Phosphorylation of movement proteins by the plasmodesmal-associated protein kinase.

Plant viruses encode movement proteins (MPs) which play important roles in spreading their infectious materials throughout host plants. This infection is facilitated by cell-to-cell trafficking of MPs through specialized channels termed plasmodesmata, which involves specific interactions between MPs and host factors. Recently, we have reported the identification of a host protein kinase named plasmodesmal-associated protein kinase (PAPK) which specifically phosphorylates a subset of noncell autonomous proteins in vitro, including MPs of Tobacco mosaic virus (TMV) and Bean dwarf mosaic virus (BDMV). Biochemical purification of PAPK was achieved by developing a method in which a series of liquid chromatographic separations of plasmodesmal-enriched subcellular fractions was coupled with phosphorylation assays using TMV MP as a substrate. Application of this approach may prove useful in isolating other host kinases that interact with various viral components.

Comparative single-turnover kinetic analyses of trans-cleaving hammerhead ribozymes with naturally derived non-conserved sequence motifs.

trans-Cleaving hammerhead ribozyme variants were generated with mimicked non-conserved internal loop motifs derived from five structurally diverse natural cis-cleaving ribozymes. Most modified trans-cleaving variants showed enhanced single-turnover cleavage rates relative to minimal counterparts that lack tertiary interactions between internal loop motifs I and II, and relative to controls with sequence changes in loop I. The trans-cleaving ribozyme derived from the positive strand of peach latent mosaic viroid had the highest observed cleavage rate, suggesting a structurally optimized motif that facilitates rapid formation of the ribozyme catalytic center in a trans-reaction.

Mutational analysis of the sequence and structural requirements in brome mosaic virus RNA for minus strand promoter activity.

An RNA-dependent RNA polymerase (replicase) activity that specifically copies brome mosaic virus (BMV) RNAs in vitro can be prepared from BMV-infected barley leaves. The signals directing complementary (minus) strand synthesis reside within the 3' 134-nucleotide-long tRNA-like structure that is common to each of the virion RNAs. By studying the influence of minus strand synthesis of numerous mutations introduced throughout this region of the RNA, we have mapped in detail the sequence and structural elements necessary for minus strand promoter activity. Sequence alterations (either substitutions or small, structurally discrete deletions) in most parts of the tRNA-like structure resulted in decreased minus strand synthesis. This suggests that BMV replicase is a large enzyme, possibly composed of several subunits. The lowest activities, 5 to 8% of wild type, were observed for mutants with substitutions at three separate loci, identifying one structural and two sequence-specific elements essential for optimal promoter activity. (1) Destabilization of the pseudoknot structure in the aminoacyl acceptor stem resulted in low promoter activity, demonstrating the importance of a tRNA-like conformation. (2) Substitution of the C residue adjacent to the 3' terminus resulted in low promoter activity, probably by interfering with strand initiation. (3) The low activities resulting from substitutions and a small deletion in arm C suggest this region of the RNA to be a major feature involved in replicase binding. In particular, nucleotides within the loop of arm C appear to be involved in a sequence-specific interaction with the replicase.

Soybean mosaic virus helper component-protease enhances somatic embryo production and stabilizes transgene expression in soybean.

Soybean mosaic virus (SMV) helper component protease (HC-Pro), a suppressor of post-transcriptional gene silencing, was evaluated for its ability to enhance production of soybean hygromycin-resistant somatic embryos (HR-SEs), and stabilize transgene expression. Immature soybean cotyledonary explants were co-cultured with Agrobacterium tumefaciens strain KYRT1 harboring either pCAMBIA1302, carrying a hygromycin phosphotransferase gene (hpt) and a gene encoding green fluorescent protein; pCAMBIA1305.1, carrying hpt and beta-glucuronidase (uidA) genes; pG2-HC-Pro, a derivative of pCAMBIA1305.1 containing SMV G2 HC-Pro; or pG5-HC-Pro, a derivative of pCAMBIA1305.1 containing SMV G5 HC-Pro, but lacking uidA. Significantly (rho<0.02) higher numbers of HR-SEs were obtained from explants transformed with Agrobacterium harboring either pG2-HC-Pro or pG5-HC-Pro than with either of the vector controls (pCAMBIA1302 or pCAMBIA1305.1). Beta-glucuronidase (GUS) expression was significantly (rho<0.003) higher in 50-day-old transgenic plants expressing GUS along with SMV-HC-Pro and in SMV-infected GUS transgenic plants than in transgenic plants expressing GUS alone. Together, these data suggest that SMV-HC-Pro enhanced recovery of HR-SEs by suppressing silencing of the hygromycin phosphotransferase gene.

High-level synthesis of cowpea mosaic virus RNA polymerase and protease in Escherichia coli.

An expression system for the production of polymerase proteins of cowpea mosaic virus (CPMV) in Escherichia coli cells is described. High-level synthesis of proteins containing protease and polymerase moieties (110-kDa protein) and polymerase alone (87-kDa protein) were obtained from cells containing different plasmid constructions. Precursor and processed forms of CPMV proteins were detected by immunoblotting with antisera directed against 170-kDa precursor polyprotein and 24-kDa viral protease. Crude lysates and supernatant fractions of the lysates from E. coli cells harboring the various plasmid constructions were analysed for poly(A)-oligo(U) polymerase activity and found to be negative for CPMV activity under conditions where similar expression systems for the production of poliovirus RNA polymerase activity were positive. Thus, conditions for CPMV RNA replication may indeed be different from those for poliovirus even though the genomic organization of these viruses is similar.

Characterization of cucumber mosaic virus RNA-dependent RNA polymerase.

Cucumber mosaic virus (CMV) RNA-dependent RNA polymerase (RdRp) was purified form CMV-infected tobacco. The purified enzyme is completely dependent on exogenous template. The enzyme utilizes a variety of viral RNAs and CMV satellite RNA as template for minus-strand synthesis. Cellular RNAs are not used as templates. Ribosomal RNA inhibits the viral RNA synthesis by the CMV RdRp.

Sobemovirus genome appears to encode a serine protease related to cysteine proteases of picornaviruses.

A putative serine protease was identified among non-structural proteins of southern bean mosaic virus (SBMV) by sequence comparison with cellular and viral proteases. The predicted SBMV protease displayed a significant similarity to cysteine proteases of picornaviruses, providing a possible evolutionary link between the two enzyme classes. It is suggested that SBMV follows the general expression strategy characteristic of other positive-strand RNA viruses containing 5'-terminal covalently linked proteins (VPg), i.e. generation of functional proteins by polyprotein processing.

Effect of removal of zinc on alfalfa mosaic virus RNA-dependent RNA polymerase.

The necessity of coat protein for infection of plants by alfalfa mosaic virus (AIMV) and other ilarviruses distinguishes this virus group from other plant virus groups. Recently, the presence of both a zinc-finger type motif and zinc in AIMV coat protein was described [(1989) Virology 168, 48-56]. We studied the effect of a zinc chelator on viral RNA synthesis. Strong inhibition of AIMV RNA-dependent RNA polymerase (RdRp) by ortho-phenanthroline (OP) was observed.

mRNA amplification system by viral replicase in transgenic plants.

We have constructed transgenic tobacco plants (M1x2-FCP2IFN plants) expressing viral RNA replication genes of brome mosaic virus (BMV) and BMV RNA3 derivative (FCP2IFN) carrying the human gamma interferon (IFN-gamma) gene. In M1x2-FCP2IFN plants the RNA3 derivative expressed from the integrated cDNA was replicated and subgenomic RNA (i.e. mRNA of IFN-gamma) was produced by BMV replicase. The accumulation level of the mRNA of IFN-gamma was approximately 5-fold higher than that by the cauliflower mosaic virus (CaMV) 35S RNA promoter. In addition IFN-gamma accumulated in M1x2-FCP2IFN plants.

Nonsense mutations of replicase and movement protein genes contribute to the attenuation of an avirulent tomato mosaic virus.

Three recovery mutants of an avirulent Tomato mosaic virus genus: (Tobamovirus) (ToMV-K) with back mutations of the replicase and/or movement protein (MP) genes, have been constructed by site-directed mutagenesis, and infectious plasmids (pToMV-K) were obtained. The rescued phenotypes of the progeny viruses showed that the replicase and MP recovery mutant (ToMV-K(rase-mp)) induced severe symptoms on both systemic and necrotic plants similar to those induced by the virulent strain. The replicase back mutant (ToMV-K(rase)) produced chlorosis and mosaic symptoms on N. tabacum cv. Huangmiaoyu (systemic host), while the MP recovery mutant (ToMV-K(mp)) produced no systemic symptoms on Huangmiaoyu tobacco. Sequencing of the cDNA of progeny viruses revealed that the "back mutants" maintained these mutation sites during infection. Protein immunoblots indicated that the 98 and 126 kDa proteins were expressed in the plants systemically infected by ToMV-K and pToMV-K, whereas no 98 kDa protein was detected in the plants infected by ToMV. The MPs (27 kDa) of ToMV-K and pToMV-K in the plants were smaller in size than those (30 kDa) of ToMV and pToMVK(rase-mp). These data suggest that ToMV-K replicates and spreads by expressing the truncated 98 and 126 kDa replicases and 27 kDa MP in plants. The opal mutation at nucleotides (nt) 2670-2672 of the replicase gene mainly contributes to the attenuation of ToMV-K, whereas the mutations at nt 5632-5664 of the MP gene attenuate the induced symptoms.

Evolution of bamboo mosaic virus in a nonsystemic host results in mutations in the helicase-like domain that cause reduced RNA accumulation.

A mutant population of bamboo mosaic potexvirus (BaMV) was isolated after serial passage using Chenopodium quinoa plants. While the wild type inoculum induced indistinct chlorotic lesions, the mutant produced obvious lesions on C. quinoa although RNA accumulation of the mutant in Nicotiana benthamiana protoplasts was significantly reduced compared to wild type. Mutations were identified in the helicase-like domain. One RT-PCR-generated cDNA clone (designated pL1-33) representing the helicase-like region showed four nucleotide mutations encoding three amino acid changes that were shown to result in dramatically decreased viral accumulation. Independent analyses of the effects of these substitutions showed that nucleotide changes at position 1722 resulting in a leucine to proline switch and position 2129 resulting in a histidine to tyrosine switch had the greatest effect on viral accumulation. Combination of these two mutations resulted in a undetectable viral accumulation. We have identified that amino acids within the helicase domain but outside the universally conserved helicase-like motifs that play an important role in viral amplification.

The partial purified RNA-dependent RNA polymerases from bamboo mosaic potexvirus and potato virus X infected plants containing the template-dependent activities.

RNA-dependent RNA polymerases (RdRp) isolated from bamboo mosaic potexvirus (BaMV) and potato virus X infected Nicotiana benthamiana plants and solubilized with the detergent NP-40, generated a full-length genomic and two subgenomic double-stranded RNAs of respective viruses in an in vitro RdRp assay containing endogenous RNA templates. Template-dependent and species-specific RdRp activity could be detected after the removal of endogenous RNA templates. The 3' untranslated regions (UTR) containing a stretch of 40 adenylate residues were shown to be an efficient exogenous RNA template for in vitro RdRp reactions. Solution hybridization and nuclease digestion studies revealed that the products transcribed in vitro were minus-sense. Besides using the 3' UTR for minus-sense RNA synthesis, the BaMV RdRp can also recognize 3' terminal 77 nucleotides of the minus-strand for plus-sense RNA synthesis. Promoter studies with BaMV RdRp showed that domain D containing the potexviral hexamer motif of the 3' UTR would be the major contributor of minus-sense RNA synthesis in vitro. On the other hand, the pseudoknot domain containing the poly(A) sequences would be sufficient for minus-sense RNA synthesis.

In vitro activity of the hairpin ribozyme derived from the negative strand of arabis mosaic virus satellite RNA.

The negative strand of the satellite RNA of tobacco ringspot virus [(-)sTRSV] is a self-cleaving RNA, of which self-cleaving domain is called the hairpin ribozyme. The negative strand of the satellite RNA of arabis mosaic virus [(-)sArMV] has been suggested to have a hairpin ribozyme-like secondary structure, and we have previously shown that this hairpin domain of (-)sArMV has ribozyme activity. Here we report characterization of the cleavage reaction of the (-)sArMV hairpin ribozyme. Mutagenesis analyses in a trans-acting system revealed, surprisingly, that the wild-type ribozyme was less active than almost all the other mutant ribozymes tested. In a cis-acting system (self-cleaving reaction), however, the reaction of the RNA containing the wild-type sequence proceeds highly efficiently. This result suggests that the inefficient cleavage of the wild-type substrate in trans-acting system may be due to low efficiency at the substrate-binding step but not at the chemical cleavage step in the reaction. We also constructed a chimeric ribozyme between the catalytic hairpin domain from (-)sArMV and the substrate-binding site from (-)sTRSV. This chimeric ribozyme had the highest activity among the trans-acting hairpin ribozymes tested.

[Amino acid sequence analysis of barley stripe mosaic viral proteins: tentative identification of viral serine proteases]. / Analiz aminokislotnykh posledovatel'nostei belkov virusa shtrikhovatoi mozaiki iachmenia: predpolozhitel'naia identifikatsiia virusnoi serinovoi proteazy.

Analysis of amino acid sequences of barley stripe mosaic virus (BSMV) proteins revealed the pentapeptide GDSGG, the sequence unique for catalytic centers of serine chymotrypsin-like proteases, in protein p14 encoded by open reading frame 4 of RNA beta. Computer-assisted comparisons revealed a statistically significant similarity between amino acid sequences of p14 and chymotrypsin-like proteases. The catalytic His and Asp residues tentatively identified in p14 together with the Ser residue of the GDSGG sequence, presumably, constitute the "catalytic triad" characteristic of chymotrypsin-like proteases. Based on these observations and on the presence of a potential N-proximal transmembrane domain in p14, this protein may be suggested to be a serine protease involved in processing of the replicase precursor within a membrane-bound replication complex of BSMV.

Development of an Efficient Virus Induced Gene Silencing Strategy in the Non-Model Wild Ginger-Zingiber zerumbet and Investigation of Associated Proteome Changes.

Zingiber zerumbet (Zingiberaceae) is a wild, tropical medicinal herb that shows a high degree of resistance to diseases affecting cultivated ginger. Barley stripe mosaic virus (BSMV) silencing vectors containing an endogenous phytoene desaturase (PDS) gene fragment were agroinfiltrated into young leaves of Z. zerumbet under controlled growth conditions to effect virus-induced gene silencing (VIGS). Infiltrated leaves as well as newly emerged leaves and tillers showed visual signs of PDS silencing after 30 days. Replication and systemic movement of the viral vectors in silenced plants were confirmed by RT-PCR. Real-time quantitative PCR analysis verified significant down-regulation of PDS transcripts in the silenced tissues. Label-free proteomic analysis was conducted in leaves with established PDS transcript down regulation and buffer-infiltrated (mock) leaves. A total of 474 proteins were obtained, which were up-regulated, down-regulated or modulated de novo during VIGS. Most of these proteins were localized to the chloroplast, as revealed by UniprotKB analysis, and among the up-regulated proteins there were abiotic stress responsive, photosynthetic, metabolic and membrane proteins. Moreover, the demonstration of viral proteins together with host proteins proved successful viral infection. We report for the first time the establishment of a high-throughput gene functional analysis platform using BSMV-mediated VIGS in Z. zerumbet, as well as proteomic changes associated with VIGS.

Expression, purification and molecular modeling of the NIa protease of Cardamom mosaic virus.

The NIa protease of Potyviridae is the major viral protease that processes potyviral polyproteins. The NIa protease coding region of Cardamom mosaic virus (CdMV) is amplified from the viral cDNA, cloned and expressed in Escherichia coli. NIa protease forms inclusion bodies in E.coli. The inclusion bodies are solubilized with 8 M urea, refolded and purified by Nickel-Nitrilotriacetic acid affinity chromatography. Three-dimensional modeling of the CdMV NIa protease is achieved by threading approach using the homologous X-ray crystallographic structure of Tobacco etch mosaic virus NIa protease. The model gave an insight in to the substrate specificities of the NIa proteases and predicted the complementation of nearby residues in the catalytic triad (H42, D74 and C141) mutants in the cis protease activity of CdMV NIa protease.

The nuclear inclusion a (NIa) protease of turnip mosaic virus (TuMV) cleaves amyloid-ß.

BACKGROUND: The nuclear inclusion a (NIa) protease of turnip mosaic virus (TuMV) is responsible for the processing of the viral polyprotein into functional proteins. NIa was previously shown to possess a relatively strict substrate specificity with a preference for Val-Xaa-His-Gln↓, with the scissile bond located after Gln. The presence of the same consensus sequence, Val(12)-His-His-Gln(15), near the presumptive α-secretase cleavage site of the amyloid-ß (Aß) peptide led us to hypothesize that NIa could possess activity against Aß. METHODOLOGY/PRINCIPAL FINDINGS: Western blotting results showed that oligomeric as well as monomeric forms of Aß can be degraded by NIa in vitro. The specific cleavage of Aß was further confirmed by mass spectrometry analysis. NIa was shown to exist predominantly in the cytoplasm as observed by immunofluorescence microscopy. The overexpression of NIa in B103 neuroblastoma cells resulted in a significant reduction in cell death caused by both intracellularly generated and exogenously added Aß. Moreover, lentiviral-mediated expression of NIa in APP(sw)/PS1 transgenic mice significantly reduced the levels of Aß and plaques in the brain. CONCLUSIONS/SIGNIFICANCE: These results indicate that the degradation of Aß in the cytoplasm could be a novel strategy to control the levels of Aß, plaque formation, and the associated cell death.

The 3'-terminal sequence of Bamboo mosaic virus minus-strand RNA interacts with RNA-dependent RNA polymerase and initiates plus-strand RNA synthesis.

A 3'-terminal, 77-nucleotide sequence of Bamboo mosaic virus (BaMV) minus-strand RNA (Ba-77), comprising a 5' stem-loop, a spacer and a 3'-CUUUU sequence, can be used to initiate plus-strand RNA synthesis in vitro. To understand the mechanism of plus-strand RNA synthesis, mutations were introduced in the 5' untranslated region of BaMV RNA, resulting in changes at the 3' end of minus-strand RNA. The results showed that at least three uridylate residues in 3'-CUUUU are required and the changes at the penultimate U are deleterious to viral accumulation in Nicotiana benthamiana protoplasts. Results from UV-crosslinking and in vitro RNA-dependent RNA polymerase competition assays suggested that the replicase preferentially interacts with the stem structure of Ba-77. Finally, CMV/83 + UUUUC, a heterologus RNA, which possesses about 80 nucleotides containing the 3'-CUUUU pentamer terminus, and which folds into a secondary structure similar to that of Ba-77, could be used as template for RNA production by the BaMV replicase complex in vitro.