Amino acid sequence of southern bean mosaic virus coat protein and its relation to the three-dimensional structure of the virus

Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae

The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses.

Rottboellia yellow mottle virus is a distinct species within the genus Sobemovirus

Once considered a tentative member of the genus Sobemovirus, rottboellia yellow mottle virus (RoMoV) was excluded from the latest species list of the ICTV after the discovery of imperata yellow mottle virus (IYMV), which resembles RoMoV in host range and geographic origin. Here, sequence analysis of the complete genome of RoMoV suggested that it should be considered a distinct species within the genus Sobemovirus. It has the highest sequence identity (55 %) to ryegrass mottle virus (RGMoV), whereas its sequence identity to IYMV is lower (44 %). In a phylogenetic tree, RoMoV clusters together with RGMoV and artemisia virus A (ArtVA), a dicot-infecting sobemovirus.

Structure of viruses: a short history

This review is a partially personal account of the discovery of virus structure and its implication for virus function. Although I have endeavored to cover all aspects of structural virology and to acknowledge relevant individuals, I know that I have favored taking examples from my own experience in telling this story. I am anxious to apologize to all those who I might have unintentionally offended by omitting their work. The first knowledge of virus structure was a result of Stanley's studies of tobacco mosaic virus (TMV) and the subsequent X-ray fiber diffraction analysis by Bernal and Fankuchen in the 1930s. At about the same time it became apparent that crystals of small RNA plant and animal viruses could diffract X-rays, demonstrating that viruses must have distinct and unique structures. More advances were made in the 1950s with the realization by Watson and Crick that viruses might have icosahedral symmetry. With the improvement of experimental and computational techniques in the 1970s, it became possible to determine the three-dimensional, near-atomic resolution structures of some small icosahedral plant and animal RNA viruses. It was a great surprise that the protecting capsids of the first virus structures to be determined had the same architecture. The capsid proteins of these viruses all had a 'jelly-roll' fold and, furthermore, the organization of the capsid protein in the virus were similar, suggesting a common ancestral virus from which many of today's viruses have evolved. By this time a more detailed structure of TMV had also been established, but both the architecture and capsid protein fold were quite different to that of the icosahedral viruses. The small icosahedral RNA virus structures were also informative of how and where cellular receptors, anti-viral compounds, and neutralizing antibodies bound to these viruses. However, larger lipid membrane enveloped viruses did not form sufficiently ordered crystals to obtain good X-ray diffraction. Starting in the 1990s, these enveloped viruses were studied by combining cryo-electron microscopy of the whole virus with X-ray crystallography of their protein components. These structures gave information on virus assembly, virus neutralization by antibodies, and virus fusion with and entry into the host cell. The same techniques were also employed in the study of complex bacteriophages that were too large to crystallize. Nevertheless, there still remained many pleomorphic, highly pathogenic viruses that lacked the icosahedral symmetry and homogeneity that had made the earlier structural investigations possible. Currently some of these viruses are starting to be studied by combining X-ray crystallography with cryo-electron tomography.

Cocksfoot mottle virus coat protein is dispensable for the systemic infection

BACKGROUND

The Sobemovirus genome consists of polycistronic single-stranded positive-sense RNA. The first ORF encodes P1, a suppressor of RNA silencing required for virus movement. The coat protein (CP) is expressed from the 3' proximal ORF3 via subgenomic RNA. In addition to its structural role, the CP of some sobemoviruses has been reported to be required for systemic movement and to interact with P1. The aim of this study was to analyse the role of Cocksfoot mottle virus (CfMV) CP in the suppression of RNA silencing and virus movement.

METHODS

Agrobacterium-mediated transient expression method was used for testing CfMV CP capacity to suppress RNA silencing. CP substitution and deletion mutants were generated to examine the role of this protein in CfMV infection, using three host plants (oat, barley and wheat). The viral movement was characterised with CfMV expressing EGFP fused to the C-terminus of CP.

RESULTS

In the current study we show that CfMV CP is an additional RNA silencing suppressor. Interestingly, we observed that all CP mutant viruses were able to infect the three tested host plants systemically, although usually with reduced accumulation. CfMV expressing EGFP was detected in epidermal and mesophyll cells of inoculated leaves. Although EGFP fluorescence was not detected in upper leaves, some plants displayed CfMV symptoms. Analysis of the upper leaves revealed that the viruses had lost the EGFP sequence and sometimes also most of the CP gene.

CONCLUSIONS

The present study demonstrates that CfMV CP suppresses RNA silencing but, surprisingly, is dispensable for systemic movement. Thus, CfMV does not move as virion in the tested host plants. The composition of the movement RNP complex remains to be elucidated.

Nucleotide sequence diversity in Velvet tobacco mottle virus: a virus with a unique Australian pathosystem

Velvet tobacco mottle virus (VTMoV) is a naturally occurring mirid-transmitted sobemovirus of native velvet tobacco (Nicotiana velutina) plants in the Australian arid zone. We have sequenced the coding region of a typical field isolate of VTMoV (isolate I-17-04, satellite-plus) and show that it differed by nine polymorphisms from the previously sequenced atypical ‘satellite-minus’ variant VTMoV-K1 (represented here as L-K1-04), while retaining the same genomic and amino acid sequence motifs. We also report that although L-K1-04 was confirmed to be free of detectable satellite RNA by gel electrophoretic assay, the satellite sequence was detected in it by RT-PCR assay. Nucleotide sequence variation among the RNA-dependent RNA polymerase open reading frames of 15 field and laboratory isolates identified four phylogenetic groups, but these did not show a pattern related to site or time of sampling. This result would be consistent with nucleotide sequence variants of VTMoV being dispersed widely by migrating adult mirid vectors.

Complete nucleotide sequence of Velvet tobacco mottle virus isolate K1

Velvet tobacco mottle virus (VTMoV) infects the native Australian plant Nicotiana velutina, which is endemic to central Australia. This virus is included in the genus Sobemovirus based on virion morphology and serological relationships. We report here the full genome sequence of VTMoV, attained using a genome-walking strategy with both degenerate and specific primers. This sequence confirms that VTMoV is a sobemovirus, with the same open reading frame (ORF) organisation as other described sobemoviruses. The VTMoV sequence is closest to those sobemoviruses isolated from monocotyledonous plants, although the narrow host range of VTMoV is limited to dicotyledonous plants.

The EDTA-treated expanded satellite tobacco necrosis virus: biochemical properties and crystallization

The calcium ions normally present in the protein shell of the satellite tobacco necrosis virus (STNV) have been removed by EDTA. The radius of the EDTA-treated virion was found to be dependent upon pH. The radial increase was 2% at pH 5.0,4.5% at pH 6.5, and 7% at pH 7.0 as determined by analytical ultracentrifugation and X-ray crystallography. The virion could be recontracted by lowering the pH or by the addition of divalent cations, calcium ions being the most efficient. At pH 7.0 and above, the EDTA-treated virion was sensitive to ribonucleases and to trypsin. The cleavage site for trypsin is at Arg 28, which is near the N terminus of the shell domain of the subunit, but at a point which is well buried in the native structure. Crystals of the expanded STNV particles at pH 5.0 and 6.5 have been produced.

Evidence for pH-induced release of RNA from belladonna mottle virus and the stabilizing effect of polyamines and cations

The RNA of belladonna mottle virus (BDMV) is released from virions by increasing the pH to neutrality or above, leaving behind intact protein shells. In contrast, much harsher conditions are required to release the RNA from the closely related turnip yellow mosaic virus (TYMV). The heat-induced or pH-dependent escape of RNA from BDMV has been investigated by 31P NMR spectroscopy and ultracentrifugation. The methods show a transition pH near 6.8 at which the RNA undergoes a structural alteration probably caused by disruption of protein-RNA linkages. Addition of cations or polyamines to BDMV prevents the RNA loss at alkaline pH; the virions become stable to pH values up to 11.5 as observed for TYMV. We suggest that repulsion of the negatively charged phosphate groups of the nucleic acid provides the driving force for RNA release at pH values above the threshold point where protein-RNA interactions are broken. The polyamines effectively counter the phosphate charge in BDMV and thereby prevent RNA loss. Since TYMV is packaged with polyamines and BDMV is not (R. Virudachalam, K. Sitaraman, K. L. Heuss, P. Argos, and J. L. Markley, Virology 130, 360-371, 1983), the different conditions required for RNA escape from the two viruses are explained. Heating of BDMV virions at pH 7.0 to 40 degrees resulted in their partial disruption; the product some intact particles, empty capsids, and RNA fragments with a sedimentation coefficient of 5S.

Carbon-13 and proton nuclear magnetic resonance spectroscopy of plant viruses: evidence for protein-nucleic acid interactions in belladonna mottle virus and detection of polyamines in turnip yellow mosaic virus

Belladonna mottle virus (BDMV) enriched in carbon-13 was isolated from infected tobacco plants grown in a 2% 13C02, 8% 12CO2 atmosphere. The enrichment led to a fivefold improvement in the signal to noise ratio of the (13)C NMR spectrum of BDMV. 1H and 13C NMR peaks of the intact virion are broad. However, upon removal of the RNA, many sharp peaks appear in spectra of the empty capsid which are attributed to aliphatic amino acid side chains at the inner surface of the protein shell that have gained segmental mobility. These include resonances assigned to the side chain of glutamate. Internal motions are necessary to account for the experimental 13C NMR linewidths. Aliphatic 13CHn (n = 1-3) groups must have correlation times on the order of 10 nsec and quaternary carbons must have correlation times between 50 and 300 nsec to explain the narrow line widths. No sharp peaks were observed in the aromatic regions of 1H or 13C NMR spectra; thus all the aromatic side chains seem to be tightly packed in the capsid as well as the virion. 1H and 13C NMR have been used for the first time to detect polyamines in virus particles. 1H NMR studies confirmed the presence of polyamines, apparently packaged during assembly, in turnip yellow mosaic virus (TYMV) and demonstrated their absence in BDMV. Sedimentation analysis has shown that the RNA is released upon increasing the pH above neutrality for BDMV but only above pH 11.5 for TYMV (R. Virudachalam, K. Sitaraman, K. L. Heuss, J. L. Markley, and P. Argos, Virology 130, 351-359, 1983). 1H NMR studies demonstrated that the BDMV capsid is permeable to polyamines and that the pH stability of BDMV with added spermidine is comparable to that of TYMV.

Epitope mapping of the major capsid protein of type 2 porcine circovirus (PCV2) by using chimeric PCV1 and PCV2

Type 2 porcine circovirus (PCV2) is associated with postweaning multisystemic wasting syndrome in pigs, whereas the genetically related type 1 PCV (PCV1) is nonpathogenic. In this study, seven monoclonal antibodies (MAbs) against PCV2-ORF2 capsid protein were generated, biologically characterized, and subsequently used to map the antigenic sites of PCV2 capsid protein by using infectious PCV DNA clones containing PCV1/PCV2-ORF2 chimeras. The PCV1/PCV2-ORF2 chimeras were constructed by serial deletions of PCV2-ORF2 and replacement with the corresponding sequences of the PCV1-ORF2. The reactivities of chimeric PCV1/PCV2 clones in transfected PK-15 cells with the seven MAbs were detected by an immunofluorescence assay (IFA). The chimera (r140) with a deletion of 47 amino acids at the N terminus of PCV2-ORF2 reacted strongly to all seven MAbs. Expanding the deletion of PCV2-ORF2 from residues 47 to 57 (r175) abolished the recognition of MAb 3B7, 3C11, 4A10, 6H2, or 8F6 to the chimera. Further deletion of PCV2-ORF2 to 62 residues disrupted the binding of this chimera to all seven MAbs. IFA reactivities with all MAbs were absent when residues 165 to 233 at the C terminus of PCV2-ORF2 was replaced with that of PCV1-ORF2. Extending the sequence of PCV2-ORF2 from residues 165 (r464) to 185 (r526), 200 (r588), or 224 (r652) restored the ability of the three chimeras to react with MAbs 3C11, 6H2, 9H7, and 12G3 but not with 8F6, 3B7, or 4A10. When the four amino acids at the C terminus of r588 were replaced with that of PCV2-ORF2, the resulting chimera (r588F) reacted with all seven MAbs. The results from this study suggest that these seven MAbs recognized at least five different but overlapping conformational epitopes within residues 47 to 63 and 165 to 200 and the last four amino acids at the C terminus of the PCV2 capsid protein.

Membrane activity of the southern cowpea mosaic virus coat protein: the role of basic amino acids, helix-forming potential, and lipid composition

Southern cowpea mosaic virus (SCPMV) is a spherical RNA virus with T = 3 icosahedral symmetry. The particle is composed of 180 subunits of the coat protein (CP) and one copy of the positive-sense viral RNA. The CP has two domains, the random (R) domain formed by the N-terminal 64 aa and the shell (S) domain (aa 65--260). The R domain is highly charged, with 11 of the N-terminal 30 residues being basic. It is localized to the interior of the native particle where it may interact with the viral RNA, but under certain pH and salt conditions the topology of the particle changes to externalize the R domain. Since the CPs of several spherical RNA viruses have been shown to interact with host membranes during infection, we have begun investigating the membrane interactions of the SCPMV CP using the artificial liposome membranes. Both the native CP and the R domain overexpressed in Escherichia coli were observed to interact with liposomes. The interaction between the R domain and liposomes required either anionic phospholipids or non-bilayer-forming lipids and involved electrostatic interactions since it was shown to be both pH and ionic strength dependent. The analysis of four different deletion and six different site-directed substitution mutations partially mapped the region responsible for this interaction to residues 1--30. Analysis of this region of the R domain by circular dichroism indicated that it assumes an alpha-helical structure when exposed to liposomes composed of anionic lipids. Mutations, which extend the helical nature of this region, promoted an increased interaction. The possible role of the CP/lipid interaction in the SCPMV infection is discussed.

In vitro analysis of an RNA binding site within the N-terminal 30 amino acids of the southern cowpea mosaic virus coat protein

Southern cowpea mosaic virus (SCPMV) is a positive-sense RNA virus with T = 3 icosahedral symmetry. The coat protein (CP) has two domains, the random (R) domain and the shell (S) domain. The R domain is formed by the N-terminal 64 amino acids (aa) and is localized to the interior of the particle where it is expected to interact with the viral RNA. The R domain (aa 1--57) was expressed in Escherichia coli as a recombinant protein (rWTR) containing a nonviral C-terminal extension with two histidine tags. The RNA binding site of the R domain was identified by Northwestern blotting and electrophoretic mobility shift assay (EMSA) using recombinant wild-type and mutant R domain proteins. Deletions within the R domain revealed that the RNA binding site is localized to its N-terminal 30 aa. RNA binding by this element was found to be nonspecific with regard to RNA sequence and was sensitive to high salt concentrations, suggesting that electrostatic interactions are important for RNA binding by the R domain. The RNA binding site includes 11 basic residues, eight of which are located in the arginine-rich region between aa 22 and 30. It was demonstrated using alanine substitution mutants that the basic residues of the arginine-rich region but not those present at positions 3, 4, and 7 are necessary for RNA binding. None of the basic residues within the arginine-rich region are specifically required for RNA binding, but the overall charge of the N-terminal 30 aa is important. Proline substitution mutations within the N-terminal 30 aa, and alanine substitutions for prolines at positions 18, 20, and 21, did not affect the RNA binding activity of the R domain. However, it was demonstrated by circular dichroism (CD) that the conformation of the N-terminal 30 aa of the R domain changes from a random coil to an alpha-helix in the presence of 50% trifluoroethanol (TFE). The possible role for this structural change in RNA binding by the R domain is discussed.

Primary structure and phylogenetic analysis of the coat protein of a Toyama isolate of tobacco necrosis virus

The amino acid sequence of the coat protein (CP) of a tobacco necrosis virus (TNV) strain, Toyama isolate, was determined by a combination of peptide and cDNA sequencing. The deduced sequence of 276 residues was compared with CPs of other TNV isolates and other plant virus isolates of Tombusviridae. It showed the highest similarity to the TNV Nebraska isolate with 92% identity and moderate similarity to the TNV strain A with 51% identity, confirming the previous serological analysis. It also showed overall similarity with CPs of mostly genera Necrovirus and Sobemovirus, and partial similarity with CPs of genera Tombusvirus and Carmovirus. Among 13 CPs that showed overall similarity, there were 10 completely conserved residues. These included three residues that participate in Ca2+ ligation at the interfaces of virion subunits in TNV crystal structure, suggesting that similar metal binding occur in the viruses of genera Necrovirus and Sobemovirus.

Crystal structure of tobacco necrosis virus at 2.25 A resolution

The crystal structure of tobacco necrosis virus (TNV) has been determined by real-space averaging with 5-fold non-crystallographic symmetry, and refined to R=25.3 % for diffraction data to 2.25 A resolution. A total of 180 subunits form a T=3 virus shell with a diameter of about 280 A and a small protrusion at the 5-fold axis. In 276 amino acid residues, the respective amino terminal 86, 87 and 56 residues of the A, B and C subunits are disordered. No density for the RNA was found. The subunits have a "jelly roll" beta-barrel structure, as have the structures of the subunits of other spherical viruses. The tertiary and quaternary structures of TNV are, in particular, similar to those of southern bean mosaic virus, although they are classified in different groups. Invisible residues 1 to 56 with a high level of basic residues are considered to be located inside the particle. Sequence comparison of the coat proteins of several TNV strains showed that the sequences of the disordered segment diverge considerably as compared with those of the ordered segment, consistent with a small tertiary structural constraint being imposed on the N-terminal segment. Basic residues are localized on the subunit interfaces or inner surface of the capsid. Positive charges of the basic residues facing the interior, as well as those of the N-terminal segment, may neutralize the negative charge of the RNA inside. Five calcium ions per icosahedral asymmetric unit are located at the subunit interfaces; three are close to the exterior surface, the other two away from it. The environments of the first three are similar, and those of the other two sites are similar. These calcium ions are assumed to be responsible for the stabilization/transition of the quaternary structure of the shell. Three peptide segments ordered only in the C subunits are clustered around each 3-fold (quasi-6-fold) axis forming a beta-annulus, and may lead to quasi-equivalent interactions for the organization of the T=3 shell.

Mapping and expression of southern bean mosaic virus genomic and subgenomic RNAs

The coat protein of the cowpea strain of southern bean mosaic sobemovirus (SBMV-C) is translated from a subgenomic RNA (sgRNA) that is synthesized in the virus-infected cell. Like the SBMV-C genomic RNA, the sgRNA has a viral protein (VPg) covalently bound to its 5' end. The mechanism(s) by which ribosomes initiate translation on the SBMV-C RNAs is not known. To begin to characterize the translation of the sgRNA it was first necessary to precisely map its 5' end. Primer extension was used to identify SBMV-C nucleotide (nt) 3241 as the transcription start site. As a control, the 5' end of the genomic RNA was also mapped. Surprisingly, the 5' terminal nt of this RNA was identified as SBMV-C nt 2. The primary structure of the 5' ends of these two RNAs is therefore expected to be VPg-ACAAAA. Precise mapping of the 5' end of the sgRNA of the bean strain of SBMV (SBMV-B) demonstrated that it has these same elements. Translation of coat protein from the SBMV-C sgRNA and p21 from the SBMV-C genomic RNA was compared using a cell-free system. The results of these experiments were consistent with translation of these proteins by a 5' end-dependent scanning mechanism rather than by internal ribosome binding.

Nucleotide sequence of the bean strain of southern bean mosaic virus

The genome of the bean strain of southern bean mosaic virus (SBMV-B) comprises 4109 nucleotides and thus is slightly shorter than those of the two other sequenced sobemoviruses (southern bean mosaic virus, cowpea strain (SBMV-C) and rice yellow mottle virus (RYMV)). SBMV-B has an overall sequence similarity with SBMV-C of 55% and with RYMV of 45%. Three potential open reading frames (ORFs) were recognized in SBMV-B which were in similar positions in the genomes of SBMV-C and RYMV. However, there was no analog of SBMV-C and RYMV ORF 3. From a comparison of the predicted sequences of the ORFs of these three sobemoviruses and of the noncoding regions, it is suggested that the two SBMV strains differ from one another as much as they do from RYMV and that they should be considered as different viruses.

Molecular cloning and nucleotide sequence of the coat protein gene of a Cuban isolate of potato leafroll virus and its expression in Escherichia coli

Total RNA from infected Physalis floridana was isolated to generate complementary DNA corresponding to the coat protein (GP) gene of a Cuban isolate of potato leaf roll virus (PLRV). This cDNA was amplified by the polymerase chain reaction (PCR) and cloned into the bacterial expression vectors pEX(1-3) for fusion protein expression in E. coli. The product was detected by antibodies specific for the PLRV CP. The coding sequence of the CP gene was determined, and the predicted length of the CP was 208 amino acids (23 kD). The nucleotide sequences and deduced amino acid sequences were compared with the other PLRV isolates and found to be 97-99.5% identical at both the nucleotide and amino acid sequence level of other isolates. Comparison of the deduced amino acid sequences of the PLRVcub CP revealed considerable homology to other luteoviruses. We believe that the protocol described could be applicable to other plant viruses of low abundance or of cumbersome isolation, since this method is less time consuming than the traditional methods of cloning coat protein genes of plant viruses with known sequences.

Analysis of epitopes on potato leafroll virus capsid protein

Pepscan hexapeptides prepared to the capsid protein amino acid sequence of potato leafroll luteovirus (PLRV) were tested against both polyclonal and monoclonal antibodies. Twelve continuous epitopes were identified: 11 were detected by two different PLRV polyclonal antisera, but only 4 were detected by both antisera. The 12th epitope reacted with monoclonal antibody BG3. The location of most of the epitopes did not correlate well with antigenic areas predicted by computer algorithms. Comparison of the amino acid sequences of PLRV and southern bean mosaic virus capsid proteins allowed a preliminary assignment of epitopes 4-12 to different regions of the putative S domain of the PLRV subunit. Five out of 14 monoclonal antibodies and both of the polyclonal antisera reacted with epitope 1 at the N-terminus. ELISA data indicated that even though the N-terminus is hydrophobic, it is exposed at the surface of the particles.

Nucleotide sequence of the 3' terminal region of belladonna mottle virus-Iowa (renamed Physalis mottle virus) RNA and an analysis of the relationships of tymoviral coat proteins

The 3' terminal 1255 nt sequence of Physalis mottle virus (PhMV) genomic RNA has been determined from a set of overlapping cDNA clones. The open reading frame (ORF) at the 3' terminus corresponds to the amino acid sequence of the coat protein (CP) determined earlier except for the absence of the dipeptide, Lys-Leu, at position 110-111. In addition, the sequence upstream of the CP gene contains the message coding for 178 amino acid residues of the C-terminus of the putative replicase protein (RP). The sequence downstream of the CP gene contains an untranslated region whose terminal 80 nucleotides can be folded into a characteristic tRNA-like structure. A phylogenetic tree constructed after aligning separately the sequence of the CP, the replicase protein (RP) and the tRNA-like structure determined in this study with the corresponding sequences of other tymoviruses shows that PhMV wrongly named belladonna mottle virus [BDMV(I)] is a separate tymovirus and not another strain of BDMV(E) as originally envisaged. The phylogenetic tree in all the three cases is identical showing that any subset of genomic sequence of sufficient length can be used for establishing evolutionary relationships among tymoviruses.

Genome structure of tobacco necrosis virus strain A

An almost complete sequence of the RNA genome of tobacco necrosis virus (TNV) strain A has been determined. The genome organization is very similar to that of carnation mottle virus (CarMV) and turnip crinkle virus (TCV). The 5'-proximal open reading frame (ORF) encodes a 23-kDa protein and read-through of its amber codon into the second ORF is presumably used for the translation of a 82-kDa protein. The third large ORF encodes the 30-kDa coat protein. Two small ORFs are located upstream and one immediately downstream of this coat protein cistron. Extensive sequence similarity was found between the TNV 82-kDa protein and the putative polymerases of TCV, CarMV, cucumber necrosis virus (CNV), maize chlorotic mottle virus (MCMV), red clover necrotic mosaic virus (RCNMV), and barley yellow dwarf virus (BYDV). The TNV coat protein is very similar to southern bean mosaic virus (SBMV) capsid protein. Of the predicted small proteins only a 7.9-kDa protein shows some sequence similarity with a corresponding protein of MCMV, CarMV, and TCV. The others are unique to TNV. Except for the first four nucleotides at the 5' end no homology was found with the RNA of STNV (satellite of TNV).

Nucleotide sequence of a circular single-stranded DNA associated with coconut foliar decay virus

A circular single-stranded (ss) covalently closed (ccc) DNA associated with coconut foliar decay virus (CFDV) was purified, amplified by the polymerase chain reaction, and subcloned and its sequence established by analysis of overlapping subgenomic cDNA clones. The complete CFDV sequence comprised 1291 nucleotides and contained open reading frames for six proteins of molecular weight larger than 5 kDa. One of these (ORF1, 33.4 kDa) codes for a leucine-rich protein with the nucleoside triphosphate-binding motif GXGKS and may possibly participate in virus replication. The putative viral protein encoded by ORF3 (6.4 kDa) is a positively charged arginine-rich protein with homology to the capsid protein of nuclear polyhedrosis virus, and may represent the CFDV coat protein. CFDV DNA can form a stable stem structure of 10 GC base pairs subtending a loop sequence which in one orientation closely resembles the motif TAATATTAC conserved in a similar structural arrangement within the geminivirus group. Otherwise no sequence homology to DNA-containing plant viruses of the gemini- or caulimovirus groups was found. CFDV therefore represents a new taxonomic group of plant viruses.

Structure-function relationships of icosahedral plant viruses

X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary organization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.

A method to identify distinctive charge configurations in protein sequences, with application to human herpesvirus polypeptides

Charge interactions are of great importance for protein function and structure, and for a variety of cellular and biochemical processes. We present a systematic approach to the detection of distinctive clusters, runs and periodic patterns of charged residues in a protein sequence. Criteria and formulae are set forth to assess statistical significance of these charge configurations. For the 80-odd proteins potentially encoded by the Epstein-Barr virus, only the major nuclear antigens of the latent state and the transactivator of the lytic cycle contain separated charge clusters of opposite sign as well as periodic charge patterns. From our studies of the polypeptides of the human herpesviruses and of a broad collection of human and other viral protein sequences, distinctive charge configurations appear to be associated with viral capsid and core proteins (positive clusters or runs, mostly at the carboxyl terminus), with many viral glycoproteins and membrane-associated proteins (negative charge clusters), and with transactivators and transforming proteins (multiple charge structures). The statistics developed in this paper apply more generally to other than charge properties of a protein and should aid in the evaluation of a large variety of sequence features.

Sequence and identification of the barley yellow dwarf virus coat protein gene

The nucleotide sequence of the coat protein gene of barley yellow dwarf virus (BYDV, PAV serotype) was determined, and the amino acid sequence was deduced. The open reading frame, encoding a protein of relative molecular mass (Mr) 22,047, was confirmed as the coat protein gene by comparison with amino acid sequences of tryptic peptides derived from dissociated virions. In addition, a fragment of this gene expressed in Escherichia coli produced a product which was recognized by antibodies prepared against purified BYDV virions. An overlapping reading frame encoding an Mr 17,147 protein is contained completely within the coat protein gene.

The dynamical structure of the RNA in alfalfa mosaic virus studied by 31P-nuclear magnetic resonance

The structure of the viral RNA in alfalfa mosaic virus (AlMV) was investigated by means of 31P-nuclear magnetic resonance (NMR). It was found that the 31P-NMR line width of AlMV Top a particles is significantly smaller than that of the larger Bottom particles. At low temperatures, the totational correlation time of the 31P nuclei essentially equals the tumbling rate of the virus particle, indicating that the RNA is contained rigidly inside the virion. At more elevated temperatures, the NMR line width sharpens more than expected on the basis of viscosity changes and the RNA exhibits internal mobility. The occurrence of internal mobility is paralleled by an increased internal mobility of the N-terminal part of the coat protein, as could be observed by 1H-NMR spectroscopy. The influence of EDTA on the 31P-NMR line width appeared to be negligible, which is in agreement with the idea that AlMV does not 'swell' like several other RNA-containing plant viruses.

Sequence and organization of southern bean mosaic virus genomic RNA

The genomic RNA sequence of the cowpea strain of southern bean mosaic virus (SBMV-C) has been determined. The genome is 4194 nucleotides in length and has four open reading frames. A 5' proximal open frame, from base 49 to base 603, corresponds to the length of the P4 proteins translated in cell-free extracts from full-length and smaller virion RNA. The largest open frame extends from base 570 to base 3437 and encodes the two largest proteins translated in cell-free extracts from full-length virion RNA. Segments of this open reading frame's predicted amino acid sequence resemble those of known viral RNA polymerases, ATP-binding proteins, and viral genome-linked proteins. A third open frame extends from base 1895 to base 2380 and has not been correlated with an in vitro translation product. The fourth open reading frame is located in the 3' terminal region of the genome extending from base 3217 to base 4053. This frame encodes the SBMV capsid protein which is translated from subgenomic, virion RNA.

Refined structure of southern bean mosaic virus at 2.9 A resolution

The T = 3 capsid of southern bean mosaic virus is analyzed in detail. The beta-sheets of the beta-barrel folding motif that form the subunits show a high degree of twist, generated by several beta-bulges. Only 34 water molecules were identified in association with the three quasi-equivalent subunits, most of them on the external viral surface. Subunit contacts related by quasi-3-fold axes are similar, are dominated by polar interactions and have almost identical calcium binding sites. There is no metal ion on the quasi-3-fold axis, as previously reported. Subunits related by quasi-2-fold and icosahedral 2-fold axes have different contacts but nevertheless display almost identical interactions between the antiparallel helices alpha A. A dipole-dipole type interaction between these helices may produce an energetically stable hinge that allows two types of dimers in a T = 3 assembly. The temperature factor distribution, the hydrogen-bonding pattern, and the contacts across the icosahedral 2-fold axes suggest that one of the dimer types is present in the intact virion and probably also in solution; the other is produced only during capsid assembly. Interactions along the 5-fold axes are mainly polar and possibly form an ion channel. The beta-sheet structures of the three subunits can be superimposed with considerable precision. Significant relative distortions between quasi-equivalent subunits occur mainly in helices and loops. The two dimeric forms and the subunit distortions are the consequence of the non-equivalent subunit environments in the capsid.

Structure of tomato bushy stunt virus. V. Coat protein sequence determination and its structural implications

We report the chemically determined sequence of most of the polypeptide chain of the coat protein of tomato bushy stunt virus. Peptide locations have been determined by comparison with the high-resolution electron density map from X-ray crystallographic analysis as well as by conventional chemical overlaps. Three small gaps remain in the 387-residue sequence. Positively charged side-chains are concentrated in the N-terminal part of the polypeptide (the R domain) as well as on inward-facing surfaces of the S domain. There is homology of S-domain sequences with structurally corresponding residues in southern bean mosaic virus.

Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution

The structure of the protein subunit of satellite tobacco necrosis virus has been solved at 3.7 A resolution. We have now crystallographically refined the original model and extended the resolution ot 2.5 A in order to get a model accurate enough to explain the details of the subunit interactions. The refinement was done with a novel method utilizing the icosahedral symmetry of the virus particle. The final model shows a complicated network of interactions, involving salt linkages, hydrogen bonds and hydrophobic contacts. In addition, we have located three different metal ion sites in the protein shell, linking the protein subunits together. These sites are probably occupied by calcium ions. One site is found in a general position near the icosahedral 3-fold axis of the virus. The ligands form an octahedral arrangement, with two main chain carbonyl oxygens (0-61 and 0-64), one carboxylate oxygen (OD1 from Asp194) of the same subunit and a second carboxylate oxygen (OE1 of Glu25) from a 3-fold related subunit. Two water molecules complete the octahedral arrangement. A second site is on the icosahedral 3-fold axis and is liganded by the carboxylate oxygens of the 3-fold related Asp55 residues. The third metal ion site is found on the 5-fold axis, liganded by the five carbonyl oxygens of Thr138 and two water molecules. We are unable to locate the first 11 N-terminal amino acid residues, which point into the virus interior. No interpretable density for RNA has been found, indicating that the nucleic acid of the virus does not have a unique orientation in the crystal.

RNA-protein interactions in some small plant viruses

The structure of the three quasi-equivalent protein subunits A, B and C of the spherical, T = 3 southern bean mosaic virus (SBMV) have been carefully built in accordance with a refined electron density map of the complete virus. The lower electron density in the RNA portion of the map could not be explicitly interpreted in terms of a preferred RNA structure on which some icosahedral symmetry might have been imposed. However, the extremely basic nature of the interior surface of the coat protein must be associated with the binding and organization of the RNA. Comparison with the small spherical, T = 1 satellite tobacco necrosis virus (STNV; Liljas et al., J. Mol. Biol. 159, 93-108, 1982) and the T = 1 aggregate of alfalfa mosaic virus (AMV) protein (Fukuyama et al., J. Mol. Biol. 150, 33-41, 1981) showed similar results. The pattern of basic residues on the SBMV coat protein surface facing the RNA is able to dock a 9 base pair double-helical A-RNA structure with surprising accuracy. The basic residues are each associated with a different phosphate and the protein can make interactions with five bases in the minor groove. This may be one of a small number of ways in which the RNA interacts with SBMV coat protein. The self-assembly of SBMV has been studied in relation to the presence of the 63 basic amino-terminal coat protein sequence, pH, Ca2+ and Mg2+ ions and RNA. These results have led to a two-state model where the "relaxed" dimers initially self-assemble into 10-mer caps which nucleate the assembly of T = 1 or T = 3 capsids depending on the charge state of the carboxyl group clusters in the subunit contact region. The two-state condition of dimers in a viral coat protein extends the range of structures originally envisaged by Caspar and Klug (Cold Spring Harbor Symp. Quant. Biol. 27, 1-24, 1962).

Structure of a T = 1 aggregate of alfalfa mosaic virus coat protein seen at 4.5 A resolution

A T = 1 empty aggregate of alfalfa mosaic virus coat protein had been crystallized in a hexagonal unit cell and its orientation was determined with the rotation function. A single heavy-atom derivative has now been prepared and the position of the two Hg atoms per protein subunit were determined using a systematic Patterson search procedure, given the particle orientation. Phases, initially determined by single isomorphous replacement, were refined by six cycles of electron density averaging and solvent leveling to produce a 4.5 A resolution electron density map. The protein coat is confined between 95 and 58 A radius. The subunit boundary could be delineated easily. It has a central cavity reminiscent of the beta-barrel in other spherical plant viruses, but its topology could not be determined unambiguously. The spherical particle has large holes at the 5-fold axes, consistent with previous observations. The subunits have substantial interactions at the 2 and 3-fold axes. The structure of the elongated particles is discussed in relation to these results.

Structural comparisons of some small spherical plant viruses

The structures of tomato bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been compared quantitatively. The organization of the shell domains of tomato bushy stunt virus and southern bean mosaic virus within the icosahedral envelope is identical. The wedge-shaped end of the subunit is closer to the fivefold or quasi-sixfold axes in all three viruses but the packing about the three- and twofold axes is quite different in satellite tobacco necrosis virus as compared to tomato bushy stunt virus or southern bean mosaic virus. The polypeptide folds of these viruses have greatest similarity in the beta-sheet region of the eight-stranded anti-parallel beta-barrel. The largest differences occur in the connecting segments. There is no clear indication of homologous amino acid sequences between southern bean mosaic virus and satellite tobacco necrosis virus. However, there is some conservation of the following functional groups. (1) Threonines and serines at the hexagonal-pentagonal wedge-shaped end of the subunit. (2) Lysines and arginines at the protein-RNA interface. (3) Hydrophobic residues in the cavity within the anti-parallel beta-barrel. (4) An aspartic acid near a site which binds Ca in tomato bushy stunt virus. (5) Ionic interactions in the contacts between fivefold-related subunits. These virus coat protein structures are not as similar to each other as the alpha and beta chains of hemoglobin but have greater likeness to one another than the NAD-binding domains of dehydrogenases or lysozymes from hen egg-white and T4 phage. The surface domains of tomato bushy stunt virus and southern bean mosaic virus are more like each other than like satellite tobacco necrosis virus. A divergent evolutionary tree is proposed on the basis of these observations.