Pseudovirions of tobacco mosaic virus

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.

Facile Purification and Use of Tobamoviral Nanocarriers for Antibody-Mediated Display of a Two-Enzyme System

Immunosorbent turnip vein clearing virus (TVCV) particles displaying the IgG-binding domains D and E of Staphylococcus aureus protein A (PA) on every coat protein (CP) subunit (TVCVPA) were purified from plants via optimized and new protocols. The latter used polyethylene glycol (PEG) raw precipitates, from which virions were selectively re-solubilized in reverse PEG concentration gradients. This procedure improved the integrity of both TVCVPA and the wild-type subgroup 3 tobamovirus. TVCVPA could be loaded with more than 500 IgGs per virion, which mediated the immunocapture of fluorescent dyes, GFP, and active enzymes. Bi-enzyme ensembles of cooperating glucose oxidase and horseradish peroxidase were tethered together on the TVCVPA carriers via a single antibody type, with one enzyme conjugated chemically to its Fc region, and the other one bound as a target, yielding synthetic multi-enzyme complexes. In microtiter plates, the TVCVPA-displayed sugar-sensing system possessed a considerably increased reusability upon repeated testing, compared to the IgG-bound enzyme pair in the absence of the virus. A high coverage of the viral adapters was also achieved on Ta2O5 sensor chip surfaces coated with a polyelectrolyte interlayer, as a prerequisite for durable TVCVPA-assisted electrochemical biosensing via modularly IgG-assembled sensor enzymes.

The Tobacco Mosaic Virus Origin of Assembly Sequence is Dispensable for Specific Viral RNA Encapsidation but Necessary for Initiating Assembly at a Single Site

We have investigated whether the presence of the origin of assembly sequence (OAS) of tobacco mosaic virus (TMV) is necessary for the specific encapsidation of replicating viral RNA. To this end TMV coat protein was expressed from replicating RNA constructs with or without the OAS in planta. In both cases the replicating RNA was specifically encapsidated to give nucleoprotein nanorods, though the yield in the absence of the OAS was reduced to about 60% of that in its presence. Moreover, the nanorods generated in the absence of the OAS were more heterogeneous in length and contained frequent structural discontinuities. These results strongly suggest that the function of the OAS is to provide a unique site for the initiation of viral assembly, leading to a one-start helix, rather than the selection of virus RNA for packaging.

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.

Encapsidation of Host RNAs by Cucumber Necrosis Virus Coat Protein during both Agroinfiltration and Infection

Next-generation sequence analysis of virus-like particles (VLPs) produced during agroinfiltration of cucumber necrosis virus (CNV) coat protein (CP) and of authentic CNV virions was conducted to assess if host RNAs can be encapsidated by CNV CP. VLPs containing host RNAs were found to be produced during agroinfiltration, accumulating to approximately 1/60 the level that CNV virions accumulated during infection. VLPs contained a variety of host RNA species, including the major rRNAs as well as cytoplasmic, chloroplast, and mitochondrial mRNAs. The most predominant host RNA species encapsidated in VLPs were chloroplast encoded, consistent with the efficient targeting of CNV CP to chloroplasts during agroinfiltration. Interestingly, droplet digital PCR analysis showed that the CNV CP mRNA expressed during agroinfiltration was the most efficiently encapsidated mRNA, suggesting that the CNV CP open reading frame may contain a high-affinity site or sites for CP binding and thus contribute to the specificity of CNV RNA encapsidation. Approximately 0.09% to 0.7% of the RNA derived from authentic CNV virions contained host RNA, with chloroplast RNA again being the most prominent species. This is consistent with our previous finding that a small proportion of CNV CP enters chloroplasts during the infection process and highlights the possibility that chloroplast targeting is a significant aspect of CNV infection. Remarkably, 6 to 8 of the top 10 most efficiently encapsidated nucleus-encoded RNAs in CNV virions correspond to retrotransposon or retrotransposon-like RNA sequences. Thus, CNV could potentially serve as a vehicle for horizontal transmission of retrotransposons to new hosts and thereby significantly influence genome evolution.

IMPORTANCE

Viruses predominantly encapsidate their own virus-related RNA species due to the possession of specific sequences and/or structures on viral RNA which serve as high-affinity binding sites for the coat protein. In this study, we show, using next-generation sequence analysis, that CNV also encapsidates host RNA species, which account for ∼0.1% of the RNA packaged in CNV particles. The encapsidated host RNAs predominantly include chloroplast RNAs, reinforcing previous observations that CNV CP enters chloroplasts during infection. Remarkably, the most abundantly encapsidated cytoplasmic mRNAs consisted of retrotransposon-like RNA sequences, similar to findings recently reported for flock house virus (A. Routh, T. Domitrovic, and J. E. Johnson, Proc Natl Acad Sci U S A 109:1907-1912, 2012). Encapsidation of retrotransposon sequences may contribute to their horizontal transmission should CNV virions carrying retrotransposons infect a new host. Such an event could lead to large-scale genomic changes in a naive plant host, thus facilitating host evolutionary novelty.

Replication of Plant Viruses

Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses co-infecting cells.

Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses coinfecting cells.

Tobacco mosaic virus RNA enters chloroplasts in vivo

Several lines of evidence are presented to allow us to conclude that tobacco mosaic virus (TMV) RNA enters the chloroplast in vivo. Chloroplasts were prepared from either directly inoculated or systemically infected leaves of tobacco plants inoculated with one of several strains of the virus and from uninfected control plants. Intact chloroplasts were isolated on Percoll gradients and treated with pancreatic RNase and thermolysin to destroy potential TMV virions and RNA on the outside or bound to their surfaces. Northern blot analysis of RNA extracted from these chloroplasts demonstrated that full-length TMV RNA was present within the chloroplasts prepared from both directly inoculated and systemically invaded leaves. Only genomic length, but not subgenomic length, RNA was found in the chloroplast extracts, indicating a selectivity of the transport of the viral RNA into the chloroplast. A temperature-sensitive TMV mutant (Ts 38), in which no virions are formed at 35 degrees C, was used to demonstrate that at that restrictive temperature viral RNA is detected in the chloroplast, indicating that free viral RNA can enter the chloroplast rather than intact virions. To our knowledge, the transport of a foreign RNA species into chloroplasts has not been reported previously.

Extensive and widespread homologies between mitochondrial DNA and chloroplast DNA in plants

We used hybridization techniques to demonstrate that numerous sequence homologies exist between cloned mung bean and spinach chloroplast DNA (ctDNA) restriction fragments and mtDNAs from corn, mung bean, spinach, and pea. The strongest cross-homologies are between clones derived from the ctDNA inverted repeat and mtDNA from corn and pea, although all the ctDNA clones tested hybridized to at least one mtDNA restriction fragment. Known chloroplast genes showing strong mtDNA homologies include those for the large subunit of ribulosebisphosphate carboxylase, which hybridizes to corn mtDNA, and the beta subunit of the chloroplast ATPase, which hybridizes to mung bean mtDNA. Certain of these homologies were confirmed by using cloned spinach mtDNA restriction fragments as probes in reciprocal hybridizations to ctDNA. Several of these ctDNA-homologous mtDNA sequences were shown to be much more closely related to ctDNA from the same species than to that of a distantly related species. We interpret these differential homologies as evidence for relatively recent DNA sequence transfer events, suggesting that transpostion between the two genomes is an ongoing evolutionary process.

Chloroplast DNA transcripts are encapsidated by tobacco mosaic virus coat protein

Preparations of tobacco mosaic virus contain pseudovirions, particles resembling virions but containing host rather than viral RNA. The encapsidated host RNA was found to be composed of discrete-sized species derived from a large portion of the chloroplast genome except that very little, if any, ribosomal RNA is present. Pseudovirions contain the same chloroplast DNA transcripts as those detected in extracts from uninfected leaves, although not always in the same relative amounts. Several strains of tobacco mosaic virus were tested and all were found to contain pseudovirions, with the U2 strain containing more than the others.

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 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.

Ty1-copia group retrotransposons as ubiquitous components of plant genomes

Ty1-copia group retrotransposons were searched for in 35 plant species by amplification of the reverse transcriptase coding region using the polymerase chain reaction. Sequences of the expected size were amplified from all of these plant species, including a liverwort, a horsetail, a bracken, gymnosperms and angiosperms. Sequences of 72 clones from 17 species were determined, all of which showed clear homology to the reverse transcriptase sequence of Ty1-copia type retrotransposons. More than half of the sequences carried stop codons or frame shifts. Twenty three new retrotransposon sequences with no interruption by these mutations were revealed. The mechanisms of the evolution of retrotransposons and accumulation of mutations were discussed.

On the relationship between X-bodies and symptom development in plants infected with different tobamoviruses

The relationship between systemic mosaic symptoms and the occurrence of viral 126-kDa protein in X-bodies was studied in tobacco infected with the tobacco mild green mosaic virus (TMGMV) strains U2, U5, and ribgrass mosaic virus (RMV) strain HR, and in other plant species infected with tobacco mosaic virus (TMV) strain W U 1. Strains U2, U5, and HR coded for proteins of 126, 126, and 130 kDa, respectively, but these were not recognized by antisera against the corresponding protein from W U 1. Only the HR 130-kDa protein reacted with an antiserum raised against a peptide of amino acids 849-863 from the sequence of W U 1. Electron microscopic analysis established the presence of virus clusters in the cytoplasm, as well as in chloroplasts, in leaf tissue infected with U 2 or U 5, and adjacent to nuclei and chloroplasts in scattered cells infected with HR. X-bodies were not detected after infection with any of these strains, but were large and adjacent to nuclei in W U 1-infected tomato displaying severe mosaic symptoms. Large X-bodies were detected near nuclei in W U 1-infected tomato displaying severe mosaic symptoms, but none were detected after infection of tobacco with any of the other tobamoviruses. The induction of X-bodies appears to be characteristic of some tobamovirus only and, at best, can only be associated with, rather than causative of, the severity of symptoms induced by those viruses.

The nucleotide sequence of abutilon mosaic virus reveals prokaryotic as well as eukaryotic features

The complete nucleotide sequence of abutilon mosaic virus (West Indian isolate, AbMVa) is presented. The resulting genomic structure resembles that of other geminiviruses which are transmitted by the whitefly Bemisia tabaci: AbMV possesses a bipartite circular genome with bidirectional orientation of the open reading frames (ORF). Both components have a common region of 180 bases with 99% homology while the rest of their sequence is distinct. Eukaryotic regulatory transcription elements precede most ORFs and polyadenylation signals are present at the end of most ORFs. However, two ORFs show features of prokaryotic genes. This chimaeric genome organisation is discussed with reference to the finding that AbMV DNA is present in plastids as well as in the nucleus of infected cells.

Localization of multiple TMV encapsidation initiation sites on rbcL gene transcripts

TMV capsid protein reacts with and encapsidates many of the chloroplast DNA transcripts both in vivo and in vitro to form pseudovirions. We report on the encapsidation initiation reaction with one of the major RNA species found in in vivo formed pseudovirions, the mRNA for the chloroplast-encoded large subunit of ribulose bisphosphate carboxylase/oxygenase (rbcL). This mRNA is found to contain at least three sites which are independently capable of reacting with capsid protein oligomers to initiate encapsidation. All three sites react with capsid protein less efficiently in vitro than does the functional viral RNA encapsidation initiation site (ei). The 5' portion of the region that contains the most reactive rbcL site, ei-3, shows significant nucleotide sequence homology with the encapsidation initiation sites of the U1 and Cc strains of TMV and it can assume a folding structure that resembles that postulated for the Cc strain site. A site that acts as a block to rod elongation is present in transcripts from the region just 3' to the segment from which the rbcL mRNA is transcribed, probably close to, or at the transcription termination signal.

Selective encapsidation of CAT gene transcripts in TMV-infected transgenic tobacco inhibits CAT synthesis

Young tobacco seedlings (F1-progeny), transformed to express chloramphenicol acetyltransferase (CAT) mRNA with or without a 3'-proximal copy of the origin-of-assembly sequence (OAS) from tobacco mosaic virus (TMV) RNA (residues 5118-5550), were inoculated with TMV. After 21 days, virus symptoms were observed and systemic TMV infections were confirmed by Western blotting for viral coat protein and by electron microscopy of leaf saps. CAT activities were measured in extracts of leaf discs taken before, and 21 days after, virus inoculation. On average, the systemic leaves from TMV-infected CAT-transgenic plants containing the OAS exhibited 3.2-fold less CAT activity than the equivalent leaves from CAT-transgenic control plants lacking the OAS. Hence selective, OAS-dependent encapsidation of nuclear DNA transcripts into TMV-like (pseudovirus) particles can reduce expression of a particular mRNA, post-transcriptionally, in vivo. Furthermore, these data indicate that TMV self-assembly is not restricted to an exclusive subcellular compartment in vivo, and that formation of natural pseudovirions (A. Siegel, Virology 46, 50-59 (1971)) may shut off specific host RNA functions.

Selective recovery of foreign gene transcripts as virus-like particles in TMV-infected transgenic tobaccos

A short origin-of-assembly sequence (OAS) located in the 30kDa movement protein gene, about 1.0kb from the 3'-end of the common strain of tobacco mosaic virus (TMV) RNA, nucleates encapsidation of the 6395-nucleotide-long genome by TMV coat protein in vitro, and presumably also in vivo. Single-stranded RNAs containing a foreign reporter gene sequence and the TMV OAS at their 5' - and 3' -ends, respectively, can be synthesized in vitro from recombinant SP6-transcription plasmids and will assemble spontaneously in vitro to form TMV-like 'pseudovirus' particles. In this paper, we show that foreign gene transcripts derived from the nuclear DNA of plants transformed by Agrobacterium tumefaciens, and which contain the TMV OAS, can be assembled into stable 'pseudovirus' particles in vivo during a systemic infection by TMV (helper). This is the first report of structural complementation between a heritable function bestowed on a transgenic plant and an infecting virus. As a route to protect, accumulate and recover a specific mRNA in vivo, in transgenic plant cells, this novel approach may find wider applications in developmental plant molecular biology.

Association of TMV coat protein with chloroplast membranes in virus-infected leaves

The polypeptide composition of extracts of chloroplasts from tobacco leaves systemically infected with different strains of Tobacco Mosaic Virus (TMV) was analyzed by one- and two-dimensional gel electrophoresis. There were no changes in the protein profiles of chloroplasts from infected leaves when compared to control leaves except for the presence of coat protein (CP) of TMV, identified by immunoblotting. When protease-treated intact chloroplasts isolated on Percoll gradients were osmotically disrupted the CP could be detected in both stroma and membrane fractions. The majority of the CP associated with the thylakoid membranes (about 1-5% of the total thylakoid proteins) was in the form of free molecules while stroma contained aggregated or assembled CP (about 0.1% of the soluble proteins). Thylakoid-associated CP was insensitive to protease digestion unless the membranes were first treated with a detergent, indicating that the CP was embedded inside or otherwise complexed with the thylakoid membranes.Chloroplasts isolated from leaves infected with TMV-PV42, a symptomless strain, contained approximately 10-50 times less CP than did chloroplasts isolated from leaves bearing mosaic symptoms induced by other strains of TMV (U1, PV230 or PV39). A possible role of CP in symptom development is discussed.

Encapsidation of 18 S rRNA by tobacco mosaic virus coat protein

It has been reported that tobacco mosaic virus capsid protein encapsidates discretesized truncated portions of host 18 S rRNA in vitro. This paper presents further information concerning the nature and specificity of this reaction. We have found that it is only the 5' portions of 18 S rRNA that are encapsidated. The structure recognized by capsid protein is highly conserved; bovine as well as plant 18 S rRNA becomes encapsidated. It is further demonstrated that assembly of 18 S rRNA is slow in comparison to assembly of TMV RNA and that this is due to a slow rate of initiation. Synthetic 18 S rRNA, prepared by in vitro transcription of an 18 S rRNA coding sequence, differs from native 18 S rRNA in that full length, rather than a truncated portion, is encapsidated. The possible reasons for this are discussed.

Polyoma pseudovirions. I. Sequence of events in primary mouse embryo cells leading to pseudovirus production

The relationship of the intracellular events leading to the production of polyoma pseudovirions in primary mouse embryo cells has been investigated. Replication of polyoma deoxyribonucleic acid (DNA) began 18 hr after infection. Assembly of viral capsid protein occurred 12 hr later. Intracellular fragments of host cell DNA, of the size found in pseudovirions, were first detected 36 hr after infection. The amount of intracellular 14S host DNA that was produced during infection was seven times greater than the amount of polyoma DNA synthesized. The relative pool sizes of polyoma DNA and 14S DNA at the time of virus assembly may dictate the amounts of polyoma virus and pseudovirus produced.