RNA-protein interactions in the assembly of tobacco mosaic virus

Potyviral coat protein and genomic RNA: A striking partnership leading virion assembly and more

Potyvirus genus clusters a significant and expanding number of widely distributed plant viruses, responsible for large losses impacting most crops of economic interest. The potyviral genome is a single-stranded, linear, positive-sense RNA of around 10kb that is encapsidated in flexuous rod-shaped filaments, mostly made up of a helically arranged coat protein (CP). Beyond its structural role of protecting the viral genome, the potyviral CP is a multitasking protein intervening in practically all steps of the virus life cycle. In particular, interactions between the CP and the viral RNA must be tightly controlled to allow the correct assignment of the RNA to each of its functions through the infection process. This review attempts to bring together the most relevant available information regarding the architecture and modus operandi of potyviral CP and virus particles, highlighting significant discoveries, but also substantial gaps in the existing knowledge on mechanisms orchestrating virion assembly and disassembly. Biotechnological applications based on potyvirus nanoparticles is another important topic addressed here.

From stars to stripes: RNA-directed shaping of plant viral protein templates-structural synthetic virology for smart biohybrid nanostructures

The self-assembly of viral building blocks bears exciting prospects for fabricating new types of bionanoparticles with multivalent protein shells. These enable a spatially controlled immobilization of functionalities at highest surface densities-an increasing demand worldwide for applications from vaccination to tissue engineering, biocatalysis, and sensing. Certain plant viruses hold particular promise because they are sustainably available, biodegradable, nonpathogenic for mammals, and amenable to in vitro self-organization of virus-like particles. This offers great opportunities for their redesign into novel "green" carrier systems by spatial and structural synthetic biology approaches, as worked out here for the robust nanotubular tobacco mosaic virus (TMV) as prime example. Natural TMV of 300 x 18 nm is built from more than 2,100 identical coat proteins (CPs) helically arranged around a 6,395 nucleotides ssRNA. In vitro, TMV-like particles (TLPs) may self-assemble also from modified CPs and RNAs if the latter contain an Origin of Assembly structure, which initiates a bidirectional encapsidation. By way of tailored RNA, the process can be reprogrammed to yield uncommon shapes such as branched nanoobjects. The nonsymmetric mechanism also proceeds on 3'-terminally immobilized RNA and can integrate distinct CP types in blends or serially. Other emerging plant virus-deduced systems include the usually isometric cowpea chlorotic mottle virus (CCMV) with further strikingly altered structures up to "cherrybombs" with protruding nucleic acids. Cartoon strips and pictorial descriptions of major RNA-based strategies induct the reader into a rare field of nanoconstruction that can give rise to utile soft-matter architectures for complex tasks. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.

Building expanded structures from tetrahedral DNA branching elements, RNA and TMV protein

By combining both chemical and enzymatic ligation with procedures guiding the self-assembly of nanotubular tobacco mosaic virus (TMV)-like particles (TLPs), novel nucleoprotein structures based on DNA-terminated branching elements, RNA scaffolds and TMV coat protein (CP) are made accessible. Tetrahedral tetrakis(hydroxybiphenyl)adamantane cores with four 5'-phosphorylated dinucleotide arms were coupled to DNA linkers by chemical ligation. The resulting three-dimensional (3D) branching elements were enzymatically ligated to the 3' termini of RNA scaffolds either prior to or after the RNAs' incorporation into TLPs. Thus, architectures with interconnected nanotube domains in two different length classes were generated, each containing 70 CP subunits per 10 nm length. Short TMV origin-of-assembly-containing RNA scaffolds ligated to the DNA allowed the growth of protein-coated 34 nm tubes on the terminal RNA strands in situ. Alternatively, 290 nm pre-fabricated tubes with accessible RNA 3' termini, attained by DNA blocking elements hybridized to the RNAs, were ligated with the branched cores. Both approaches resulted in four-armed nanoobjects, demonstrating a so far unique combination of organic synthesis of branching elements, enzymatic modifications, nucleic acid-based scaffolding and RNA-guided and DNA-controlled assembly of tubular RNA-encapsidating protein domains, yielding a novel class of 3D nucleoprotein architectures with polyvalent protein elements. In the long term, the production route might give rise to supramolecular systems with complex functionalities, installed via the orthogonal coupling of effector molecules to TLP domains.

Bottom-Up Assembly of TMV-Based Nucleoprotein Architectures on Solid Supports

RNA-guided self-assembly of tobacco mosaic virus (TMV)-like nucleoprotein nanotubes is possible using 3'-terminally surface-linked scaffold RNAs containing the viral origin of assembly (OAS). In combination with TMV coat protein (CP) preparations, these scaffold RNAs can direct the growth of selectively addressable multivalent carrier particles directly at sites of interest on demand. Serving as adapter templates for the installation of functional molecules, they may promote an integration of active units into miniaturized technical devices, or enable their presentation on soft-matter nanotube systems at high surface densities advantageous for, for example, biodetection or purification applications. This chapter describes all procedures essential for the bottom-up fabrication of "nanostar" colloids with gold cores and multiple TMV-like arms, immobilized in a programmable manner by way of hybridization of the RNA scaffolds to oligodeoxynucleotides exposed on the gold beads.

Dynamic DNA-controlled "stop-and-go" assembly of well-defined protein domains on RNA-scaffolded TMV-like nanotubes

A DNA-based approach allows external control over the self-assembly process of tobacco mosaic virus (TMV)-like ribonucleoprotein nanotubes: their growth from viral coat protein (CP) subunits on five distinct RNA scaffolds containing the TMV origin of assembly (OAs) could be temporarily blocked by a stopper DNA oligomer hybridized downstream (3') of the OAs. At two upstream (5') sites tested, simple hybridization was not sufficient for stable stalling, which correlates with previous findings on a non-symmetric assembly of TMV. The growth of DNA-arrested particles could be restarted efficiently by displacement of the stopper via its toehold by using a release DNA oligomer, even after storage for twelve days. This novel strategy for growing proteinaceous tubes under tight kinetic and spatial control combines RNA guidance and its site-specific but reversible interruption by DNA blocking elements. As three of the RNA scaffolds contained long heterologous non-TMV sequence portions that included the stopping sites, this method is applicable to all RNAs amenable to TMV CP encapsidation, albeit with variable efficiency most likely depending on the scaffolds' secondary structures. The use of two distinct, selectively addressable CP variants during the serial assembly stages finally enabled an externally configured fabrication of nanotubes with highly defined subdomains. The "stop-and-go" strategy thus might pave the way towards production routines of TMV-like particles with variable aspect ratios from a single RNA scaffold, and of nanotubes with two or even more adjacent protein domains of tightly pre-defined lengths.

RNA-controlled assembly of tobacco mosaic virus-derived complex structures: from nanoboomerangs to tetrapods

The in vitro assembly of artificial nanotubular nucleoprotein shapes based on tobacco mosaic virus-(TMV-)-derived building blocks yielded different spatial organizations of viral coat protein subunits on genetically engineered RNA molecules, containing two or multiple TMV origins of assembly (OAs). The growth of kinked nanoboomerangs as well as of branched multipods was determined by the encapsidated RNAs. A largely simultaneous initiation at two origins and subsequent bidirectional tube elongation could be visualized by transmission electron microscopy of intermediates and final products. Collision of the nascent tubes' ends produced angular particles with well-defined arm lengths. RNAs with three to five OAs generated branched multipods with a maximum of four arms. The potential of such an RNA-directed self-assembly of uncommon nanotubular architectures for the fabrication of complex multivalent nanotemplates used in functional hybrid materials is discussed.

The use of tobacco mosaic virus and cowpea mosaic virus for the production of novel metal nanomaterials

Due to the nanoscale size and the strictly controlled and consistent morphologies of viruses, there has been a recent interest in utilizing them in nanotechnology. The structure, surface chemistries and physical properties of many viruses have been well elucidated, which have allowed identification of regions of their capsids which can be modified either chemically or genetically for nanotechnological uses. In this review we focus on the use of such modifications for the functionalization and production of viruses and empty viral capsids that can be readily decorated with metals in a highly tuned manner. In particular, we discuss the use of two plant viruses (Cowpea mosaic virus and Tobacco mosaic virus) which have been extensively used for production of novel metal nanoparticles (<100nm), composites and building blocks for 2D and 3D materials, and illustrate their applications.

TMV nanorods with programmed longitudinal domains of differently addressable coat proteins

The spacing of functional nanoscopic elements may play a fundamental role in nanotechnological and biomedical applications, but is so far rarely achieved on this scale. In this study we show that tobacco mosaic virus (TMV) and the RNA-guided self-assembly process of its coat protein (CP) can be used to establish new nanorod scaffolds that can be loaded not only with homogeneously distributed functionalities, but with distinct molecule species grouped and ordered along the longitudinal axis. The arrangement of the resulting domains and final carrier rod length both were governed by RNA-templated two-step in vitro assembly. Two selectively addressable TMV CP mutants carrying either thiol (TMVCys) or amino (TMVLys) groups on the exposed surface were engineered and shown to retain reactivity towards maleimides or NHS esters, respectively, after acetic acid-based purification and re-assembly to novel carrier rod types. Stepwise combination of CP(Cys) and CP(Lys) with RNA allowed fabrication of TMV-like nanorods with a controlled total length of 300 or 330 nm, respectively, consisting of adjacent longitudinal 100-to-200 nm domains of differently addressable CP species. This technology paves the way towards rod-shaped scaffolds with pre-defined, selectively reactive barcode patterns on the nanometer scale.

Mechanism of tobacco mosaic virus assembly: Incorporation of 4S and 20S protein at pH 7.0 and 20 degrees C

The mechanism of assembly of tobacco mosaic virus (TMV) has been investigated at pH 7.0 and 20 degrees C by analytical ultracentrifugation. Under these conditions the overall rates of interconversion of 4S and 20S TMV coat protein are sufficiently slow to make possible measurements of the concentrations of remaining 4S and 20S TMV coat protein after addition of homologous RNA to solutions containing, initially, various mass ratios of 20S protein to 4S protein. It has been possible to measure, by schlieren boundary analysis, the relative rates of incorporation of 4S and 20S TMV protein into the growing nucleoprotein rod over the range of initial 20S:4S protein mass ratios from 93:7 to 18:82. The results show that the amount of incorporation of 20S TMV protein depends on the initial 20S:4S mass ratio between approximately 100% and 60% 20S protein but that reconstitution can proceed with approximately 100% 20S TMV protein to form full virus-size rods. However, when the initial protein solutions have less than 60% 20S protein, approximately 80% of the reconstituted nucleoprotein is preferentially formed from 4S coat protein. The remaining approximately 20% appears to require preformed 20S coat protein. These results suggest that a larger region of RNA than previously estimated is involved in the rate-limiting nucleation step in assembly and may explain previously conflicting results concerning the elongation phase of assembly when starting with partially assembled rods.

Elongation in the major direction of tobacco mosaic virus assembly

Butler and Lomonossoff [Butler, P. J. G. & Lomonossoff, G. P. (1978) J. Mol. Biol. 126, 877-882] claim that the elongation in the major direction (3'-->5') proceeds by incorporation of disk protein in tobacco mosaic virus (TMV) assembly. The strongest argument they have for this theory is the periodicity of 50 or 100 nucleotides that they observed in the banding pattern of the protected RNAs during the first few minutes of the assembly reaction. We repeated their experiment using TMV-OM (a common Japanese strain) disk protein and TMV-OM RNA. We observed a banding pattern similar to theirs, but we found the long protected RNA at 6 min to be from the 260-nm intermediate particle rather than from the full-length TMV RNA. We also carried out the assembly reaction between TMV-OM disk protein, as well as cucumber green mottle mosaic virus (CGMMV) protein, and three strains of TMV RNAs. During the course of each assembly reaction, we examined the banding patterns. We demonstrated that the banding pattern of the protected RNA differs depending on what kind of RNA is used, rather than on what kind of aggregational state the protein is in. Specifically, the similar banding pattern observed for CGMMV subunit protein was also observed for TMV disk protein in the assembly reaction with TMV (OM) RNA. We showed previously that the assembly reaction between CGMMV protein and TMV RNA proceeds by incorporation of CGMMV subunit protein. This strongly indicates that the banding pattern of the protected RNA does not arise from the stepwise addition of the 20S disk protein.

Assembly of tobacco mosaic virus into fibrous and macroscopic bundled arrays mediated by surface aniline polymerization

One-dimensional (1D) polyaniline/tobacco mosaic virus (TMV) composite nanofibers and macroscopic bundles of such fibers were generated via a self-assembly process of TMV assisted by in-situ polymerization of polyaniline on the surface of TMV. At near-neutral reaction pH, branched polyaniline formed on the surface of TMV preventing lateral association. Therefore, long 1D nanofibers were observed with high aspect ratios and excellent processibility. At a lower pH, transmission electron microscopy (TEM) analysis revealed that initially long nanofibers were formed which resulted in bundled structures upon long-time reaction, presumably mediated by the hydrophobic interaction because of the polyaniline on the surface of TMV. In-situ time-resolved small-angle X-ray scattering study of TMV at different reaction conditions supported this mechanism. This novel strategy to assemble TMV into 1D and 3D supramolecular composites could be utilized in the fabrication of advanced materials for potential applications including electronics, optics, sensing, and biomedical engineering.

Direct visualization of the structure of the "20 S" aggregate of coat protein of tobacco mosaic virus. The "disk" is the major structure at pH 7.0 and the Proto-helix at lower pH

We have employed the rapid-freeze technique to prepare specimens for electron microscopy of a coat protein solution of tobacco mosaic virus at equilibrium at pH 7.0 and 6.8, ionic strength 0.1 M and 20 degrees C. The former are the conditions for the most rapid assembly of the virus from its isolated protein and RNA. At both pH values, the equilibrium mixture contains approximately 80% of a "20 S" aggregate and 20% of a "4 S" aggregate (the so-called A-protein). The specimens were prepared either totally unstained or positively stained with methyl mercury nitrate, which binds to an amino acid residue (Cys27) internally located within the subunit, which we show not to affect the virus assembly. The images in the electron microscope are compatible only with the major structure for the "20 S" aggregate at pH 7.0 containing two rings of subunits and these aggregates display the same binding contacts as those seen between the aggregate that forms the asymmetric unit in the crystal, which has been shown by X-ray crystallography to be a disk containing two rings, each of 17 subunits, oriented in the same direction. In contrast, the images from specimens prepared at pH 6.8 show the major structure to be a proto-helix at this slightly lower pH, demonstrating that the technique of cryo-electron microscopy is capable of distinguishing between these aggregates of tobacco mosaic virus coat protein. The main structure in solution at pH 7.0 must therefore be very similar to that in the crystal, although slight differences could occur and there are probably other, minor, components in a mixture of species sedimenting around 20 S under these conditions. The equilibrium between aggregates is extremely sensitive to conditions, with a drop of 0.2 pH unit tipping the disk to proto-helix ratio from approximately 10:1 at pH 7.0 to 1:10 at pH 6.8. This direct determination of the structure of the "20 S" aggregate in solution, under conditions for virus assembly, contradicts some recent speculation that it must be helical, and establishes that, at pH 7.0, it is in fact predominantly a two-layer disk as it had been modelled before.

Assembly of hybrid RNAs with tobacco mosaic virus coat protein. Evidence for incorporation of disks in 5'-elongation along the major RNA tail

We have shown that during the reassembly of tobacco mosaic virus (TMV) RNA, with the coat protein supplied as a "disk preparation", the lengths of RNA protected from nuclease are "quantized" with steps which correspond to incorporation of the subunits from either a single or, more commonly, both rings of a disk. This interpretation has been challenged and it was suggested that the pattern was due to special, though unspecified features of the sequence of TMV RNA. To test whether the specific sequence of TMV RNA is important during the elongation, rather than just during nucleation, we have now followed growth of particles containing hybrid RNAs, with the TMV RNA origin of assembly but otherwise non-TMV sequences. We have prepared in vitro RNA transcripts containing heterologous RNA 5' to the origin of assembly sequence from TMV RNA, i.e. with a heterologous RNA tail in place of the natural major 5'-tail and no minor tail, and used these for assembly experiments. In each case we observe a banding pattern very similar to that which we had found with native TMV RNA and with a dominant quantum step of just over 100 bases, and sometimes also a step of 50 bases, strongly suggesting that this is not due to any feature of the TMV RNA. This same repeat is also visible even with a heterologous RNA chosen because it had a sequence repeat of 135 or 136 bases, confirming that the quantization is due to a feature of the elongation reaction and in no way to the RNA sequence being encapsidated. We have also followed elongation with the origin of assembly located 5' to the heterologous RNA. This leads to a slower elongation along this 3'-tail, after the initial rapid encapsidation of the origin RNA, which lacks any quantization of length protected. These results are fully compatible with the hypothesis we had advanced earlier, that the major growth along the 5'-tail is from performed aggregates ("disks") while the minor growth along the 3'-tail is from subunits in the "A-protein" adding singly or a few at a time.

Bidirectional assembly of tobacco mosaic virus in vitro

THE TIMING OF THE BIDIRECTIONAL GROWTH IN THE ASSEMBLY REACTION OF TOBACCO MOSAIC VIRUS HAS BEEN THE SUBJECT OF CONTROVERSY: Does elongation actually occur simultaneously to 5' and 3' ends or sequentially, first to the 5' end and then to the 3' end? To determine the timing of elongation toward the 3' end directly, using the S1 nuclease mapping method on a cloned cDNA with micrococcal nuclease-digested tobacco mosaic virus RNA, we analyzed encapsidation of the RNA region that was located downstream from the assembly origin. The results clearly showed that elongation toward the 3' end did not occur for at least the first 4 min. Actually it was first observed at 8 min. It is concluded that, in the first 5-7 min, a rapid elongation of the nucleation complex occurs only toward the 5' end of the RNA and that this gives rise to an intermediate particle 260 nm long. Furthermore, the lengths of the RNA that were protected against S1 nuclease digestion showed a clear banding pattern that had a spacing of approximately 100 nucleotides. This supports the hypothesis that the 20S aggregate is kinetically favored as the protein source for elongation to the 3' end.

Potential length determiner and DNA injection protein is extruded from bacteriophage T4 tail tubes in vitro

Bacteriophage T4 tails contain a set of extended protein molecules in the central channel of the tail tube through which the DNA must exit during infection. Treatment of tails with guanidine hydrochloride separates the baseplates, leaving the tail tube and several specific tube-associated proteins. Methods were developed to purify these structures. Using specific antisera, immunoblotting, and electrophoretic analysis, these structures were shown to contain proteins gp19, 29, and 48. Electron microscopy showed specifically defined stain penetration into the tail tube, a bulge at one end, and a short fiber extruded from the tube. These structures could be removed by proteases but the gp19 tube itself was resistant. Structural studies of tails and intact phage show that the bulge and fiber are at the end of the tube that interacts with the cell membrane during infection. Since the fiber did not protrude from baseplates or from incomplete (short) tube-baseplates, we propose that it is first assembled as a compact structure formed of six copies of a tube-associated protein, which elongates during tail tube formation to fill the central channel, span the length of the tube, and regulate its length. We suggest that the exit of this fiber during infection signals DNA ejection.

Sequence specificity of trinucleoside diphosphate binding to polymerized tobacco mosaic virus protein

The binding of trinucleoside diphosphates to long helical rods of tobacco mosaic virus (TMV) protein is shown to depend on base sequence, 5' AAG 3' binding being the strongest of the 25 trinucleoside diphosphate sequences measured. As TMV has a stoichiometry of three nucleotides per protein subunit, the sequence of TMV RNA suggested to be the nucleation site for self-assembly of the virus has three possible binding frames. From our binding constant data the most likely frame is predicted and shown to have two contiguous AAG sequences in a hairpin loop region.