protein

Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA-coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein's amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.

Electron Microscopy Methods for Virus Diagnosis and High Resolution Analysis of Viruses

The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).

Non-structural Functions of Hordeivirus Capsid Protein Identified in Plants Infected by a Chimeric Tobamovirus

Capsid proteins (CPs) of (+)RNA-containing plant viruses are multifunctional proteins involved in many stages of viral infection cycle, in addition to their main function of virus capsid formation. For example, the tobamoviral CP ensures virus systemic transport in plants and defines the virus-host interactions, thereby influencing the virus host range, virus infectivity, pathogenicity, and manifestation of infection symptoms. Hordeiviruses and tobamoviruses belong to the Virgaviridae family and have rod-shaped virions with a helical symmetry; their CPs are similar in structure. However, no non-structural functions of hordeiviral CPs have been described so far. In this study, we assayed possible non-structural functions of CP from the barley stripe mosaic virus (BSMV) (hordeivirus). To do this, the genome of turnip vein clearing virus (TVCV) (tobamovirus) was modified by substituting the TVCV CP gene with the BSMV CP gene or its mutants. We found that BSMV CP efficiently replaced TVCV CP at all stages of viral infection. In particular, BSMV CP performed the role of tobamoviral CP in the long-distance transport of the chimeric virus, acted as a hypersensitive response elicitor, and served as a pathogenicity determinant that influenced the symptoms of the viral infection. The chimeric tobamovirus coding for the C-terminally truncated BSMV CP displayed an increased infectivity and was transported in plants in a form of atypical virions (ribonucleoprotein complexes).

Electron Microscopy Methods for Virus Diagnosis and High Resolution Analysis of Viruses

The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).

Structure and properties of virions and virus-like particles derived from the coat protein of Alternanthera mosaic virus

Plant viruses and their virus-like particles (VLPs) have a lot of advantages for biotechnological applications including complete safety for humans. Alternanthera mosaic virus (AltMV) is a potentially promising object for design of novel materials. The 3D structures of AltMV virions and its VLPs were obtained by single particle EM at ~13Å resolution. The comparison of the reconstructions and a trypsin treatment revealed that AltMV CPs possesses a different fold in the presence (virions) and absence of viral RNA (VLPs). For the first time, the structure of morphologically similar virions and virus-like particles based on the coat protein of a helical filamentous plant virus is shown to be different. Despite this, both AltMV virions and VLPs are stable in a wide range of conditions. To provide a large amount of AltMV for biotechnology usage the isolation procedure was modified.

BSMV as a Biotemplate for Palladium Nanomaterial Synthesis

The vast unexplored virus biodiversity makes the application of virus templates to nanomaterial synthesis especially promising. Here, a new biotemplate, Barley stripe mosaic virus (BSMV) was successfully used to synthesize organic-metal nanorods of similarly high quality to those produced with Tobacco mosaic virus (TMV). The mineralization behavior was characterized in terms of the reduction and adsorption of precursor and nanocrystal formation processes. The BSMV surface-mediated reduction of Pd⁽²⁺⁾ proceeded via first-order kinetics in both Pd⁽²⁺⁾ and BSMV. The adsorption equilibrium relationship of PdCl₃H₂O^- on the BSMV surface was described by a multistep Langmuir isotherm suggesting alternative adsorbate-adsorbent interactions when compared to those on TMV. It was deduced that the first local isotherm is governed by electrostatically driven adsorption, which is then followed by sorption driven by covalent affinity of metal precursor molecules for amino acid residues. Furthermore, the total adsorption capacity of palladium species on BSMV is more than double of that on TMV. Finally, study of the BSMV-Pd particles by combining USAXS and SAXS enabled the characterization of all length scales in the synthesized nanomaterials. Results confirm the presence of core-shell cylindrical particles with 1-2 nm grains. The nanorods were uniform and monodisperse, with controllable diameters and therefore, of similar quality to those synthesized with TMV. Overall, BSMV has been confirmed as a viable alternate biotemplate with unique biomineralization behavior. With these results, the biotemplate toolbox has been expanded for the synthesis of new materials and comparative study of biomineralization processes.

Structural Study of Heterogeneous Biological Samples by Cryoelectron Microscopy and Image Processing

In living organisms, biological macromolecules are intrinsically flexible and naturally exist in multiple conformations. Modern electron microscopy, especially at liquid nitrogen temperatures (cryo-EM), is able to visualise biocomplexes in nearly native conditions and in multiple conformational states. The advances made during the last decade in electronic technology and software development have led to the revelation of structural variations in complexes and also improved the resolution of EM structures. Nowadays, structural studies based on single particle analysis (SPA) suggests several approaches for the separation of different conformational states and therefore disclosure of the mechanisms for functioning of complexes. The task of resolving different states requires the examination of large datasets, sophisticated programs, and significant computing power. Some methods are based on analysis of two-dimensional images, while others are based on three-dimensional studies. In this review, we describe the basic principles implemented in the various techniques that are currently used in the analysis of structural conformations and provide some examples of successful applications of these methods in structural studies of biologically significant complexes.

Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images

Thanks to latest technical advances in cryo-electron microscopy (cryo-EM), structures of macromolecular complexes (viruses, ribosomes, etc.) are now often obtained at near-atomic resolution. Also, studies of conformational changes of complexes, in connection with their function, are gaining ground. Conformational variability analysis is usually done by classifying images in a number of discrete classes supposedly representing all conformational states present in the specimen. However, discrete classes cannot be meaningfully defined when the conformational change is continuous (the specimen contains a continuum of states instead of a few discrete states). For such cases, first image analysis methods that explicitly consider continuous conformational changes were recently developed. The latest developments in cryo-EM image analysis methods for conformational variability analysis are the focus of this review.

Structural Properties of Potexvirus Coat Proteins Detected by Optical Methods

It has been shown by X-ray analysis that cores of coat proteins (CPs) from three potexviruses, flexible helical RNA-containing plant viruses, have similar α-helical structure. However, this similarity cannot explain structural lability of potexvirus virions, which is believed to determine their biological activity. Here, we used circular dichroism (CD) spectroscopy in the far UV region to compare optical properties of CPs from three potexviruses with the same morphology and similar structure. CPs from Alternanthera mosaic virus (AltMV), potato aucuba mosaic virus (PAMV), and potato virus X (PVX) have been studied in a free state and in virions. The CD spectrum of AltMV virions was similar to the previously obtained CD spectrum of papaya mosaic virus (PapMV) virions, but differed significantly from the CD spectrum of PAMV virions. The CD spectrum of PAMV virions resembled in its basic characteristics the CD spectrum of PVX virions characterized by molar ellipticity that is abnormally low for α-helical proteins. Homology modeling of the CP structures in AltMV, PAMV, and PVX virions was based on the known high-resolution structures of CPs from papaya mosaic virus and bamboo mosaic virus and confirmed that the structures of the CP cores in all three viruses were nearly identical. Comparison of amino acid sequences of different potexvirus CPs and prediction of unstructured regions in these proteins revealed a possible correlation between specific features in the virion CD spectra and the presence of disordered N-terminal segments in the CPs.

Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes

Cryo-electron microscopy (cryo-EM) has for a long time been a technique of choice for determining structure of large and flexible macromolecular complexes that were difficult to study by other experimental techniques such as X-ray crystallography or nuclear magnetic resonance. However, a fast development of instruments and software for cryo-EM in the last decade has allowed that a large range of complexes can be studied by cryo-EM, and that their structures can be obtained at near-atomic resolution, including the structures of small complexes (e.g., membrane proteins) whose size was earlier an obstacle to cryo-EM. Image analysis to identify multiple coexisting structures in the same specimen (multiconformation reconstruction) is now routinely done both to solve structures at near-atomic resolution and to study conformational dynamics. Methods for multiconformation reconstruction and latest examples of their applications are the focus of this review.

Modified TMV Particles as Beneficial Scaffolds to Present Sensor Enzymes

Tobacco mosaic virus (TMV) is a robust nanotubular nucleoprotein scaffold increasingly employed for the high density presentation of functional molecules such as peptides, fluorescent dyes, and antibodies. We report on its use as advantageous carrier for sensor enzymes. A TMV mutant with a cysteine residue exposed on every coat protein (CP) subunit (TMVCys) enabled the coupling of bifunctional maleimide-polyethylene glycol (PEG)-biotin linkers (TMVCys/Bio). Its surface was equipped with two streptavidin [SA]-conjugated enzymes: glucose oxidase ([SA]-GOx) and horseradish peroxidase ([SA]-HRP). At least 50% of the CPs were decorated with a linker molecule, and all thereof with active enzymes. Upon use as adapter scaffolds in conventional "high-binding" microtiter plates, TMV sticks allowed the immobilization of up to 45-fold higher catalytic activities than control samples with the same input of enzymes. Moreover, they increased storage stability and reusability in relation to enzymes applied directly to microtiter plate wells. The functionalized TMV adsorbed to solid supports showed a homogeneous distribution of the conjugated enzymes and structural integrity of the nanorods upon transmission electron and atomic force microscopy. The high surface-increase and steric accessibility of the viral scaffolds in combination with the biochemical environment provided by the plant viral coat may explain the beneficial effects. TMV can, thus, serve as a favorable multivalent nanoscale platform for the ordered presentation of bioactive proteins.