RECONSTITUTION OF TOBACCO MOSAIC VIRUS. IV. INHIBITION BY ENZYMES AND OTHER PROTEINS, AND USE OF POLYNUCLEOTIDES

How do RNA viruses select which RNA to package? The plant virus experience

The process whereby viral RNA is specifically selected for packaging within viral particles has been extensively studied over many years. As a result, two broad hypotheses have emerged to explain this specificity, though these are not mutually exclusive. The first proposes that the viral RNA contains specific sequences or "packaging signals" that enable it to be recognised from a mixture of RNAs within an infected cell. The second suggests that there is a functional coupling between RNA replication and packaging that leads to only replicating, viral RNA being packaged. This review is aimed at analysing the evidence for the two hypotheses from both in vitro and in vivo studies on positive-strand RNA plant viruses. Overall, it seems probable that the selectivity of packaging results from replication of the viral RNAs rather than the presence of any specific RNA sequence. However, it is also likely that the presence of packaging signals with high affinity for the viral coat protein is involved in the efficient incorporation of RNA into particles, thereby favouring the correct assembly of fully formed and infectious particles.

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.

Finding our roots and celebrating our shoots: Plant virology in Virology, 1955-1964

To celebrate the sixtieth anniversary of Virology a survey is made of the plant viruses, virologists and their institutions, and tools and technology described in the first decade of plant virus publications in Virology. This was a period when plant viruses increasingly became tools of discovery as epistemic objects and plant virology became a discipline discrete from plant pathology and other life sciences.

Self-assembly of tobacco mosaic virus: the role of an intermediate aggregate in generating both specificity and speed

The tobacco mosaic virus (TMV) particle was the first macromolecular structure to be shown to self-assemble in vitro, allowing detailed studies of the mechanism. Nucleation of TMV self-assembly is by the binding of a specific stem-loop of the single-stranded viral RNA into the central hole of a two-ring sub-assembly of the coat protein, known as the 'disk'. Binding of the loop onto its specific binding site, between the two rings of the disk, leads to melting of the stem so more RNA is available to bind. The interaction of the RNA with the protein subunits in the disk cause this to dislocate into a proto-helix, rearranging the protein subunits in such a way that the axial gap between the rings at inner radii closes, entrapping the RNA. Assembly starts at an internal site on TMV RNA, about 1 kb from its 3'-terminus, and the elongation in the two directions is different. Elongation of the nucleated rods towards the 5'-terminus occurs on a 'travelling loop' of the RNA and, predominantly, still uses the disk sub-assembly of protein subunits, consequently incorporating approximately 100 further nucleotides as each disk is added, while elongation towards the 3'-terminus uses smaller protein aggregates and does not show this 'quantized' incorporation.

Assembly of influenza ribonucleoprotein in vitro using recombinant nucleoprotein

The influenza A virus nucleoprotein previously expressed in Escherichia coli after fusion to 32 heterologous amino acids has now been purified and tested for its ability to form complexes with RNA in vitro. By using a simple filter binding assay, we show that ribonucleoprotein (RNP) complexes form readily with single-stranded RNA of viral or nonviral origin but not with double-stranded RNA. The RNP complexes formed were similar to authentic influenza virus RNPs in appearance under the electron microscope, in buoyant density in gradients of cesium chloride, and in sensitivities to pancreatic ribonuclease, to chaotropic reagents, and to high salt. We conclude that nucleoprotein synthesized in E. coli has all the properties required for correct assembly into ribonucleoprotein.

Essential features of the assembly origin of tobacco mosaic virus RNA as studied by directed mutagenesis

The assembly origin of tobacco mosaic virus RNA contains three stable hairpin loops. Coat protein disks bind first to loop 1 (the 3' most) during virus assembly, but the whole region is coated in a concerted fashion even in conditions of limiting protein. It is shown by in vitro packaging assays using mutant assembly origin transcripts that rapid and specific assembly initiation occurs in the absence of loops 2 and 3, but is abolished on removal of loop 1. Deletion or alteration of the unpaired AAGAAGUCG sequence at the apex of loop 1 also abolishes rapid packaging; this sequence is therefore instrumental in disk binding. Alteration of this sequence to (A)9 leads to packaging at a very low rate (half time 12 hours) which is apparently non-sequence specific. Substitution of (CCG)3 evokes packaging with a half time of 3 hours, as compared to 15 seconds for the wild type assembly origin. These results suggest that the three-base G periodicity within this sequence element is an important feature in assembly nucleation.

Coordinated two-disk nucleation, growth and properties, of virus-like particles assembled from tobacco-mosaic-virus capsid protein with poly(A) or oligo(A) of different length

Assembly of nucleoprotein rods from tobacco mosaic virus (TMV) coat protein and poly(A) depends on the presence of 20S disks in a manner very similar to nucleation and growth of virions in reconstitution with TMV RNA. Products assembled with (A) approximately equal to 5000 appear to have the same buoyant density in CsCl, the same nucleotide/protein ratio and the same nuclease stability, as reconstituted and native TMV. Their rate of formation is very similar to the rate of reconstitution with TMV RNA when high-molecular-mass (A) approximately equal to 5000 is used, but becomes a function of chain length particularly with (A) less than or equal to 185. The composition of assembly products can be described sufficiently with the relation between number of capsid polypeptide monomers/particle, np, to the number of nucleotide residues/chain, nnt, of np = 1/3 (nnt + 50) with two important restrictions: (1) particles of less than four turns of helically arranged capsid subunits are unstable, and (2) particles with about 150 or less nucleotides per chain deviate in structure from mature virus and virus-like (= longer) assembly products. This is indicated by changes in both buoyant density in CsCl and optical properties, while 'dislocation' of the disk to the helical arrangement of capsid subunits ('helicalization') and nuclease stability already become established with chains as short as (A) approximately equal to 58 +/- 20. Consequently, we suggest that assembly proceeds through three distinct phases: (1) nucleation (resulting in helicalization) by interaction of nucleic acid with the first disk; (2) stabilization of the primary (unstable!) nucleation complex by addition of a second disk and formation of a four-turn virus-like and stable nucleoprotein helix, which is then fit for (3) elongation by addition of further disks. The question of what makes the TMV protein disk select specifically TMV RNA during virion assembly is discussed in some detail.

The H protein isolated from tobacco mosaic virus reassociates with virions reconstituted in vitro

Virions of two strains of tobacco mosaic virus (U1 and Cc) have associated with them a small amount of a minor protein called H protein (A. Asselin and M. Zaitlin, 1978, Virology 91, 173-181), now known to be related to the viral coat protein (C.W. Collmer, V.M. Vogt, and M. Zaitlin, 1983, Virology 126, 429-448.). In the present study, a quantification technique involving disruption of virions followed by direct analysis of the component parts on SDS polyacrylamide gels was used to confirm an average of one molecule of H protein per virion for U1 TMV. H protein was separated from coat protein and purified by electrofocusing in a flatbed of granulated gel under stringent dissociating conditions. When assayed in the presence of urea, H protein has a pI of approximately 5.4, coat protein has a pI of approximately 4.9. Proteinase K-treated TMV RNA and H-protein-free TMV coat protein were reconstituted in vitro with or without H protein and the resulting virions were analyzed. A small amount of H protein reassociated with virions reconstituted in vitro (less than 10% of the amount found in native virions) and became resistant to degradation by trypsin, but such virions were no different from virions reconstituted without H protein in terms of yield of reconstituted particles or infectivity. In mixed reconstitution experiments with RNA and coat protein from strains U1 and Cc in all four possible combinations and with U1 H protein, the H protein always associated with the U1 coat protein. This demonstrated U1-H protein affinity for a specific coat protein rather than a specific RNA. It is unlikely that H protein functions in the early stages of viral infection, although the possibility of its having some other role in the life cycle of TMV remains.

Mechanism of RNA-protein interactions in tobacco mosaic virus: analysis of the pH stability of virus protein complexes with synthetic polynucleotides

TMV-like RNP complexes were reconstituted from TMV protein and synthetic polynucleotides. Analysis of the pH stability of RNP with polynucleotides containing U, G, or their analogues reveals a correlation between the stability of their structure and the pK values of the bases, and indicates that the -NH-CO-groups of U and G are involved in hydrogen bonding with protein. It is suggested that TMV protein has two U- and one G-specific binding sites which, according to the phase position of the protein subunits relative to the origin of TMV assembly (D. Zimmern (1977), Cell 11, 463) are likely to be organized as UGU. The binding of the A and C residues of RNA with TMV protein is nonspecific. TMV protein groups with pK 6.3, 7.5 and 9.7 were found to be essential in the protein-protein interactions in RNP. A group of the protein with pK 8.2 is also involved in RNP stabilization. Both protein-protein interactions and interactions of protein with RNA phosphate groups were shown to be mediated by a conformational change in the protein induced by base binding. The effect of bases on both types of interactions changes in the order G approximately equal to much greater than A, and incorporation of C in RNP proceeds in a compulsory way at the expense of interaction of the neighbouring nucleotide residues in polynucleotides with protein. The data obtained are used to discuss the principles of the cooperativity of the interactions between TMV components and the mechanism of initiation and elongation in TMV self-assembly.

RNA-protein interactions in the assembly of tobacco mosaic virus

Assembly of tobacco mosaic virus is initiated by the binding of a specific loop of the RNA into the central hole of the disk aggregate of protein subunits. Since the nucleation loop is located about five-sixths along the RNA molecule, subsequent elongation must be bidirectional. We have now measured the rates of elongation in the two directions by determining the lengths of RNA protected from nuclease digestion at different times and using either intact TMV rNA, or RNA with most of the longer tail removed. Comparison of the rates with the protein supplied as either a mixture of disks with A-protein (a mixture of less aggregated states) or just A-protein, shows that different mechanisms and protein aggregates are used for the most rapid growth. When disks are present, they add more rapidly along the longer RNA tail but do not appear to add directly on the shorter tail. In contrast, smaller aggregates (A-protein) can add at both ends of the rod, but do so more slowly. Mechanisms for these processes are discussed. Preliminary results on the binding of the specific hexanucleotide AAGAAG to the disk are given and compared with the known changes on binding nonspecific hexanucleotides or the trinucleotide AAG.

Infectivity and reconstitution of TMV RNA modified with N-acetoxy-2-acetylaminofluorene or benzol [a] pyrene 7,8-dihydrodiol 9,10 oxide

TMV RNA was modified by two bulky carcinogens, N-acetoxy-2-acetylamino-fluorene (AAAF) and (+/-)-7beta, 8alpha- dihydroxy-9alpha, 10alpha-epoxy-7,8,9,10-tetrahydrobenzo[alpha]pyrene (BPDE), and the effects of such substituents on biological and physical properties was studied. For both types of modification, the loss of infectivity was directly proportional to the number of chemical modifications indicating that all modifications are lethal. Neither AAAF nor BPDE produced measurable mutations. Reconstitution of modified RNA with TMV protein was partially inhibited, but such inhibition occurred to similar extents with either carcinogen and a varying levels of modification. The data suggest that both types of substitution of TMV RNA generally permit the TMV coat protein to aggregate normally around the RNA, but that AAAF and BPDE may induce some conformational change in the initiation region that inhibits the initiation step.

Interaction of tobacco mosaic virus protein with synthetic polynucleotides containing a fluorescent label: optical properties of poly(A,epsilonA) and poly(C,epsilonC) copolymers and energy migration from the tryptophan to 1,N6-ethenoadenine or 3,N4-ethenocytosine residues in RNP

A spectrophotometric method for determination of the modification degrees and molar extinction coefficients for poly(A, epsilonA) and poly(C, epsilonC) copolymers has been developed. Dependence of some absorption and fluorescence parameters of the copolymers on the modification degree has been studied. Distribution of modified residues in copolymers differs from random and depends on modification conditions. Interaction between the TMV protein and copolymers has been investigated. The protein interacts with poly(A, epsilonA) of low or medium modification degree and displays no activity with respect to poly(epsilonA). On the contrary, introduction of epsilonC to the polynucleotide promotes complex formation between poly(C, epsilonC) and TMV protein. Analysis of the fluorescence emission and excitation spectra has revealed energy transfer from tryptophan to epsilonA or epsilon C in the RNP to occur and permits one to estimate the average distance between Trp (presumably Trp 52)o and the RNA base binding region in the virus to be 17 to 20 A.

Tobacco mosaic virus protein: sedimentation equilibrium studies of the initial stages of polymerization

The lowest stages of polymerization of tobacco mosaic virus protein were studied by means of high-speed sedimentation equilibrium experiments. Several distinct modes of polymerization were found. At pH 7.1 the expected monomer-trimer-higher polymer equilibrium was observed--very little dimer was detected at this pH. At pH 7.5, however, a strong dimerization was observed--neither monomer nor trimer was detected at this pH. An octamer appeared to be the only species present other than the dimer. When 0.01 M beta-mercaptoethanol was added to the solvent pH 7.5, the dimer was dissociated, resulting in a monomer-trimer association. The dimerization may be the basis for the larger "doubled" polymers formed by the protein at alkaline pH, while the octamer may correspond to the 8S peak frequently observed in sedimentation velocity experiments at alkaline pH. On the other hand, the monomer-trimer-higher polymer equilibrium may correspond to the single helix formed by the protein at slightly acid pH and to the combination of 4S and 20S peaks seen in sedimentation velocity experiments at slightly acid pH.

Tobacco rattle virus RNA-protein interactions

For the purpose of attempting to generalize the rules concerning morphogenesis of helical viruses, the in vitro reconstitution of the CAM strain of TRV was studied. The conditions for reconstitution and the importance of the aggregation state of the protein for initiation and elongation are compared with those of TMV. The initiation step consisting of the binding of RNA with the 36S disk of protein was easily accomplished. The polarity and the specificity of encapsidation of TRV RNA by homologous and heterologous viral protein is discussed.

A prediction of the structure of tobacco-mosaic-virus protein

The location of amino acid residues within the tobacco mosaic virus protein subunit is discussed. Sequence data, X-ray crystallographic measurements, and the availability of specific residues for enzymic, immunological or chemical reaction are amongst the information used to trace roughly how the tobacco mosaic virus polypeptide chain winds in and out from the virus axis. Published rules for predicting secondary structure are then applied to obtain a diagram of the course of the polypeptide chain. This map should be useful for the interpretation of X-ray diffraction data and already permits an outline of the main features of the inner third of subunit to be suggested.

Sequence of a specifically encapsidated RNA fragment originating from the tobacco-mosaic-virus coat-protein cistron

When 25-S tobacco mosaic virus (TMV) protein aggregate and TMV RNA, which has been partially digested by T1 RNase, are mixed under conditions suitable for reconstitution, only a few RNA fragments are encapsidated. These fragments were isolated and purified by polyacrylamide gel electrophoresis. The sequence of the three main fragments, the longest of which (fragment 1) was estimated to contain 103 nucleotides, has been determined. The two smaller fragments are portions of the longer chain produced by an additional specific scission. Because of the great affinity of 25-S TMV protein for this nucleotide sequence, it will be referred to as the "specifically encapsidated RNA fragment". The occurrence of a "hidden break" in the sequence has been demonstrated: fragment 1, purified by electrophoresis on a polyacrylamide gel without 8 M urea, gives rise upon further electroporesis in the presence of urea to two new bands corresponding to the two halves of the molecule. A stable hair-pin secondary structure has been derived from the base sequence which can account for the specificity of action of the enzyme. Because of its properties, we have suggested elsewhere that the sequence of fragment 1 might correspond to the disk recognition site for reconstitution, which is known to be located at the 5' end of the intact RNA. But experiments with TMV RNA whose 5'-OH end has been radioactively phosphorylated with polynucleotide kinase show that this is not the case. Analysis of the amino acid coding capacity of the fragment has instead revealed that fragment 1 is a portion of the TMV coat protein cistron.

The specificity of different classes of ethylating agents toward various sites in RNA

The alkyl products of neutral in vitro ethylation of TMV-RNA by [14C]diethyl sulfate, [14C]ethyl methanesulfonate, and [14C]ethylnitrosourea have been determined and found to differ significantly depending on the ethylating agent. Diethyl sulfate and ethyl methanesulfonate ethylate the bases of TMV-RNA in the following order: 7-ethylguanine greater than 1-ethyladenine, 3-ethylcytidine greater than 7-ethyladenine, 3-ethyladenine, O6-ethylguanosine, 3-ethylguanine. Ethyl methanesulfonate was more specific for the 7 position of guanine, and other derivatives were found in lesser amounts than with diethyl sulfate. Neither reagent caused the formation of detectable amounts (smaller than 0.26 percent) of 1-ethylguanine, 1,7-diethylguanine, N2-ethylguanine, N6-ethyladenine, N4-ethylcytidine, or 3-ethyluridine. Identified ethyl bases account for over 85% of the total radioactivity of [14C]ethyl methanesulfonate and [14C]diethyl sulfate treated TMV-RNA. Phosphate alkylation accounts for about 13 and 1%, respectively, In contrast, [14C]ethylnitrosourea-treated TMV-RNA, while reacting to a similar extent (15-70 ethyl groups/6400 nucleotides), is found to cause considerably more phosphate alkylation. Upon either U4A RNase or acid hydrolysis up to 60% of the radioactivity is found as volatile ethyl groupw in the form of [14C]ethanol, and a further 15% appears to be primarily ethyl phosphate and nucleosides with ethylated phosphate. Of the remaining radioactivity, half is found as O6-ethylguanosine, the major identified ethyl nucleoside. Other ethyl bases found in ethylnitrosourea-treated TMV-RNA are 7-ethylguanine greater than 1-ethyladenine, 3-ethyladenine, 7-ethyladenine, 3-ethylcytidine, and 3-ethylguanine. It appears that ethylnitrosourea preferentially alkylates oxygens, and that formation of phosphotriesters is by far the predominant chemical event. Since the number of ethyl groups introduced into TMV-RNA by ethylnitrosourea is similar to the number of lethal events, one may conclude that phosphate alkylation leads to loss of infectivity. None of the three ethylating agents studied are strongly mutagenic on TMV-RNA or TMV. The role of phosphate alkylation in regard to in vivo mutagenesis and oncogenesis remains to be established. At present it appears possible that the extent of this reaction may correlate better with the oncogenic effectiveness of different ethylating agents, than the extent of any base reaction. Unfractionated HeLa cell RNA is ethylated primarily in acid labile manner even by diethyl sulfate and ethyl methanesulfonate, a fact that is attributed to its high content of low molecular weight trna rich in terminal phosphates which alkylate readily.