Purification of cowpea mosaic virus RNA replication complex: Identification of a virus-encoded 110,000-dalton polypeptide responsible for RNA chain elongation

Grapevine Pathogenic Microorganisms: Understanding Infection Strategies and Host Response Scenarios

Grapevine (Vitis vinifera L.) is one of the most important fruit crop worldwide. Commercial cultivars are greatly affected by a large number of pathogenic microorganisms that cause diseases during pre- and/or post-harvest periods, affecting production, processing and export, along with fruit quality. Among the potential threats, we can find bacteria, fungi, oomycete, or viruses with different life cycles, infection mechanisms and evasion strategies. While plant-pathogen interactions are cycles of resistance and susceptibility, resistance traits from natural resources are selected and may be used for breeding purposes and for a sustainable agriculture. In this context, here we summarize some of the most important diseases affecting V. vinifera together with their causal agents. The aim of this work is to bring a comprehensive review of the infection strategies deployed by significant types of pathogens while understanding the host response in both resistance and susceptibility scenarios. New approaches being used to uncover grapevine status during biotic stresses and scientific-based procedures needed to control plant diseases and crop protection are also addressed.

Investigating the role of viral integral membrane proteins in promoting the assembly of nepovirus and comovirus replication factories

Formation of plant virus membrane-associated replication factories requires the association of viral replication proteins and viral RNA with intracellular membranes, the recruitment of host factors and the modification of membranes to form novel structures that house the replication complex. Many viruses encode integral membrane proteins that act as anchors for the replication complex. These hydrophobic proteins contain transmembrane domains and/or amphipathic helices that associate with the membrane and modify its structure. The comovirus Co-Pro and NTP-binding (NTB, putative helicase) proteins and the cognate nepovirus X2 and NTB proteins are among the best characterized plant virus integral membrane replication proteins and are functionally related to the picornavirus 2B, 2C, and 3A membrane proteins. The identification of membrane association domains and analysis of the membrane topology of these proteins is discussed. The evidence suggesting that these proteins have the ability to induce membrane proliferation, alter the structure and integrity of intracellular membranes, and modulate the induction of symptoms in infected plants is also reviewed. Finally, areas of research that need further investigation are highlighted.

Inhibition of cleavage of a plant viral polyprotein by an inhibitor activity present in wheat germ and cowpea embryos

In rabbit reticulocyte lysate, the bottom component RNA of cowpea mosaic virus directs the synthesis of a 200,000-molecular-weight precursor protein (200K protein) that is cleaved during synthesis by a reticulocyte enzyme to form a 32K protein and a 170K protein. Cleavage of the 200K protein was found to be effectively inhibited by inhibitor activity in wheat germ and cowpea embryo extracts. The inhibitor was nondialyzable, precipitatable by ammonium sulfate, and partially stable at high temperatures. The activity appeared to be specific in that it caused no inhibition of the secondary cleavage reactions (cleavage of the 170K protein) at concentrations that were sufficient to cause complete inhibition of the primary cleavage reaction (cleavage of the 200K protein).

Small nuclear inclusion protein encoded by a plant potyvirus genome is a protease

Tobacco etch virus, a plant potyvirus, expresses its RNA genome as a large polyprotein precursor which undergoes extensive proteolytic processing to yield seven or more mature products. Two of these products, proteins with apparent molecular weights of 49,000 and 54,000 (49K and 54K proteins), aggregate in the form of crystalline inclusions within the nuclei of infected cells. Cell-free translation of synthetic transcripts was used to map the genes for these two products on the viral genome and to express an enzymatically active protein. The 49K protein was determined to be a viral protease responsible for several cleavages of the polyprotein, including its own autocatalytic excision. Analyses of products expressed from the 49K protein genes which were altered by deletion revealed that only the carboxyl-terminal half was required for proteolytic activity.

RNAi-mediated resistance to Potato spindle tuber viroid in transgenic tomato expressing a viroid hairpin RNA construct

Because of their highly ordered structure, mature viroid RNA molecules are assumed to be resistant to degradation by RNA interference (RNAi). In this article, we report that transgenic tomato plants expressing a hairpin RNA (hpRNA) construct derived from Potato spindle tuber viroid (PSTVd) sequences exhibit resistance to PSTVd infection. Resistance seems to be correlated with high-level accumulation of hpRNA-derived short interfering RNAs (siRNAs) in the plant. Thus, although small RNAs produced by infecting viroids [small RNAs of PSTVd (srPSTVds)] do not silence viroid RNAs efficiently to prevent their replication, hpRNA-derived siRNAs (hp-siRNAs) appear to effectively target the mature viroid RNA. Genomic mapping of the hp-siRNAs revealed an unequal distribution of 21- and 24-nucleotide siRNAs of both (+)- and (-)-strand polarities along the PSTVd genome. These data suggest that RNAi can be employed to engineer plants for viroid resistance, as has been well established for viruses.

Peripheral association of a polyprotein precursor form of the RNA-dependent RNA polymerase of Tomato ringspot virus with the membrane-bound viral replication complex

Replication of Tomato ringspot virus (ToRSV) occurs in association with endoplasmic reticulum (ER)-derived membranes. We have previously shown that the putative nucleotide triphosphate-binding protein (NTB) of ToRSV is an ER-targeted protein and that an intermediate polyprotein containing the domains for NTB and for the genome-linked viral protein (VPg) is associated with the replication complex. We now report the detection of a 95-kDa polyprotein that contains the domains for the RNA-dependent RNA polymerase (Pol), the proteinase (Pro) and the VPg. This polyprotein appears to be a truncated version of the full-length 111-kDa VPg-Pro-Pol polyprotein and was termed VPg-Pro-Pol'. A subpopulation of VPg-Pro-Pol' was peripherally associated with ER-derived membranes active in viral replication. However, the VPg, Pro and Pol domains did not target to membranes in the absence of viral infection. We propose a model in which VPg-Pro-Pol' is brought to the site of replication through interaction with a viral membrane protein.

Nomenclature and functions of RNA-directed RNA polymerases

There is little relationship between eukaryotic RNA-directed RNA polymerases (RDRs), viral RNA-dependent RNA polymerases (RdRps) and DNA-dependent RNA polymerases, indicating that RDRs evolved as an independent class of enzymes early in evolution. In fungi, plants and several animal systems, RDRs play a key role in RNA-mediated gene silencing [post-transcriptional gene silencing (PTGS) in plants and RNA interference (RNAi) in non-plants] and are indispensable for heterochromatin formation, at least, in Schizosaccharomyces pombe and plants. Recent findings indicate that PTGS, RNAi and heterochromatin formation not only function as host defence mechanisms against invading nucleic acids but are also involved in natural gene regulation. RDRs are required for these processes, initiating a broad interest in this enzyme class.

Replication of positive-strand RNA viruses in plants: contact points between plant and virus components

Positive-strand RNA viruses constitute the largest group of plant viruses and have an important impact on world agriculture. These viruses have small genomes that encode a limited number of proteins and depend on their hosts to complete the various steps of their replication cycle. In this review, the contact points between positive-strand RNA plant viruses and their hosts, which are necessary for the translation and replication of the viral genomes, are discussed. Special emphasis is placed on the description of viral replication complexes that are associated with specific membranous compartments derived from plant intracellular membranes and contain viral RNAs and proteins as well as a variety of host proteins. These complexes are assembled via an intricate network of protein–protein, protein–membrane, and protein–RNA interactions. The role of host factors in regulating the assembly, stability, and activity of viral replication complexes are also discussed.

Cowpea mosaic virus: effects on host cell processes

SUMMARY Taxonomy: Cowpea mosaic virus (CPMV) is the type member of the Comoviridae and bears a strong resemblance to animal picornaviruses, both in gene organization and in the amino acid sequence of replication proteins. Little systematic work has been done to compare isolates of the virus from different parts of the world. Physical properties: Purified preparations of virus contain three centrifugal components; empty protein shells without RNA (T) and two nucleoprotein components (M and B), containing 24% and 34% RNA, respectively. The icosahedral particles have with a diameter of 28 nm, consist of 60 copies of two coat proteins, and are heat stable. Hosts: CPMV causes one of the most commonly reported virus diseases of cowpea (Vigna unguiculata), in which it produces chlorotic spots with diffuse borders in inoculated primary leaves. Trifoliate leaves develop a bright yellow or light green mosaic of increasing severity in younger leaves. The host range is rather limited, and few hosts are known outside the Leguminosae. The virus is transmitted by various beetles with biting mouthparts. Reported in Africa, the Philippines and Iran. Is apparently absent from North and South America. Useful website: http://mmtsb.scripps.edu/viper/1cpmv.html (structure); http://image.fs.uidaho.edu/vide/descr254.htm (general information).

The GCD10 subunit of yeast eIF-3 binds the methyltransferase-like domain of the 126 and 183 kDa replicase proteins of tobacco mosaic virus in the yeast two-hybrid system

The tobacco mosaic virus (TMV) replicase complex contains virus- and host-encoded proteins. In tomato, one of these host proteins was reported previously to be related serologically to the GCD10 subunit of yeast eIF-3. The yeast two-hybrid system has now been used to show that yeast GCD10 interacts selectively with the methyltransferase domain shared by the 126 and 183 kDa TMV replicase proteins. These findings are consistent with a role for a GCD10-like protein in the TMV replicase complex and suggest that, in TMV-infected cells, the machinery of virus replication and protein synthesis may be closely connected.

Cellular factors in the transcription and replication of viral RNA genomes: a parallel to DNA-dependent RNA transcription

Viral RNA replication and transcription involves not only viral RNA-dependent RNA polymerases, but also cellular proteins, the majority of which are subverted from the RNA-processing or translation machineries of host cells. These factors interact with viral RNA or polymerases to form transcription or replication ribonucleoprotein complexes and may provide template specificity for RNA-dependent RNA synthesis, suggesting a close parallel to the mechanism of DNA-dependent RNA synthesis. The types of cellular proteins involved and their modes of action are reviewed.

Comparison of the replication of positive-stranded RNA viruses of plants and animals

It is clear from the experimental data that there are some similarities in RNA replication for all eukaryotic positive-stranded RNA viruses—that is, the mechanism of polymerization of the nucleotides is probably similar for all. It is noteworthy that all mechanisms appear to utilize host membranes as a site of replication. Membranes appear to function not only as a way of compartmentalizing virus RNA replication but also appear to have a central role in the organization and functioning of the replication complex, and further studies in this area are needed. Within virus supergroups, similarities are evident between animal and plant viruses—for example, in the nature and arrangements of replication genes and in sequence similarities of functional domains. However, it is also clear that there has been considerable divergence, even within supergroups. For example, the animal alpha-viruses have evolved to encode proteinases which play a central controlling function in the replication cycle, whereas this is not common in the plant alpha-like viruses and even when it occurs, as in the tymoviruses, the strategies that have evolved appear to be significantly different. Some of the divergence could be host-dependent and the increasing interest in the role of host proteins in replication should be fruitful in revealing how different systems have evolved. Finally, there are virus supergroups that appear to have no close relatives between animals and plants, such as the animal coronavirus-like supergroup and the plant carmo-like supergroup.

Complementation of tobacco etch potyvirus mutants by active RNA polymerase expressed in transgenic cells

A genetic complementation system was developed in which tobacco etch virus (TEV) polymerase (NIb)-expressing transgenic plants or protoplasts were inoculated with NIb-defective TEV mutants. A beta-glucuronidase (GUS) reporter gene integrated into the genomes of parental and four mutant viruses was used to assay RNA amplification. Two mutants (termed VNN and EDE) contained substitutions affecting the conserved "GDD" polymerase motif or a nuclear localization signal sequence, respectively; one (aD/b) contained a mutation debilitating the NIb N-terminal cleavage site, whereas the other (delta b) lacked the entire NIb sequence. Each mutant was unable to amplify in nontransformed tobacco protoplasts. In contrast, the VNN, EDE, and delta b mutants were complemented to various degrees in NIb-expressing cells, whereas the aD/b mutant was not complemented. The VNN mutant was complemented most efficiently, reaching an average of 11-12% the level of parental TEV-GUS, although in some experiments the level was near 100%. This mutant also replicated in, and spread through, whole transgenic plants to the same level as parental virus. The EDE mutant was complemented relatively poorly, reaching 1% or less of the level of parental TEV-GUS. Despite the close proximity of the EDE substitution to the N-terminal cleavage site, proteolytic processing of NIb was unaffected in an in vitro assay. The delta b mutant was complemented to an intermediate degree in protoplasts, reaching 3.5% the level of parental virus, and replicated and moved systemically in transgenic plants. These data indicate that free NIb supplied entirely in trans can provide all NIb functions essential for RNA amplification. The relative inefficient complementation of the EDE mutant suggests that the resulting mutant protein was transinhibitory.

RNA-dependent RNA polymerase from plants infected with turnip crinkle virus can transcribe (+)- and (-)-strands of virus-associated RNAs

RNA-dependent RNA polymerase (RdRp) was solubilized from membranes of turnip infected with turnip crinkle virus (TCV), a single-stranded, monopartite RNA virus. The RdRp activity could be separated into three peaks by Sephacryl S500HR chromatography. RdRp from peak I, which contained substantial amounts of endogenous TCV genomic RNA, and peak II were template-specific, synthesizing full-length complementary strands of exogenous TCV subviral RNAs but not control RNA templates. Peak III RdRp was nonspecific, synthesizing full-sized products for all added RNA templates. Peak II RdRp transcribed several different TCV satellite (sat) and defective interfering RNA templates in both (+)- and (-)-sense orientations but did not transcribe (+)-strands of satellite RNAs associated with unrelated viruses. Monomeric-length sat-RNA C was synthesized from a template containing as many as 220 nonsatellite bases at the 3' ends of either (+)- or (-)-strands, indicating that the RdRp was able to recognize 3'-end sequences in an internal location. Deletion of 95-242 bases from the 3' end of (+)-strand sat-RNA C abolished the synthesis of template-length product. However, transcription of template-length products was not affected by the deletion of at least 257 bases from the 3' end of (-)-strand sat-RNA C template (leaving only the 100 5'-terminal residues), implying that different mechanisms exist for synthesis of (+)-and (-)-strand satellite RNA in vitro.

Clustered charged-to-alanine mutagenesis of poliovirus RNA-dependent RNA polymerase yields multiple temperature-sensitive mutants defective in RNA synthesis

To generate a collection of conditionally defective poliovirus mutants, clustered charged-to-alanine mutagenesis of the RNA-dependent RNA polymerase 3D was performed. Clusters of charged residues in the polymerase coding region were replaced with alanines by deoxyoligonucleotide-directed mutagenesis of a full-length poliovirus cDNA clone. Following transfection of 27 mutagenized cDNA clones, 10 (37%) gave rise to viruses with temperature-sensitive (ts) phenotypes. Three of the ts mutants displayed severe ts plaque reduction phenotypes, producing at least 10(3)-fold fewer plaques at 39.5 degrees C than at 32.5 degrees C; the other seven mutants displayed ts small-plaque phenotypes. Constant-temperature, single-cycle infections showed defects in virus yield or RNA accumulation at the nonpermissive temperature for eight stable ts mutants. In temperature shift experiments, seven of the ts mutants showed reduced accumulation of viral RNA at the nonpermissive temperature and showed no other ts defects. The mutations responsible for the phenotypes of most of these ts mutants lie in the N-terminal third of the 3D coding region, where no well-characterized mutations responsible for viable mutants had been previously identified. Clustered charged-to-alanine mutagenesis (S. H. Bass, M. G. Mulkerrin, and J. A. Wells, Proc. Natl. Acad. Sci. USA 88:4498-4502, 1991; W. F. Bennett, N. F. Paoni, B. A. Keyt, D. Botstein, J. J. S. Jones, L. Presta, F. M. Wurm, and M. J. Zoller, J. Biol. Chem. 266:5191-5201, 1991; and K. F. Wertman, D. G. Drubin, and D. Botstein, Genetics 132:337-350, 1992) is designed to target residues on the surfaces of folded proteins; thus, extragenic suppression analysis of such mutant viruses may be very useful in identifying components of the viral replication complex.

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.

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.

Mutational analysis of tobacco etch virus polyprotein processing: cis and trans proteolytic activities of polyproteins containing the 49-kilodalton proteinase

The genome of tobacco etch virus contains a single open reading frame with the potential to encode a 346-kilodalton (kDa) polyprotein. The large polyprotein is cleaved at several positions by a tobacco etch virus genome-encoded, 49-kDa proteinase. The locations of the 49-kDa proteinase-mediated cleavage sites flanking the 71-kDa cytoplasmic pinwheel inclusion protein, 6-kDa protein, 49-kDa proteinase, and 58-kDa putative polymerase have been determined by using cell-free expression, proteolytic processing, and site-directed mutagenesis systems. Each of these sites is characterized by the conserved sequence motif Glu-Xaa-Xaa-Tyr-Xaa-Gln-Ser or Gly (in which cleavage occurs after the Gln residue). The amino acid residue (Gln) predicted to occupy the -1 position relative to the scissile bond has been substituted, by mutagenesis of cloned cDNA, at each of four cleavage sites. The altered sites were not cleaved by the 49-kDa proteinase. A series of synthetic polyproteins that contained the 49-kDa proteinase linked to adjoining proteins via defective cleavage sites were expressed, and their proteolytic activities were analyzed. As part of a polyprotein, the proteinase was found to exhibit cis (intramolecular) and trans (intermolecular) activity.

Detection of a Novel Protein Encoded by the Bottom-Component RNA of Cowpea Mosaic Virus, Using Antibodies Raised against a Synthetic Peptide

A peptide was synthesized that corresponded to a sequence in the cowpea mosaic virus bottom-component RNA-encoded 200-kilodalton polyprotein showing homology to the picornaviral 3C proteases. By injecting a rabbit with this peptide, antibodies were obtained that allowed the detection of a novel viral protein derived from the 200-kilodalton polyprotein. This protein, which had a size of 24 kilodaltons was found in both infected cowpea leaves and cowpea protoplasts.