A genetic map for the cowpea strain on TMV

The Forgotten Tobamovirus Genes Encoding the 54 kDa Protein and the 4-6 kDa Proteins

This article reviews the literature concerning the largely forgotten tobamovirus gene products for which no functions have been ascribed. One of these gene products is the 54 kDa protein, representing the RNA-dependent RNA polymerase segment of the 183 kDa protein translated from the I1-subgenomic mRNA, but which has been found only by in vitro translation and not in plants. The other is a collection of small proteins, expressed from alternative reading frames (likely from internal ribosome entry sites) in either or both the movement protein gene or the capsid protein gene. Previously, two small proteins were referred to as the 4-6 kDa proteins, since only single proteins of such size had been characterized from tobacco mosaic virus and tomato mosaic virus genomes. Such putative proteins will be referred to here as P6 proteins, since many new proposed P6 open reading frames could be discerned, from an analysis of 45 of 47 tobamovirus genomes, with a coding capacity of >15 amino acids up to 94 amino acids, whereas other peptides with ≤15 amino acids were not considered here. The distribution of the putative P6 proteins among these tobamoviruses is described, as well as the various classes they fall into, based on their distribution with regard to the organization of other genes in the viral genomes. Models also are presented for possible functions of the 54 kDa protein and the P6 proteins, based on data in the literature.

tRNA-like structures and their functions

tRNA-like structures (TLSs) were first identified in the RNA genomes of turnip yellow mosaic virus. Since then, TLSs have been found in many other species including mammals, and the RNAs harboring these structures range from viral genomic RNAs to mRNAs and noncoding RNAs. Some progress has also been made on understanding their functions that include regulation of RNA replication, translation enhancement, RNA-protein interaction, and more. In this review, we summarize the current knowledge about the regulations and functions of these TLSs. Possible future directions of the field are also briefly discussed.

Analysis of RNA structure using small-angle X-ray scattering

In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well-defined 3D structure of tRNA, the structures of many of the other RNAs recognized by aaRSs have not been solved. Despite advances in the use of X-ray crystallography (XRC), nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (cryo-EM) for structural characterization of biomolecules, significant challenges to solving RNA structures still exist. Recently, small-angle X-ray scattering (SAXS) has been increasingly employed to characterize the 3D structures of RNAs and RNA-protein complexes. SAXS is capable of providing low-resolution tertiary structure information under physiological conditions and with less intensive sample preparation and data analysis requirements than XRC, NMR and cryo-EM. In this article, we describe best practices involved in the process of RNA and RNA-protein sample preparation, SAXS data collection, data analysis, and structural model building.

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.

Sequence determination of the capsid protein gene and flanking regions of tobacco etch virus: Evidence for synthesis and processing of a polyprotein in potyvirus genome expression

The nucleotide sequence of the 3'-terminal portion of the tobacco etch virus (TEV) genome was determined. The 2324-nucleotide sequence represented approximately one-fourth of the TEV genome and included the capsid protein gene and flanking regions. An open reading frame of 2135 nucleotides and an untranslated region of 189 nucleotides adjacent to a polyadenylate tract were identified. The sequence began within an open reading frame, indicating that the initiation codon was upstream of the available sequence data. The sequence of the 20 NH(2)-terminal amino acids of the TEV capsid protein was established chemically. An identical amino acid sequence, predicted from the nucleotide sequence, was located, commencing at amino acid - 263. These data indicated that maturation of the capsid protein required a post-translational cleavage of a larger protein precursor, with a probable cleavage site between the amino acids glutamine and glycine.

Localization by immunogold cytochemistry of the virus-coded 30K protein in plasmodesmata of leaves infected with tobacco mosaic virus

The 30K protein of tobacco mosaic virus (TMV) was localized to the plasmodesmata of infected tobacco leaves by immunogold cytochemistry. This protein has been reported to be in the nuclear fraction of TMV-infected protoplasts, but as it has been proposed to function in cell-to-cell transport of virus, probably via the plasmodesmata, intact tissue was investigated with particular attention directed to plasmodesmata and nuclei. Thin sections were made from leaves mechanically inoculated with TMV at different times. Affinity-purified antibodies against a synthetic peptide corresponding to the C-terminal sequence of the 30K protein were used in the incubations, and parallel sections were incubated with antibodies against TMV. The 30K protein label accumulated inside the plasmodesmata, with a maximum 24 hr after inoculation. No specific label was found in the nuclei or at any other site in the cells.

Properties of the tobacco mosaic virus intermediate length RNA-2 and its translation

The existence of subgenomic RNAs is well established in the case of plant viruses such as tobacco mosaic virus (TMV). However, except for the subgenomic coat protein mRNA, it is not known whether the other subgenomic RNAs have a function in the life cycle of the virus. In search of more information about one of the major subgenomic RNAs-intermediate length RNA-2 or I2 RNA-of TMV, in vitro and in vivo translational studies were performed. The I2 RNA, which codes in vitro for the synthesis of a 30K (K = kilodalton) protein, appears to be uncapped as judged by the need of different in vitro translation conditions for the synthesis of this protein, compared to the conditions required for the synthesis of the 126K and 183K proteins coded by the capped genomic RNA. In vivo a protein migrating in the same position as the 30K protein synthesized in vitro can be detected in infected tobacco leaves. Since this protein occurs transiently early upon infection, whether it is virus-coded or virus-induced, it could have an early function during infection.

Nucleotide sequence of the coat protein cistron and the 3' noncoding region of cucumber green mottle mosaic virus (watermelon strain) RNA

Double-stranded cDNA copies of cucumber green mottle mosaic virus (watermelon strain, CGMMV-W) RNA polyadenylated in vitro were cloned into the pBR322 at the PstI site. The sequence of 1071 nucleotides from the Tend of the genomic RNA was determined using two recombinant plasmids and the genomic RNA. The coat protein cistron was located in residues 176-661 from the 3' end. The coat protein was composed of 160 amino acid residues with the molecular weight of 17,261. The 3' noncoding region of the CGMMVW genome was 175 nucleotides long and highly homologous to that of the common strain of TMV. The assembly origin of reconstitution is positioned within the coat protein cistron as predicted previously. In the 5' flanking region of the coat protein cistron a long open frame, probably of 30K protein, was found. The predicted 30K and the coat protein cistron would overlap each other as is the case of the cowpea strain of TMV.

Role of tRNA-like structures in controlling plant virus replication

Transfer RNA-like structures (TLSs) that are sophisticated functional mimics of tRNAs are found at the 3'-termini of the genomes of a number of plant positive strand RNA viruses. Three natural aminoacylation identities are represented: valine, histidine, and tyrosine. Paralleling this variety in structure, the roles of TLSs vary widely between different viruses. For Turnip yellow mosaic virus, the TLS must be capable of valylation in order to support infectivity, major roles being the provision of translational enhancement and down-regulation of minus strand initiation. In contrast, valylation of the Peanut clump virus TLS is not essential. An intermediate situation seems to exist for Brome mosaic virus, whose RNAs 1 and 2, but not RNA 3, need to be capable of tyrosylation to support infectivity. Other known roles for certain TLSs include: (i) the recruitment of host CCA nucleotidyltransferase as a telomerase to maintain intact 3' CCA termini, (ii) involvement in the encapsidation of viral RNAs, and (iii) presentation of minus strand promoter elements for replicase recognition. In the latter role, the promoter elements reside within the TLS but are not functionally dependent on tRNA mimicry. The phylogenetic distribution of TLSs indicates that their evolutionary history includes frequent horizontal exchange, as has been observed for protein-coding regions of plant positive strand RNA viruses.

Translation of tobacco rattle virus RNAs in vitro: four proteins from three RNAs

RNAs from the Lisse and PRN strains of tobacco rattle virus were translated in nuclease-treated reticulocyte lysates. With both strains, RNA-1 coded for two proteins of MW 170,000 and 120,000. Addition of 1-2 mM Mg2+ increased the yield of the larger product, apparently by facilitating readthrough of a leaky termination codon at the end of the region coding for the smaller protein. Experiments with yeast suppressor tRNA indicate that this is not a UAG or UAA codon. RNA-2 coded for a protein of the same size as coat protein. A product of MW 30,000 was coded by a third RNA (RNA-3) which in the case of PRN TRV had a molecular weight of 550,000 and could be separated from RNA-2 by gel electrophoresis. Translation of all three RNAs was inhibited by m7GTP. However, RNA-1 also directed a low level of m7GTP-resistant synthesis of a 30,000-dalton protein which appeared to be identical to the RNA-3 product, and it is suggested that RNA-3 corresponds to the 3' end of RNA-1. Thus the strategies of synthesis of the non-coat proteins of tobacco rattle and tobacco mosaic viruses appear to be similar.

Packaging of tobacco mosaic virus subgenomic RNAs by Brome mosaic virus coat protein exhibits RNA controlled polymorphism

The coat protein (CP) of icosahedral Brome mosaic virus (BMV) was expressed from a genetically engineered rod-shape Tobacco mosaic virus. Molecular characterization of the progeny recovered from symptomatic plants revealed that BMV CP selectively packaged the three subgenomic RNAs of the hybrid virus into two differently sized icosahedral virus-like particles (VLPs). The smaller VLPs packaged only the two smaller subgenomic RNAs. Additional in vitro reassembly assays with BMV CP subunits and transcripts of hybrid subgenomic RNAs further demonstrated that the ability of BMV capsids to display polymorphism is not dependent on the RNA size alone and appears to be controlled by some other feature(s) of the genetically engineered RNA.

Coat-protein-mediated resistance to tobacco mosaic virus: discovery mechanisms and exploitation

In 1986 we reported that transgenic plants which accumulate the coat protein of tobacco mosaic virus (TMV) are protected from infection by TMV, and by closely related tobamoviruses. The phenomenon is referred to as coat-protein-mediated resistance (CP-MR), and bears certain similarities to cross protection, a phenomenon described by plant pathologists early in this century. Our studies of CP-MR against TMV have demonstrated that transgenically expressed CP interferes with disassembly of TMV particles in the inoculated transgenic cell. However, there is little resistance to local, cell-to-cell spread of infection. CP-MR involves interaction between the transgenic CP and the CP of the challenge virus, and resistance to TMV is greater than to tobamo viruses that have CP genes more distantly related to the transgene. Using the known coordinates of the three-dimensional structure of TMV we developed mutant forms of CP that have stronger inter-subunit interactions, and confer increased levels of CP-MR compared with wild-type CP. Similarly, it is predicted that understanding the cellular and structural basis of CP-MR will lead to the development of variant CP transgenes that each can confer high levels of resistance against a range of tobamoviruses.

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.

Historical overview of research on the tobacco mosaic virus genome: genome organization, infectivity and gene manipulation

Early in the development of molecular biology, TMV RNA was widely used as a mRNA [corrected] that could be purified easily, and it contributed much to research on protein synthesis. Also, in the early stages of elucidation of the genetic code, artificially produced TMV mutants were widely used and provided the first proof that the genetic code was non-overlapping. In 1982, Goelet et al. determined the complete TMV RNA base sequence of 6395 nucleotides. The four genes (130K, 180K, 30K and coat protein) could then be mapped at precise locations in the TMV genome. Furthermore it had become clear, a little earlier, that genes located internally in the genome were expressed via subgenomic mRNAs. The initiation site for assembly of TMV particles was also determined. However, although TMV contributed so much at the beginning of the development of molecular biology, its influence was replaced by that of Escherichia coli and its phages in the next phase. As recombinant DNA technology developed in the 1980s, RNA virus research became more detached from the frontier of molecular biology. To recover from this setback, a gene-manipulation system was needed for RNA viruses. In 1986, two such systems were developed for TMV, using full-length cDNA clones, by Dawson's group and by Okada's group. Thus, reverse genetics could be used to elucidate the basic functions of all proteins encoded by the TMV genome. Identification of the function of the 30K protein was especially important because it was the first evidence that a plant virus possesses a cell-to-cell movement function. Many other plant viruses have since been found to encode comparable 'movement proteins'. TMV thus became the first plant virus for which structures and functions were known for all its genes. At the birth of molecular plant pathology, TMV became a leader again. TMV has also played pioneering roles in many other fields. TMV was the first virus for which the amino acid sequence of the coat protein was determined and first virus for which cotranslational disassembly was demonstrated both in vivo and in vitro. It was the first virus for which activation of a resistance gene in a host plant was related to the molecular specificity of a product of a viral gene. Also, in the field of plant biotechnology, TMV vectors are among the most promising. Thus, for the 100 years since Beijerinck's work, TMV research has consistently played a leading role in opening up new areas of study, not only in plant pathology, but also in virology, biochemistry, molecular biology, RNA genetics and biotechnology.

Expression of alfalfa mosaic virus coat protein in tobacco mosaic virus (TMV) deficient in the production of its native coat protein supports long-distance movement of a chimeric TMV

Alfalfa mosaic virus (AlMV) coat protein is involved in systemic infection of host plants, and a specific mutation in this gene prevents the virus from moving into the upper uninoculated leaves. The coat protein also is required for different viral functions during early and late infection. To study the role of the coat protein in long-distance movement of AlMV independent of other vital functions during virus infection, we cloned the gene encoding the coat protein of AlMV into a tobacco mosaic virus (TMV)-based vector Av. This vector is deficient in long-distance movement and is limited to locally inoculated leaves because of the lack of native TMV coat protein. Expression of AlMV coat protein, directed by the subgenomic promoter of TMV coat protein in Av, supported systemic infection with the chimeric virus in Nicotiana benthamiana, Nicotiana tabacum MD609, and Spinacia oleracea. The host range of TMV was extended to include spinach as a permissive host. Here we report the alteration of a host range by incorporating genetic determinants from another virus.

The turnip yellow mosaic virus tRNA-like structure cannot be replaced by generic tRNA-like elements or by heterologous 3' untranslated regions known to enhance mRNA expression and stability

The tRNA-like structure (TLS) at the 3' end of the turnip yellow mosaic virus genome was replaced with heterologous tRNA-like elements, and with a poly(A) tail, in order to assess its role. Replacement with the valylatable TLSs from two closely related tymoviruses resulted in infectious viruses. In contrast, no systemic symptoms on plants, and only low viral accumulations in protoplasts, were observed for three chimeric genomes with 3' sequences known to enhance mRNA stability and translatability. One of these chimeras had a poly(A) tail, and the others had the TLS with associated upstream pseudoknot tracts from the 3' ends of brome mosaic and tobacco mosaic viruses. The latter two chimeric RNAs were shown to be appropriately folded by demonstrating their aminoacylation in vitro with tyrosine and histidine, respectively. The results show that enhancement of genome stability or gene expression is not the major role of the turnip yellow mosaic virus TLS. The major role is likely to be replicational, dependent on features present in tymoviral TLSs but not in generic tRNA-like structures.

A novel open reading frame in tobacco mosaic virus genome coding for a putative small, positively charged protein

From sequence comparisons between the tobramovirus genomes an open reading frame (ORF-X) potentially encoding a small, positively charged protein (33- to 45-amino-acids long) was found to overlap the immediate 3' and 5' sides of the transport protein gene and coat protein gene, respectively. In vitro translation of the monocistronic artificial transcripts generated with T7 RNA polymerase yielded a protein of M(r) 4000 (p4) and an unexpected trypsin-sensitive complex of M(r) 54,000 that was resistant to reduction with 2-mercaptoethanol but could be dissociated by 8 M urea. Assembly of this complex was inhibited completely by site-directed mutagenesis within a conserved, positively charged 5-amino-acid long segment of the ORF-X protein. After centrifugation in low salt buffer the 54-kDa complex remained mostly associated with ribosomes. Apparently this complex represents a specific aggregate of the p4 product of ORF-X with a protein of approximate M(r) 50,000 that is a component of the translation apparatus.

Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA

Mischarging of the valine specific tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA has been tested in the presence of purified arginyl-, aspartyl-, histidinyl-, and phenylalanyl-tRNA synthetases from bakers' yeast. Important mischarging of a 264 nucleotide-long transcript was found with histidinyl-tRNA synthetase which can acylate this fragment up to a level of 25% with a loss of specificity (expressed as Vmax/KM ratios) of only 100 fold as compared to a yeast tRNA(His) transcript. Experiments on transcripts of various lengths indicate that the minimal valylatable fragment (n = 88) is the most efficient substrate for histidinyl-tRNA synthetase, with kinetic characteristics similar to those found for the control tRNA(His) transcript. Mutations in the anticodon or adjacent to the 3' CCA that severely affect the valylation capacity of the 264 nucleotide long TYMV fragment are without negative effect on its mischarging, and for some cases even improve its efficiency. A short fragment (n = 42) of the viral RNA containing the pseudoknot and corresponding to the amino acid accepting branch of the molecule is an efficient histidine acceptor.

Regulation of tobamovirus gene expression

This chapter discusses tobacco mosaic virus (TMV) strains U1, OM, L, CGMMV, 0, and Cc. The production of each TMV protein is regulated differently, both in amounts and times of production. The chapter discusses some of the strategies that tobamoviruses uses to control gene expression: (1) different subgenomic RNA promoter/leader sequences control timing of expression of genes, (2) genes expressed via subgenomic mRNAs are expressed in decreasing amounts with increasing distances from the 3' terminus, and (3) TMV mRNAs appear to be translationally regulated differently from host mRNAs. Genome organization affects gene expression, but it appears to be equally important for the efficiency of replication and the ability of the genomic structure to be stably propagated. Different virus groups have evolved different gene arrangements. Tobamovirus genes expressed via subgenomic mRNAs appear to be expressed in increasing amounts when positioned nearer the 3’ terminus.

Similarities among plant virus (+) and (-) RNA termini imply a common ancestry with promoters of eukaryotic tRNAs

The 5' ends of brome mosaic virus (BMV) RNAs contain sequences similar to the consensus internal control region (ICR) of pol III promoters in tRNA genes. Comparison of BMV (+)RNA 5' termini with BMV (-)RNA termini revealed the presence of two (tandem) repeats of some 30 nucleotides, the more internal containing a region of 73% similarity to the tRNA consensus ICR2 (downstream) region of the ICR. Tandem repeats containing motifs similar to the ICR2 consensus were found at the 5' termini of (-)RNAs of cucumo-, tobamo-, and tymoviruses whose 3' (+)RNAs have aminoacylatable tRNA-like structures. Single regions of homology to the BMV(+)RNA 5' terminus, containing an ICR2-like motif, were detected for several tobravirus RNAs, and for satellite tobacco necrosis virus RNA. The (+)-stranded genomes of these viruses have not been shown to be capable of amino acid esterification. The ICR2 consensus (GGUUCGANUCC) is nearly palindromic, and is contained with the T psi C loop of tRNAs and viral analogs. Consequently, tRNA promoter-like motifs can be seen at both termini of (+) and (-) RNAs of bromoviruses and other viruses. The presence of ICR1 and ICR2-like sequences in BMV genomic 5' (+)RNAs and the tobamovirus 5' (-)RNAs may reflect promoter arrangements of primordial genomic RNAs ancestral to both modern plant viruses and eukaryotic tRNAs. Several derivative concepts related to genome evolution are discussed, including the origin of asymmetric strand synthesis of RNAs.

Sequence and structure at the genome 3' end of the U2-strain of tobacco mosaic virus, a histidine-accepting tobamovirus

The primary sequence of the 3' noncoding region of U2-TMV RNA was determined. A structural model was proposed based on chemical and enzymatic structure mapping as well as on analyses of nuclease protection by aminoacyl-tRNA-synthetase. The model agrees with those proposed for TMV "vulgare" RNA and confirms their general validity for the tobamoviruses. The RNA appears to have a tRNA-like, L-shaped structure at the 3' terminus, linked to a quasi-continuous double-helical stalk, with five pseudoknots involved in the formation of the whole structure. However, the structure of U2-TMV RNA is less stringently conserved than the 3' termini of "vulgare" and other histidine-accepting tobamoviruses. This difference is reflected in the kinetics of aminoacylation of the RNA.

Complementary oligodeoxynucleotide mediated inhibition of tobacco mosaic virus RNA translation in vitro

Two different "antisense" oligodeoxynucleotides and their RNA analogues, each complementary to non-overlapping sequences of 51 bases near the 5' end of TMV RNA, inhibit in vitro translation of the genomic RNA in a rabbit reticulocyte lysate. Inhibition is dependent upon complementarity, concentration, and hybridization of the oligomers with TMV RNA. Inhibition is observed at molar ratios of TMV RNA to antisense oligomers as low as 1:1.5. A plateau of inhibition at which 10-25% of the control signal remains is achieved by molar ratios of TMV RNA:antisense DNA or RNA greater than or equal to 1:15. The extent of inhibition is not increased by the simultaneous presence of both complementary fragments. Oligodeoxynucleotides and their RNA analogues identical to the same regions of TMV RNA have no direct effect on translation, however, they can block inhibition by the antisense fragments. Translation of BMV RNA is not affected by any of the oligodeoxynucleotides. Polyacrylamide gel electrophoresis shows translation of TMV p126 is selectively inhibited. We conclude that the observed inhibition of translation is due to direct interference with ribosome function.

The 30-Kilodalton Gene Product of Tobacco Mosaic Virus Potentiates Virus Movement

The proposed role of the 30-kilodalton(kD) protein of tobacco mosaic virus is to facilitate cell-to-cell spread of the virus-during infection. To directly define the function of the protein, a chimeric gene containing a cloned complementary DNA of the 30-kD protein gene was introduced into tobacco cells via a Ti plasmid-mediated transformation system of Agrobacterium tumefaciens. Transgenic plants regenerated from transformed tobacco cells expressed the 30-kD protein messenger RNA and accumulated 30-kD protein. Seedlings expressing the 30-kD protein gene complemented the Lsl mutant of TMV, a mutant that is temperature-sensitive in cell-to-cell movement. In addition, enhanced movement of the Lsl virus at the permissive temperature was detected in seedlings that express the 30-kD protein gene. These results conclusively demonstrate that the 30-kD protein of tobacco mosaic virus potentiates the movement of the virus from cell to cell.

In vitro transcription and translation of cloned cDNAs encoding the 30-kDa protein gene of TMV

A cDNA clone encoding the nonstructural, 30-kDa protein of the common (U1) strain of tobacco mosaic virus (TMV) was isolated and characterized. cDNA clones representing the intact gene as well as deletions from the 5' end of the gene were subcloned into SP6 vectors. Capped RNAs produced by in vitro transcription reactions were translated in a wheat germ cell-free system. The resultant proteins were compared to proteins obtained from the in vitro translation of intermediate length (I2) rods of TMV. Transcripts of the cDNA clones encoded polypeptides of 30, 28, or 18 kDa that were immunoprecipitated by antibody prepared against a synthetic peptide representing the carboxy terminus of the 30-kDa protein. cDNA clones containing the intact 30-kDa sequence coded for 30-kDa polypeptides while clones lacking the 30-kDa initiation codon produced 28-kDa polypeptides. Surprisingly, translation of a transcript from a cDNA clone containing the 30-kDa gene plus 390 nucleotides 5' of the initiator AUG yielded a polypeptide with an approximate molecular mass of 18 kDa. The results indicate that an intact and functional 30-kDa protein gene has been cloned. The significance of these results, with respect to determining the function of the 30-kDa protein, is discussed.

Five pseudoknots are present at the 204 nucleotides long 3' noncoding region of tobacco mosaic virus RNA

The 104 nucleotides long 3' terminal region of TMV RNA was shown previously to contain two pseudoknotted structures (Rietveld et al. (1984), EMBO J. 3, 2613-2619). We here present evidence for the occurrence, within the 204 nucleotides long 3' noncoding region, of another highly structured domain located immediately adjacent to the tRNA-like structure of 95 nucleotides (Joshi et al. (1985) Nucleic Acids Res. 13, 347-354). A model for the three-dimensional folding of this region, containing three more pseudoknots, is proposed on the basis of chemical modification and enzymatic digestion. The existence of these three consecutive pseudoknots was supported by sequence comparisons with the RNA from the related tobamoviruses TMV-L, CcTMV and CGMMV. Coaxial stacking of the six double helical segments involved gives rise to the formation of a 25 basepair long quasi-continuous double helix. The results show that the three-dimensional folding of the 3' non-translated region of tobamoviral RNAs is largely maintained by the formation of five pseudoknots. The organisation of this region in the RNA of the tobamovirus CcTMV suggests that recombinational events among aminoacylatable plant viral RNAs have to be considered.

Molecular cloning and nucleotide sequence of the 30K and the coat protein cistron of TMV (tomato strain) genome

The cDNA copies of tobacco mosaic virus (TMV)-tomato strain (L) genome were cloned by the method of Okayama and Berg (Mol. Cell. Biol. 2, 161-170. (1982)) and the sequence of 1,614 nucleotides at the 3' end was determined. The sequence encompasses the 30K and the coat protein cistron which are located in residues 685-1, 479 and 203-682 from the 3' end of the genome respectively. The close relationship between the tomato and the common strain was shown on the level of the nucleotide sequence. Highly homologous regions are found in the 3' non-coding region, the assembly origin and the 5' flanking region of the 30K protein cistron. The comparison of the deduced amino acid sequence between the tomato and the common strain shows that the 30K protein is composed of the conserved N-terminal four-fifth and the highly divergent region near the C-terminus.

H protein, a minor protein of TMV virions, contains sequences of the viral coat protein

H protein, a minor protein found associated with virions of tobacco mosaic virus (TMV) at an average of about one copy per virion and previously believed to be host-coded (Asselin and Zaitlin, 1978, Virology 91, 173-181), has been shown to contain sequences of the viral capsid protein. Two-dimensional tryptic peptide maps of 125I-labeled H protein (Mr 26,500) and coat protein (Mr 17,500) from TMV strains U1 and Dahlemense show that the respective H proteins contain most if not all of the labeled peptides of the coat proteins in addition to 2-3 unique peptides. The H proteins also contain unique antigenic determinants, as antibodies can be isolated which react strongly with the H protein but not with the coat protein of Dahlemense TMV. Finally, amino acid composition analysis of the U1-TMV H protein has shown the presence of methionine and histidine, amino acids not present in the coat protein of that strain. H protein appears to contain the same NH2 terminus as coat protein, as there is an H protein tryptic peptide that both comigrates in a two-dimensional system and produces the same acid cleavage product as the NH2-terminal tryptic peptide of coat protein. H protein also seems to have the same COOH terminus as coat protein, as cyanogen bromide digestion of Dahlemense-TMV coat protein and H protein indicates that each has a methionine about 12 amino acids from one terminus (known to be the COOH terminus of the coat protein). Thus, H protein is not structurally equivalent to coat protein with an addition on either its NH2 or COOH terminus. However, H protein does not appear to be a noncovalent aggregate of coat protein and some other protein. Rather, the model we favor for H protein structure is that of a branched fusion product between coat protein and another polypeptide of host or viral origin.

Multiple proteins and subgenomic mRNAs may be derived from a single open reading frame on tobacco mosaic virus RNA

It has previously been shown that messenger activity for a protein of Mr = ca. 30k exists in RNA fractions extracted from particles of either native or alkali stripped U1 TMV, or from cowpea strain TMV, that are smaller than full genomic length. Analysis of sucrose gradient fractions containing this activity reveals a number of slightly smaller template activities directing synthesis of proteins between 18.5k and 29k in size. All of these messenger activities, including that for the 30k protein, respond to cap analogues in anomalous ways. Discrete RNA species that include active mRNAs for these proteins can be demonstrated in the same fractions by labelling with preparations of vaccinia capping enzyme and [alpha-32P] GTP without prior beta-elimination. Detailed analysis of three of these proteins (of Mr's ca. 30k, 29k and 23k) by peptide mapping and translation of purified vaccinia-labelled RNA demonstrates that all three are unrelated to the large early TMV proteins, but are related to each other in such a way as to form a nested set with staggered N termini and identical C termini. mRNAs of chain lengths ca. 1900 and 1500 bases direct synthesis of the 30k and 23k proteins respectively, an mRNA of about 1850 bases directs both 29k and (perhaps because of cross-contamination) 30k synthesis. Initiation codons for the 29k and 23k proteins have been mapped at positions 4960-4962 and 5191-5193 respectively on TMV RNA. Since all three encapsidated templates have similar properties we conclude that either there is a family of 30k-related proteins with unusual mRNAs, or that none of these in vitro translation products are directed by physiological templates.

The tRNA-like structure at the 3' terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA

The 3' terminus of TYMV RNA, which possesses tRNA-like properties, has been studied. A 3' terminal fragment of 112 nucleotides was obtained by cleavage with RNase H after hybridization of a synthetic oligodeoxynucleotide to the viral RNA. The accessibility of cytidine and adenosine residues was probed with chemical modification. Enzymatic digestion studies were performed with RNase T1, nuclease S1 and the double-strand specific RNase from the venom of the cobra Naja naja oxiana. A model is proposed for the secondary structure of the 3' terminal region of TYMV RNA comprising 86 nucleotides. The main feature of this secondary structure is the absence of a conventional acceptor stem as present in canonical tRNA. However, the terminal 42 nucleotides can be folded in a tertiary structure which bears strong resemblance with the acceptor arm of canonical tRNA. Comparison of this region of TYMV RNA with that of other RNAs from both the tymovirus group and the tobamovirus group gives support to our proposal for such a three-dimensional arrangement. The consequences for the recognition by TYMV RNA of tRNA-specific enzymes is discussed.

Length requirements for tRNA-specific enzymes and cleavage specificity at the 3' end of turnip yellow mosaic virus RNA

This paper describes the minimum length of the turnip yellow mosaic virus (TYMV) RNA necessary to fulfill the tRNA-like properties of the viral RNA: 50 to 75 nucleotides and 86 nucleotides from the 3' end of TYMV RNA are sufficient for adenylation and valylation respectively by the Escherichia coli system. The size of the tRNA-like fragments obtained in vitro in the presence of an E. coli, a reticulocyte or a chinese cabbage leaf extract has also been determined. Among the major fragments liberated from the 3' end of TYMV RNA by the three systems are fragments of 117 and 112 nucleotides. In addition, the E. coli extract liberates fragments of 139 and 61 nucleotides, and the reticulocyte lysate fragments of 109, 94, 84, 73 and 46 nucleotides. The cleavage of the viral RNA by several systems in vitro to yield RNA fragments encompassing the tRNA-like sequence suggests that such fragments might also be liberated in vivo.

Nucleotide sequence of a cloned cDNA copy of TMV (cowpea strain) RNA, including the assembly origin, the coat protein cistron, and the 3' non-coding region

The cloned cDNA derived from the 3' end of cowpea strain (Cc) RNA of tobacco mosaic virus (TMV) has been sequenced. Substantial sequence information of 1,060 nucleotides from the 3' end of the RNA reveals some interesting features: (1) the coat protein cistron corresponds to residues 210-701 from the 3' end. Some errors in the amino acid sequence previously reported have been corrected and the revised total length of the coat protein is 162 amino acid residues. The capping site of the coat protein mRNA is at residue 711 from the 3' end of genome RNA. (2) The assembly origin of reconstitution is positioned within the coat protein cistron at residue 369-461 which can be formed into a highly base-paired hairpin loop structure. The sequence, GAXGUUG, in the loop region and a triplet-repeated purine base tract surrounding the loop are found. These structural features are common to assembly origins of both Cc and vulgare strains. (3) We find the sequence highly homologous to, but distinct from, the genuine assembly origin. It will be called the pseudo-assembly origin, which is located in the corresponding region to the assembly origin of the vulgare strain, outside the coat protein cistron. There is also the sequence, GAXGUUG, in the middle of the region. (4) In the 5' flanking region of the coat protein cistron, a long reading frame, probably of 30 K protein, is found. The coding region is terminated in the coat protein cistron and thus the 30 K protein and the coat protein cistrons overlap. (5) The 3' non-coding region is 209 residues long and can be folded into a possible tRNA-like structure. Surprisingly, we find that the 3' terminal sequence of Cc RNA is not very similar to that of vulgare RNA but extensively homologous to that of turnip yellow mosaic virus (TYMV) RNA.