Brome mosaic virus coat protein inhibits viral RNA synthesis in vitro

Profiling of genes related to cross protection and competition for NbTOM1 by HLSV and TMV

Cross protection is the phenomenon through which a mild strain virus suppresses symptoms induced by a closely related severe strain virus in infected plants. Hibiscus latent Singapore virus (HLSV) and Tobacco mosaic virus (TMV) are species within the genus tobamovirus. HLSV can protect Nicotianabenthamiana against TMV-U1 strain, resulting in mild symptoms instead of severe systemic necrosis. The mechanism of cross protection between HLSV and TMV is unknown. In the past, some researchers suggest that the protecting virus strain might occupy virus-specific replication sites within a cell leaving no room for the challenge virus. Quantitative real-time RT-PCR was performed to detect viral RNA levels during cross protection. HLSV accumulation increased in cross protected plants compared with that of single HLSV infected plants, while TMV decreased in cross protected plants. This suggests that there is a competition for host factors between HLSV and TMV for replication. To investigate the mechanism under the cross protection between HLSV and TMV, microarray analysis was conducted to examine the transcriptional levels of global host genes during cross protection, using Tobacco Gene Expression Microarray, 4 x 44 k slides. The transcriptional level of some host genes corresponded to accumulation level of TMV. Some host genes were up-regulated only by HLSV. Tobamovirus multiplication gene 1 (TOM1), essential for tobamovirus multiplication, was involved in competition for replication by HLSV and TMV during cross protection. Both HLSV and TMV accumulation decreased when NbTOM1 was silenced. A large quantity of HLSV resulted in decreased TMV accumulation in HLSV+TMV (100:1) co-infection. These results indicate that host genes involved in the plant defense response and virus multiplication are up-regulated by challenge virus TMV but not by protecting virus HLSV during cross protection.

Cross-protection: a century of mystery

Cross-protection is a phenomenon in which infection of a plant with a mild virus or viroid strain protects it from disease resulting from a subsequent encounter with a severe strain of the same virus or viroid. In this chapter, we review the history of cross-protection with regard to the development of ideas concerning its likely mechanisms, including RNA silencing and exclusion, and its influence on the early development of genetically engineered virus resistance. We also examine examples of the practical use of cross-protection in averting crop losses due to viruses, as well as the use of satellite RNAs to ameliorate the impact of virus-induced diseases. We also discuss the potential of cross-protection to contribute in future to the maintenance of crop health in the face of emerging virus diseases and related threats to agricultural production.

Mutual interference between genomic RNA replication and subgenomic mRNA transcription in brome mosaic virus

Replication by many positive-strand RNA viruses includes genomic RNA amplification and subgenomic mRNA (sgRNA) transcription. For brome mosaic virus (BMV), both processes occur in virus-induced, membrane-associated compartments, require BMV replication factors 1a and 2a, and use negative-strand RNA3 as a template for genomic RNA3 and sgRNA syntheses. To begin elucidating their relations, we examined the interaction of RNA3 replication and sgRNA transcription in Saccharomyces cerevisiae expressing 1a and 2a, which support the full RNA3 replication cycle. Blocking sgRNA transcription stimulated RNA3 replication by up to 350%, implying that sgRNA transcription inhibits RNA3 replication. Such inhibition was independent of the sgRNA-encoded coat protein and operated in cis. We further found that sgRNA transcription inhibited RNA3 replication at a step or steps after negative-strand RNA3 synthesis, implying competition with positive-strand RNA3 synthesis for negative-strand RNA3 templates, viral replication factors, or common host components. Consistent with this, sgRNA transcription was stimulated by up to 400% when mutations inhibiting positive-strand RNA3 synthesis were introduced into the RNA3 5'-untranslated region. Thus, BMV subgenomic and genomic RNA syntheses mutually interfered with each other, apparently by competition for one or more common factors. In plant protoplasts replicating all three BMV genomic RNAs, mutations blocking sgRNA transcription often had lesser effects on RNA3 accumulation, possibly because RNA3 also competed with RNA1 and RNA2 replication templates and because any increase in RNA3 replication at the expense of RNA1 and RNA2 would be self-limited by decreased 1a and 2a expression from RNA1 and RNA2.

RNA-dependent RNA polymerase complex of Brome mosaic virus: analysis of the molecular structure with monoclonal antibodies

Viral RNA-dependent RNA polymerase (RdRp) plays crucial roles in the genomic replication and subgenomic transcription of Brome mosaic virus (BMV), a positive-stranded RNA plant virus. BMV RdRp is a complex of virus-encoded 1a and 2a proteins and some cellular factors, and associates with the endoplasmic reticulum at an infection-specific structure in the cytoplasm of host cells. In this study, we investigate the gross structure of the active BMV RdRp complex using monoclonal antibodies raised against the 1a and 2a proteins. Immunoprecipitation experiments showed that the intermediate region between the N-terminal methyltransferase-like domain and the C-terminal helicase-like domain of 1a protein, and the N terminus region of 2a protein are exposed on the surface of the solubilized RdRp complex. Inhibition assays for membrane-bound RdRp suggested that the intermediate region between the methyltransferase-like and the helicase-like domains of 1a protein is located at the border of the region buried within a membrane structure or with membrane-associated material.

The C terminus of brome mosaic virus coat protein controls viral cell-to-cell and long-distance movement

To investigate the functional domains of the coat protein (CP; 189 amino acids) of Brome mosaic virus, a plant RNA virus, 19 alanine-scanning mutants were constructed and tested for their infectivity in barley and Nicotiana benthamiana. Despite its apparent normal replicative competence and CP production, the C-terminal mutant F184A produced no virions. Furthermore, virion-forming C-terminal mutants P178A and D182A failed to move from cell to cell in both plant species, and mutants D181A and V187A showed host-specific movement. These results indicate that the C-terminal region of CP plays some important roles in virus movement and encapsidation. The specificity of certain mutations for viral movement in two different plant species is evidence for the involvement of host-specific factors.

Brome mosaic virus, good for an RNA virologist's basic needs

Abstract Taxonomic relationship: Type member of the Bromovirus genus, family Bromoviridae. A member of the alphavirus-like supergroup of positive-sense single-stranded RNA viruses. Physical properties: Virions are nonenveloped icosahedrals made up of 180 coat protein subunits (Fig. 1). The particles are 26 nm in diameter and contain 22% nucleic acid and 78% protein. The BMV genome is composed of three positive-sense, capped RNAs: RNA1 (3.2 kb), RNA2 (2.9 kb), RNA3 (2.1 kb) (Fig. 2). Viral proteins: RNA1 encodes protein 1a, containing capping and putative RNA helicase activities. RNA2 encodes protein 2a, a putative RNA-dependent RNA polymerase. RNA3 codes for two proteins: 3a, which is required for cell-to-cell movement, and the capsid protein. The capsid is translated from a subgenomic RNA, RNA4 (1.2 kb). Hosts: Monocots in the Poacea family, including Bromus inermis, Zea mays and Hordeum vulgare, in which BMV causes brown streaks. BMV can also infect the dicots Nicotiana benthamiana and several Chenopodium species. In N. benthamiana, the infection is asymptomatic while infection of Chenopodium can cause either necrotic or chlorotic lesions. Useful website:http://www4.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/10030001.htm.

Coat protein-mediated resistance in transgenic plants

This review describes the proposed mechanism(s) of classical virus cross-protection in plants, followed by those suggested for coat protein-mediated resistance (CP-mediated resistance). Although both have common features, cross-protection is thought to be a complex response caused by the replication and expression of the entire viral genome, whereas the resistance conferred by the expression of a virus coat protein gene is more limited. The term genetically engineered cross-protection is frequently used because in many cases the phenotype of resistance mimics that of cross-protection. However, CP-mediated resistance, although a narrow term, more accurately describes the resistance that results from the expression of a virus CP gene in transgenic plants.

Coat protein and protease activity as in vitro translation products of potato carlavirus M RNA

Genomic-size RNA isolated from purified potato carlavirus M (PVM) was translated in both the reticulocyte and the wheat germ cell-free, messenger-dependent systems. The PVM RNA translated the same set of major products in both in vitro systems. The Mr values of the most prominent polypeptides observed consistently were 185,000 (P185), 147,000 (P147), 94,000 (P94), 87,000 (P87), 72,000 (P72), 67,000 (P67), 52,000 (P52), 46,000 (P46), 35,000 (P35) and 25,000 (P25). Relatively low amounts of a translation product of Mr 200,000 (P200) were often detectable in both systems. The P35 polypeptide displayed the same molecular weight and one-dimensional peptide map as the virus coat protein (CP), and was precipitated by antibodies raised against PVM and PVM CP. The kinetics of appearance of the in vitro synthesized polypeptides suggested that primary translation products of high molecular weight undergo post-translational proteolytic cleavage.

Regulation of (+):(-)-strand asymmetry in replication of brome mosaic virus RNA

Transfection of barley protoplasts with brome mosaic virus (BMV) RNAs 1 + 2 in the absence of RNA-3 yielded a molar ratio for (+):(-)-strand progeny at 24 hr postinoculation near unity, whereas over 100-fold more (+)- than (-)-strand progeny accumulated in its presence. The presence of RNA-3 enhanced total (+)-strand RNA production 205-fold and that of RNAs 1 + 2 by 29-fold. In contrast, total (-)-strand RNA accumulation decreased by 68% and that for (-)RNAs 1 + 2 by 79% in the presence of RNA-3. Transfections containing an RNA-3 mutant (Gsgi----U RNA-3) that is incapable of yielding RNA-4 as a result of a single nucleotide substitution at the subgenomic RNA initiation site yielded only 66% of the (+):(-) asymmetry seen in the presence of wild-type RNA-3. Only 1.8-fold excess of (+)-over (-)-strand production was obtained for transfections that included delta SGP RNA-3, a deletion that includes the subgenomic promoter core and extends 43 nt into the RNA-4 sequence. Transfections containing RNA-3 mutants bearing frameshifts or deletions in the coat protein cistron yielded levels of asymmetry similar to those seen for Gsgi----U RNA-3. These findings implicate the subgenomic promoter and other sequences in the intercistronic region of RNA-3 as the primary determinants of asymmetric replication, although the coat protein may be an additional factor enhancing the accumulation of (+)-strand RNA.

Analysis of the protein composition of alfalfa mosaic virus RNA-dependent RNA polymerase

RNA-dependent RNA polymerase (RdRp) was solubilized and purified from cellular membranes isolated from alfalfa mosaic virus (AIMV)-infected tobacco by employing a procedure recently described for brome mosaic virus RdRp [R. Quadt and E.M.J. Jaspars, 1990, Virology 178, 189-194]. The purified AIMV RdRp is completely dependent on added template RNAs and exhibits a high degree of template specificity. Analysis of the protein composition of AIMV RdRp showed that AIMV-encoded proteins P1 and P2 and the coat protein (CP) are present in the active enzyme complex. Minus-strand synthesis by the AIMV RdRp is inhibited by AIMV CP. Native double-stranded AIMV RNAs are utilized as template for viral RNA synthesis by AIMV RdRp indicating that a helicase activity is present in the purified AIMV RdRp preparation.

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.

Nucleotide sequence analysis of cDNA encoding the coat protein of cucumber mosaic virus: genome organization and molecular features of the protein

The cDNA sequence coding for the coat protein of cucumber mosaic virus (Japanese Y strain) was cloned, and its nucleotide sequence was determined. The sequence contains an open reading frame that encodes the coat protein composed of 218 amino acids. The nucleotide and deduced amino acid sequences of the coat protein of this strain were compared with those of the Q strain; the homologies of the sequences were 78% and 81%, respectively. Further study of the sequences gave an insight into the genome organization and the molecular features of the coat protein. The coding region can be divided into three characteristic regions. The N-terminal region has conserved features in the positively charged structure, the hydropathy pattern and the predicted secondary structure, although the amino acid sequence is varied mainly due to frameshift mutations. It is noteworthy that the positions of arginine residues in this region are highly conserved. Both the nucleotide and amino acid sequences of the central region are well conserved. The amino acid sequence of the C-terminal region is not conserved, because of frameshift mutations, however, the total number of amino acids is conserved. The nucleotide sequence of the 3'-noncoding region is divergent, but it could form a tRNA-like structure similar to those reported for other viruses. Detailed investigation suggests that the Y and Q strains are evolutionarily distant.

Involvement of a nonstructural protein in the RNA synthesis of brome mosaic virus

RNA-dependent RNA polymerase (RdRp) was prepared from brome mosaic virus (BMV)-infected barley by a procedure including Nonidet-P40 treatment. The enzyme proved to be highly active, specific, and almost completely template dependent without the need for nuclease treatment [W. A. Miller, and T. C. Hall (1983) Virology 125, 236-241] or DEAE ion exchange chromatography [K. Maekawa and I. Furusawa (1984) Ann. Phytopathol. Soc. Japan 50, 491-499]. Two C-terminal peptides P1C and P2C derived from the nonstructural BMV proteins P1 and P2, respectively, were synthesized. Antibodies raised against these peptides were able to recognize the corresponding native proteins present in RdRp preparations. Antibodies directed against P1C were capable of completely blocking the transcription of BMV RNA in vitro. This is the first experimental evidence that a nonstructural viral protein is present in an enzyme complex involved in tricornaviral RNA synthesis.