Polarity of the RNA in the tobacco mosaic virus particle and the direction of protein stripping in sodium dodecyl sulphate

Getting Hold of the Tobamovirus Particle-Why and How? Purification Routes over Time and a New Customizable Approach

This article develops a multi-perspective view on motivations and methods for tobamovirus purification through the ages and presents a novel, efficient, easy-to-use approach that can be well-adapted to different species of native and functionalized virions. We survey the various driving forces prompting researchers to enrich tobamoviruses, from the search for the causative agents of mosaic diseases in plants to their increasing recognition as versatile nanocarriers in biomedical and engineering applications. The best practices and rarely applied options for the serial processing steps required for successful isolation of tobamoviruses are then reviewed. Adaptations for distinct particle species, pitfalls, and 'forgotten' or underrepresented technologies are considered as well. The article is topped off with our own development of a method for virion preparation, rooted in historical protocols. It combines selective re-solubilization of polyethylene glycol (PEG) virion raw precipitates with density step gradient centrifugation in biocompatible iodixanol formulations, yielding ready-to-use particle suspensions. This newly established protocol and some considerations for perhaps worthwhile further developments could serve as putative stepping stones towards preparation procedures appropriate for routine practical uses of these multivalent soft-matter nanorods.

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.

A point mutation in the tobacco mosaic virus capsid protein gene induces hypersensitivity in Nicotiana sylvestris

In Nicotiana sylvestris, the N' gene confers hypersensitive resistance to some strains of tobacco mosaic virus (TMV) but not to the common strain. TMV sequences responsible for inducing local lesion formation in this host were identified by using cDNA clones to construct genomic recombinants between the common strain genome and a local-lesion-inducing mutant. To assay for sequences conferring the mutant phenotype, in vitro transcripts of recombinants were inoculated onto leaves of N. sylvestris and observed for the formation of either local lesions or a systemic infection. Sequences from the mutant that converted the hybrid genome to the mutant phenotype were located between nucleotides 5972 and 6206. Sequence analysis of this region revealed point mutations in the mutant at nucleotides 6157 (cytosine to uracil) and 6199 (adenine to guanine). The mutation at 6157 changes the capsid protein gene to specify phenylalanine rather than serine at position 148; nucleotide 6199 occurs in the 3' nontranslated region. When each point mutation was individually substituted into the wild-type background, transcripts containing only the alteration at 6157 produced local lesions on N. sylvestris, whereas transcripts containing only the alteration at 6199 produced systemic mosaic symptoms. The frequency of mutation was examined by partially sequencing virion RNA from six additional independent local-lesion mutants. Five mutants had the same alteration at 6157 as the original mutant and none had the alteration at 6199. This work demonstrates that the capsid protein gene of TMV is multifunctional, both encoding the virion structural protein and mediating the outcome of infection in N. sylvestris.

Flexibility in Tobacco Mosaic Virus

Tobacco mosaic virus (TMV) particles are rod-like, 300 nm long and 18 nm in diameter. TMV consists of 2140 protein subunits, each with a relative molecular mass of 17420 (158 residues), arranged on a helix of pitch 2.3 nm with 16 1/3 subunits per turn. Winding through this helix is a single strand of RNA 6400 nucleotides long. Three bases are bound to each protein subunit. TMV has a central hole of diameter 4.0 nm. Assembly of TMV occurs by the threading of the RNA through the central hole of the growing rodlet of viral coat protein and involves a preassembled double disk as intermediate. Given the structure of the subunit, such a mechanism requires that the segment of polypeptide chain which separates the nucleic acid binding site from the lumen of the cylinder should be able to move out of the way during the assembly process. Evidence from diffraction studies and from proton nuclear magnetic resonance spectroscopy points to a segment of about 20 amino acid residues being very flexible in the disk. In the helical virus these residues take on a well-defined conformation which completely shields the nucleic acid from the central channel.

Elucidation of the genome organization of tobacco mosaic virus

Proteins unique to tobacco mosaic virus (TMV)-infected plants were detected in the 1970s by electrophoretic analyses of extracts of virus-infected tissues, comparing their proteins to those generated in extracts of uninfected tissues. The genome organization of TMV was deduced principally from studies involving in vitro translation of proteins from the genomic and subgenomic messenger RNAs. The ultimate analysis of the TMV genome came in 1982 when P. Goelet and colleagues sequenced the entire genome. Studies leading to the elucidation of the TMV genome organization are described below.

Viral characterization by direct analysis of capsid proteins

Matrix-assisted laser desorption/ionization mass spectrometry has enabled viral coat proteins to be characterized directly from the virus. This analysis, demonstrated here with tobacco mosaic virus U2, a bacteriophage MS2, and equine encephalitis TRD, is achieved with a combination of organic acid, UV-absorbing matrix, and high-energy desorption with a nitrogen laser. The molecular weights of these proteins are determined with sufficient accuracy to allow differentiation among viral species and strains. The abundant hydrophobic MS2 coat protein was analyzed in aliquots of culture medium and of the tobacco mosaic virus coat protein in infected leaves. This method provides rapid detection of coat protein in the low-femtomole range, as estimated by titering plaque-forming units of MS2.

Expression of tobacco mosaic virus coat protein and assembly of pseudovirus particles in Escherichia coli

The bidirectional self-assembly of tobacco mosaic virus (TMV, common or U1 strain) has been studied extensively in vitro. Foreign single-stranded RNA molecules containing the TMV origin-of-assembly sequence (OAS, 75-432 nt in length) are also packaged by TMV coat protein (CP) in vitro to form helical pseudovirus particles. To study virus assembly in vivo requires an easily manipulated model system, independent of replication in plants. The TMV assembly machinery also provides a convenient means to protect and recover chimeric gene transcripts of almost any length or sequence for a variety of applications. Native TMV CP expressed in and purified from Escherichia coli formed nonhelical, stacked aggregates after dialysis into pH 5 buffer and was inactive for in vitro assembly with TMV RNA. U1 CP derivatives in which the second amino acid was changed from Ser to Ala or Pro, nonacetylated N termini found in two natural strains of the virus, failed to remediate these anomalous properties. However, in vivo coexpression of CP and single-stranded RNAs (up to approximately 2 kb) containing the TMV OAS gave high yields of helical pseudovirus particles of the predicted length (up to 7.4 +/- 1.4 micrograms/mg of total bacterial protein). If the OAS-containing RNA was first recruited into bacterial polyribosomes, elongation of pseudovirus assembly was blocked. In vivo, E. coli expression of a full-length cDNA clone of the TMV genome (6.4 kb) resulted in high, immunodetectable levels of CP and assembly of sufficient intact genomic RNA to initiate systemic infection of susceptible tobacco plants.

Assembly of tobacco mosaic virus and TMV-like pseudovirus particles in Escherichia coli

High-level expression of plant viral proteins, including coat protein (CP), is possible in Escherichia coli. Native tobacco mosaic virus (TMV) CP expressed in E. coli remains soluble but has a non-acetylated N-terminal Ser residue and following extraction, is unable to package TMV RNA in vitro under standard assembly conditions. Changing the Ser to Ala or Pro by PCR-mutagenesis did not confer assembly competence in vitro, despite these being non-acetylated N-termini present in two natural strains of TMV. All TMV CPs made in E. coli formed stacked cylindrical aggregates in vitro at pH 5.0 and failed to be immunogold-labelled using a mouse monoclonal antibody specific for helically assembled TMV CP. TMV self-assembly has been studied extensively in vitro, and an origin of assembly sequence (OAS) mapped internally on the 6.4 kb ssRNA genome. Pseudovirus particles can be assembled mono- or bi-directionally in vitro using virus-derived CP and chimeric ssRNAs containing the cognate TMV OAS, but otherwise of unlimited length and sequence. Studies on plant virus assembly in vivo would be facilitated by a model system amenable to site-directed mutagenesis and rapid recovery of progeny particles. When chimeric transcripts containing the TMV OAS were co-expressed with TMV CP in vivo for 2-18 h, helical TMV-like ribonucleoprotein particles of the predicted length were formed in high yield (up to 7.4 micrograms/mg total bacterial protein). In addition to providing a rapid, inexpensive and convenient system to produce, protect and recover chimeric gene transcripts of any length or sequence, this E. coli system also offers a rapid approach for studying the molecular requirements for plant virus "self-assembly" in vivo. Transcription of a full-length cDNA clone of TMV RNA also resulted in high levels of CP expression and assembly of sufficient intact genomic RNA to initiate virus infection of susceptible tobacco plants.

Mutation and replacement of the 16-kDa protein gene in RNA-1 of tobacco rattle virus

The function of the 16-kDa protein encoded by tobacco rattle virus (TRV) RNA-1 was investigated by a mutational analysis of the 16-kDa protein gene. Transcripts of TRV RNA-1 produced from a full-length cDNA clone of TRV RNA-1 (SYM strain) remained infectious when the 16-kDa protein gene was disrupted by premature termination codons and a deletion which removed 73% of the coding region. A deletion which included the intergenic region between the 29-kDa protein gene and the 16-kDa protein gene, the entire 16-kDa protein coding region, and 57% of the 3' noncoding region was not infectious. Transcripts in which the 16-kDa protein coding region was replaced by the tobacco mosaic virus (TMV) (L strain) coat protein gene were also infectious and expressed TMV coat protein in infected tissue. Inclusion of the TMV origin of assembly sequence in the chimaeric constructs resulted in the accumulation of TMV-like virus particles in infected tissue.

The P30 movement protein of tobacco mosaic virus is a single-strand nucleic acid binding protein

The P30 protein of tobacco mosaic virus (TMV) is required for cell to cell movement of viral RNA, which presumably occurs through plant intercellular connections, the plasmodesmata. The mechanism by which P30 mediates transfer of TMV RNA molecules through plasmodesmata channels is unknown. We have identified P30 as an RNA and single-stranded (ss) DNA binding protein. Binding of purified P30 to ss nucleic acids is strong, highly cooperative, and sequence nonspecific with a minimal binding site of 4-7 nucleotides per P30 monomer. In-frame deletions across P30 were used to localize the ss nucleic acid binding domain to within amino acid residues 65-86 of the protein. We propose that binding of P30 to TMV RNA creates an unfolded protein-RNA complex that functions as an intermediate in virus cell to cell movement through plasmodesmata.

The effect of multiple dispersed copies of the origin-of-assembly sequence from TMV RNA on the morphology of pseudovirus particles assembled in vitro

Supercoiled plasmid DNA was used as a template to transcribe long concatameric RNA molecules containing several dispersed copies of the origin-of-assembly sequence (OAS) from tobacco mosaic virus (TMV) RNA. When incubated with TMV coat protein "disks" in vitro, these RNAs spontaneously assembled into TMV-like pseudovirus particles. However, as each OAS initiated assembly more or less simultaneously, the concatameric RNA species generated complex nucleoprotein structures of predictable morphology. Similar structures were proposed some time ago (M. E. Taliansky, I. B. Kaplan, L. V. Yarvekulg, T. I. Atabekova, A. A. Agranovsky, and J. G. Atabekov, 1982, Virology 118, 309-316) to account for the RNase-sensitive phenotype of a ts mutant of TMV, Ni2519. These results extend the utility of our RNA-packaging vector system and confirm many of the predictions based on the current model for the self-assembly of TMV.

Studies of tobacco mosaic virus reassembly with an RNA tail blocked by a hybridised and cross-linked probe

Segments of cloned cDNA to tobacco mosaic virus RNA, 150--300-bases long, have been hybridised and cross-linked to the RNA, which has then been used for reassembly experiments. This enables the elongation reaction, which does not encapsidate the double-stranded region generated, to be stopped at specific regions along the RNA and the resulting particles to be characterised, by measuring the lengths of the rods in the electron microscope. With hybridisation to the 3'-tail the entire RNA contiguous to the nucleation region is encapsidated, from the 5'-terminus up to the modified region. When the double-stranded region is on the 5'-side of the nucleation region, the mean length of the particles corresponds to a situation in which the double-stranded region is unable to enter the central hole of the growing rod, but the 3'-tail of the RNA is completely encapsidated. The longest particles hybridised on the 5'-tail (i.e. in a class longer than the mean length) show an effect complementary to those with a 3'-block, and have lengths which correspond to encapsidation from the modified region to the 3'-terminus, despite the continued presence of the 5'-tail up the rod. In all cases where there is a remaining 5'-tail the lengths observed can only be explained if elongation has occurred substantially, or probably completely, along the 3'-tail. Hence elongation must have occurred simultaneously along both the 5' and 3'-tails of the tobacco mosaic virus RNA after initiation on the internal nucleation region.

Characterization of long guanosine-free RNA sequences from the Dahlemense and U2 strains of tobacco mosaic virus

Four naturally occurring strains of tobacco mosaic virus, U2, Dahlemense, CV4, and the bean form of tobacco mosaic virus, were tested for the existence of long T1 RNAase oligonucleotides analogous to the oligonucleotide omega found in the common or U1 strain of tobacco mosaic virus and which makes up the 5' non-coding region of the RNA molecule. U2 and Dahlemense RNA were each found to contain this type of long T1 RNAase oligonucleotide with chain lengths of 54 and 74--77 residues, respectively. The sequence of the two oligonucleotides was determined mostly by using 5'-32P-labelled material in vitro and rapid polyacrylamide gel sequencing techniques.

Protein-RNA interactions during TMV assembly

A review of the structural studies of tobacco mosaic virus (TMV) is given. TMV is essentially a flat helical microcrystal with 16 1/3 subunits per turn. A single strand of RNA runs along the helix and is deeply embedded in the protein. The virus particles form oriented gels from which high-resolution X-ray fiber diffraction data can be obtained. This may be interpreted by the use of six heavy-chain derivatives to give an electron density map at 0.4 nm resolution from which the RNA configuration and the form of the inner part of the protein subunit may be determined. In addition, the protein subunits form a stable 17-fold two-layered disk which is involved in virus assembly and which crystallizes. By the use of noncrystallographic symmetry and a single heavy-atom derivative, it has been possible to solve the structure of the double disk to 0.28 nm resolution. In this structure one sees that an important structural role is played by four alpha-helices, one of which (the LR helix) appears to form the main binding site for the RNA. The main components of the binding site appear to be hydrophobic interactions with the bases, hydrogen bonds between aspartate groups and the sugars, and arginine salt bridges to the phosphate groups. The binding site is between two turns of the virus helix or between the turns of the double disk. In the disk, the region proximal to the RNA binding site is in a random coil until the RNA binds, whereupon the 24 residues involved build a well-defined structure, thereby encapsulating the RNA.

Infectivity suppressing and virus-binding activities of a membrane material isolated from tobacco leaves

TMV binding substance (R) was isolated from a tobacco leaf membrane fraction and was purified by extraction with organic solvents and by column chromatography. Experimental results suggest that the binding of R with TMV results in inactivation of TMV. When tobacco leaves were inoculated with the R-TMV complex, it was found that the formation of polysome containing infecting viral RNA was inhibited. Model experiments showed that the mode of R-TMV adsorption to the membrane is different from that of TMV adsorption and that stripping of coat protein from TMV by SDS was inhibited by R. A possible explanation for the mechanism of this inhibition by R is that the R-TMV complex follows a pathway which does not lead to establishment of infection. Although less efficient, R was still active when it was applied after virus inoculation. Due to its affinity to coat protein, R might also interfere with a later process of viral multiplication.

Location of tyrosine residues in the disk of tobacco-mosaic-virus protein and comparison of the subunit packing with that of the virus

The products of iodination of the disk of tobacco mosaic virus coat protein have been investigated in order to locate the reactive amino acid residues in the three-dimensional structure. Reaction occurs mainly with tyrosine-139 and, to a lesser extent, tyrosine-2 and the positions of these modified residues have been determined by X-ray crystallography. Different extents of reaction are found in the two rings of the disk and also, on adding the high salt concentration needed for stabilisation of the crystal during reaction, some conformational changes in the polypeptide chain in the inner part of the disk. Comparison of the relative positions of residues 27 and 139 in the disk and virus shows that little distortion occurs in the outer part of the subunit during the transition between the disk and virus structures.

Structure of RNA and RNA binding site in tobacco mosaic virus from 4-A map calculated from X-ray fibre diagrams

The structure of tobacco mosaic virus has been solved to a resolution of 4 A using fibre diffraction methods. The general fold of the protein is clear, the conformation may be deduced in many places, and the conformation of the RNA and its interaction with the protein can be seen.

Configuration of tobacco mosaic virus, RNA during virus assembly

When TMV reassembles, the uncoated RNA is folded back along the growing rod, probably down the central hole. This surprising configuration is essential for rapid elongation--presumably supplying RNA to its site of incorporation while keeping the bulk of the free RNA out of the way.