Alfalfa mosaic virus RNAs serve as cap donors for tomato spotted wilt virus transcription during coinfection of Nicotiana benthamiana

Translation Arrest: A Key Player in Plant Antiviral Response

Plants evolved several mechanisms to protect themselves against viruses. Besides recessive resistance, where compatible host factors required for viral proliferation are absent or incompatible, there are (at least) two types of inducible antiviral immunity: RNA silencing (RNAi) and immune responses mounted upon activation of nucleotide-binding domain leucine-rich repeat (NLR) receptors. RNAi is associated with viral symptom recovery through translational repression and transcript degradation following recognition of viral double-stranded RNA produced during infection. NLR-mediated immunity is induced upon (in)direct recognition of a viral protein by an NLR receptor, triggering either a hypersensitive response (HR) or an extreme resistance response (ER). During ER, host cell death is not apparent, and it has been proposed that this resistance is mediated by a translational arrest (TA) of viral transcripts. Recent research indicates that translational repression plays a crucial role in plant antiviral resistance. This paper reviews current knowledge on viral translational repression during viral recovery and NLR-mediated immunity. Our findings are summarized in a model detailing the pathways and processes leading to translational arrest of plant viruses. This model can serve as a framework to formulate hypotheses on how TA halts viral replication, inspiring new leads for the development of antiviral resistance in crops.

Molecular Characteristics of Subgenomic RNAs and the Cap-Dependent Translational Advantage Relative to Corresponding Genomic RNAs of Tomato spotted wilt virus

Tomato spotted wilt virus (TSWV) causes severe viral diseases on many economically important plants of Solanaceae. During the infection process of TSWV, a series of 3'-truncated subgenomic RNAs (sgRNAs) relative to corresponding genomic RNAs were synthesized, which were responsible for the expression of some viral proteins. However, corresponding genomic RNAs (gRNAs) seem to possess the basic elements for expression of these viral proteins. In this study, molecular characteristics of sgRNAs superior to genomic RNAs in viral protein expression were identified. The 3' ends of sgRNAs do not cover the entire intergenic region (IGR) of TSWV genomic RNAs and contain the remarkable A-rich characteristics. In addition, the 3' terminal nucleotides of sgRNAs are conserved among different TSWV isolates. Based on the eIF4E recruitment assay and subsequent northern blot, it is suggested that the TSWV sgRNA, but not gRNA, is capped in vivo; this is why sgRNA is competent for protein expression relative to gRNA. In addition, the 5' and 3' untranslated region (UTR) of sgRNA-Ns can synergistically enhance cap-dependent translation. This study further enriched the understanding of sgRNAs of ambisense RNA viruses.

Cap-snatching as a possible contributor to photosynthesis shut-off

Cap-snatching is a mechanism applied by segmented, negative strand (-) RNA viruses (NSVs) to initiate genome transcription. So far, the cap donor source of cytoplasmic-replicating NSVs has remained elusive. Recently, studies pointed to processing body (P body, PB) as the potential source for providing capped RNAs but conclusive evidence is still lacking. To attempt identifying these sources, here the 5' non-viral leader sequences of Tomato spotted wilt virus (TSWV) N mRNAs were analysed by high-throughput sequencing (HTS) from plants subjected to normal and heat-stress conditions, and subsequently mapped on host donor transcripts. The majority of non-viral heterogenous, host-derived leader sequences ranged in size between ~10-20 nt and contained A or AG residues at the cleavage site and the presence of certain sequence motifs. Mapping the capped-leader sequences to the 5' UTR region of genes encoded by the Nicotiana tabacum genome, identified 348 donor genes and which were specifically enriched in cellular photosynthesis pathway. Nineteen of those were clearly expressed differentially at normal condition versus heat-stress conditions. Although the results did not point towards snatching of capped-RNA leader sequences from certain cytoplasmic RNA granules in particular, they indicated photosynthesis downregulation (and development of disease symptoms) partially result from cap-snatching.

Bunyaviral N Proteins Localize at RNA Processing Bodies and Stress Granules: The Enigma of Cytoplasmic Sources of Capped RNA for Cap Snatching

Most cytoplasmic-replicating negative-strand RNA viruses (NSVs) initiate genome transcription by cap snatching. The source of host mRNAs from which the cytoplasmic NSVs snatch capped-RNA leader sequences has remained elusive. Earlier reports have pointed towards cytoplasmic-RNA processing bodies (P body, PB), although several questions have remained unsolved. Here, the nucleocapsid (N) protein of plant- and animal-infecting members of the order Bunyavirales, in casu Tomato spotted wilt virus (TSWV), Rice stripe virus (RSV), Sin nombre virus (SNV), Crimean-Congo hemorrhagic fever virus (CCHFV) and Schmallenberg virus (SBV) have been expressed and localized in cells of their respective plant and animal hosts. All N proteins localized to PBs as well as stress granules (SGs), but extensively to docking stages of PB and SG. TSWV and RSV N proteins also co-localized with Ran GTPase-activating protein 2 (RanGAP2), a nucleo-cytoplasmic shuttling factor, in the perinuclear region, and partly in the nucleus when co-expressed with its WPP domain containing a nuclear-localization signal. Upon silencing of PB and SG components individually or concomitantly, replication levels of a TSWV minireplicon, as measured by the expression of a GFP reporter gene, ranged from a 30% reduction to a four-fold increase. Upon the silencing of RanGAP homologs in planta, replication of the TSWV minireplicon was reduced by 75%. During in vivo cap-donor competition experiments, TSWV used transcripts destined to PB and SG, but also functional transcripts engaged in translation. Altogether, the results implicate a more complex situation in which, besides PB, additional cytoplasmic sources are used during transcription/cap snatching of cytoplasmic-replicating and segmented NSVs.

Molecular characterization and RSV Co-infection of Nicotiana benthamiana with three distinct begomoviruses

Geminiviruses constitute a family of plant viruses with characteristic twinned quasi-icosahedral virions and a small circular DNA genome. Geminiviruses, especially begomoviruses, cause substantial economic losses in tropical and subtropical regions globally. Geminiviruses use the host's transcriptional mechanisms to synthesize their mRNAs. They are considered as an attractive model to understand the transcription mechanism of their host plants. Experiments were conducted to identify transcriptional start sites (TSSs) of the three begomoviruses, i.e., Cotton leaf curl Multan virus (CLCuMuV), Corchorus yellow vein virus (CoYVV), and Ramie mosaic virus (RamV). We first rub-inoculated Rice stripe tenuivirus (RSV), a segmented negative-sense RNA virus that uses cap-snatching to produce capped viral mRNAs, into N. benthamiana. After the inoculation, RSV-infected N. benthamiana were super-infected by CoYVV, CLCuMuV, or RamV, respectively. The capped-RNA leaders snatched by RSV were obtained by determining the 5'-ends of RSV mRNA with high throughput sequencing. Afterwards, snatched capped-RNA leaders of RSV were mapped onto the genome of each begomovirus and those matching the begomoviral genome were considered to come from the 5' ends of assumed begomoviral mRNAs. In this way, TSSs of begomoviruses were obtained. After mapping these TSSs onto the genome of the respective begomovirus, it was found very commonly that a begomovirus can use many different TSSs to transcribe the same gene, producing many different mRNA isoforms containing the corresponding open reading frames (ORFs).

A convenient in vivo cap donor delivery system to investigate the cap snatching of plant bunyaviruses

Like their animal-infecting counterparts, plant bunyaviruses use capped RNA leaders cleaved from host cellular mRNAs to prime viral genome transcription in a process called cap-snatching, but in vivo systems to investigate the details of this process are lacking for them. Here, we report that Rice stripe tenuivirus (RSV) and Tomato spotted wilt tospovirus (TSWV) cleave capped RNA leaders from mRNAs transiently expressed by agroinfiltration, which makes it possible to artificially deliver defined cap donors to the two plant bunyaviruses with unprecedented convenience. With this system, some ideas regarding how plant bunyaviruses select and use capped RNA leaders can be tested easily. We were also able to obtain clear evidence that the capped RNA leaders selected by TSWV are generally longer than those by RSV. TSWV frequently uses the prime-and-realign mechanism in transcription primed by capped RNA leaders shorter than a certain length, like that has been demonstrated recently for RSV.

Alterations in cellular RNA decapping dynamics affect tomato spotted wilt virus cap snatching and infection in Arabidopsis

RNA processing and decay pathways have important impacts on RNA viruses, particularly animal-infecting bunyaviruses, which utilize a cap-snatching mechanism to translate their mRNAs. However, their effects on plant-infecting bunyaviruses have not been investigated. The roles of mRNA degradation and non-sense-mediated decay components, including DECAPPING 2 (DCP2), EXORIBONUCLEASE 4 (XRN4), ASYMMETRIC LEAVES2 (AS2) and UP-FRAMESHIFT 1 (UPF1) were investigated in infection of Arabidopsis thaliana by several RNA viruses, including the bunyavirus, tomato spotted wilt virus (TSWV). TSWV infection on mutants with decreased or increased RNA decapping ability resulted in increased and decreased susceptibility, respectively. By contrast, these mutations had the opposite, or no, effect on RNA viruses that use different mRNA capping strategies. Consistent with this, the RNA capping efficiency of TSWV mRNA was higher in a dcp2 mutant. Furthermore, the TSWV N protein partially colocalized with RNA processing body (PB) components and altering decapping activity by heat shock or coinfection with another virus resulted in corresponding changes in TSWV accumulation. The present results indicate that TSWV infection in plants depends on its ability to snatch caps from mRNAs destined for decapping in PBs and that genetic or environmental alteration of RNA processing dynamics can affect infection outcomes.

Paving the Way to Tospovirus Infection: Multilined Interplays with Plant Innate Immunity

Tospoviruses are among the most important plant pathogens and cause serious crop losses worldwide. Tospoviruses have evolved to smartly utilize the host cellular machinery to accomplish their life cycle. Plants mount two layers of defense to combat their invasion. The first one involves the activation of an antiviral RNA interference (RNAi) defense response. However, tospoviruses encode an RNA silencing suppressor that enables them to counteract antiviral RNAi. To further combat viral invasion, plants also employ intracellular innate immune receptors (e.g., Sw-5b and Tsw) to recognize different viral effectors (e.g., NSm and NSs). This leads to the triggering of a much more robust defense against tospoviruses called effector-triggered immunity (ETI). Tospoviruses have further evolved their effectors and can break Sw-5b-/Tsw-mediated resistance. The arms race between tospoviruses and both layers of innate immunity drives the coevolution of host defense and viral genes involved in counter defense. In this review, a state-of-the-art overview is presented on the tospoviral life cycle and the multilined interplays between tospoviruses and the distinct layers of defense.

The Cap Snatching of Segmented Negative Sense RNA Viruses as a Tool to Map the Transcription Start Sites of Heterologous Co-infecting Viruses

Identification of the transcription start sites (TSSs) of a virus is of great importance to understand and dissect the mechanism of viral genome transcription but this often requires costly and laborious experiments. Many segmented negative-sense RNA viruses (sNSVs) cleave capped leader sequences from a large variety of mRNAs and use these cleaved leaders as primers for transcription in a conserved process called cap snatching. The recent developments in high-throughput sequencing have made it possible to determine most, if not all, of the capped RNAs snatched by a sNSV. Here, we show that rice stripe tenuivirus (RSV), a plant-infecting sNSV, co-infects Nicotiana benthamiana with two different begomoviruses and snatches capped leader sequences from their mRNAs. By determining the 5' termini of a single RSV mRNA with high-throughput sequencing, the 5' ends of almost all the mRNAs of the co-infecting begomoviruses could be identified and mapped on their genomes. The findings in this study provide support for the using of the cap snatching of sNSVs as a tool to map viral TSSs.

Toscana virus cap-snatching and initiation of transcription

Toscana virus (TOSV) is an arthropod-borne phlebovirus within the family Phenuiviridae in the order Bunyavirales. It seems to be an important agent of human meningoencephalitis in the warm season in the Mediterranean area. Because the polymerase of Bunyavirales lacks a capping activity, it cleaves short-capped RNA leaders derived from the host cell, and uses them to initiate viral mRNA synthesis. To determine the size and nucleotide composition of the host-derived RNA leaders, and to elucidate the first steps of TOSV transcription initiation, we performed a high-throughput sequencing of the 5' end of TOSV mRNAs in infected cells at different times post-infection. Our results indicated that the viral polymerase cleaved the host-capped RNA leaders within a window of 11-16 nucleotides. A single population of cellular mRNAs could be cleaved at different sites to prime the synthesis of several viral mRNA species. The majority of the mRNA resulted from direct priming, but we observed mRNAs resulting from several rounds of prime-and-realign events. Our data suggest that the different rounds of the prime-and-realign mechanism result from the blocking of the template strand in a static position in the active site, leading to the slippage of the nascent strand by two nucleotides when the growing duplex is sorted out from the active site. To minimize this rate-limiting step, TOSV polymerase cleaves preferentially capped RNA leaders after GC, so as to greatly reduce the number of cycles of priming and realignment, and facilitate the separation of the growing duplex.

Inherent properties not conserved in other tenuiviruses increase priming and realignment cycles during transcription of Rice stripe virus

Two tenuiviruses Rice stripe virus (RSV) and Rice grassy stunt virus (RGSV) were found to co-infect rice with the same reovirus Rice ragged stunt virus (RRSV). During the co-infection, both tenuiviruses recruited 10-21 nucleotides sized capped-RNA leaders from the RRSV. A total of 245 and 102 RRSV-RGSV and RRSV-RSV chimeric mRNA clones, respectively, were sequenced. An analysis of the sequences suggested a scenario consistent with previously reported data on related viruses, in which capped leader RNAs having a 3' end complementary to the viral template are preferred and upon base pairing the leaders prime processive transcription directly or after one to several cycles of priming and realignment (repetitive prime-and-realign). Interestingly, RSV appeared to have a higher tendency to use repetitive prime-and-realign than RGSV even with the same leader derived from the same RRSV RNA. Combining with relevant data reported previously, this points towards an intrinsic feature of RSV.

Possible involvement of eEF1A in Tomato spotted wilt virus RNA synthesis

Tomato spotted wilt virus (TSWV) is a negative-strand RNA virus in the family Bunyaviridae and propagates in both insects and plants. Although TSWV can infect a wide range of plant species, host factors involved in viral RNA synthesis of TSWV in plants have not been characterized. In this report, we demonstrate that the cell-free extract derived from one of the host plants can activate mRNA transcriptional activity of TSWV. Based on activity-guided fractionation of the cell-free extract, we identified eukaryotic elongation factor (eEF) 1A as a possible host factor facilitating TSWV transcription and replication. The RNA synthesis-supporting activity decreased in the presence of an eEF1A inhibitor, suggesting that eEF1A plays an important role in RNA synthesis of TSWV.

Fig mosaic virus mRNAs show generation by cap-snatching

Fig mosaic virus (FMV), a member of the newly described genus Emaravirus, has four negative-sense single-stranded genomic RNAs, and each codes for a single protein in the viral complementary RNA (vcRNA). In this study we show that FMV mRNAs for genome segments 2 and 3 contain short (12-18 nucleotides) heterogeneous nucleotide leader sequences at their 5' termini. Furthermore, by using the high affinity cap binding protein eIF4E(K119A), we also determined that a 5' cap is present on a population of the FMV positive-sense RNAs, presumably as a result of cap-snatching. Northern hybridization results showed that the 5' capped RNA3 segments are slightly smaller than the homologous vcRNA3 and are not polyadenylated. These data suggest that FMV generates 5' capped mRNAs via cap-snatching, similar to strategies used by other negative-sense multipartite ssRNA viruses.

Repetitive prime-and-realign mechanism converts short capped RNA leaders into longer ones that may be more suitable for elongation during rice stripe virus transcription initiation

Cucumber mosaic virus (CMV) RNAs were found to serve as cap donors for rice stripe virus (RSV) transcription initiation during their co-infection of Nicotiana benthamiana. The 5' end of CMV RNAs was cleaved preferentially at residues that had multiple-base complementarity to the 3' end of the RSV template. The length requirement for CMV capped primers to be suitable for elongation varied between 12 and 20 nt, and those of 12-16 nt were optimal for elongation and generated more CMV-RSV chimeric mRNA transcripts. The original cap donors that were cleaved from CMV RNAs were predominantly short (10-13 nt). However, the CMV capped RNA leaders that underwent long-distance elongation were found to contain up to five repetitions of additional AC dinucleotides. Sequence analysis revealed that these AC dinucleotides were used to increase the size of short cap donors in multiple prime-and-realign cycles. Each prime-and-realign cycle added an AC dinucleotide onto the capped RNA leaders; thus, the original cap donors were gradually converted to longer capped RNA leaders (of 12-20 nt). Interestingly, the original 10 nt (or 11 nt) cap donor cleaved from CMV RNA1/2 did not undergo direct extension; only capped RNA leaders that had been increased to ≥12 nt were used for direct elongation. These findings suggest that this repetitive priming and realignment may serve to convert short capped CMV RNA leaders into longer, more suitable sizes to render a more stabilized transcription complex for elongation during RSV transcription initiation.

Negative-strand RNA viruses: the plant-infecting counterparts

While a large number of negative-strand (-)RNA viruses infect animals and humans, a relative small number have plants as their primary host. Some of these have been classified within families together with animal/human infecting viruses due to similarities in particle morphology and genome organization, while others have just recently been/or are still classified in floating genera. In most cases, at least two striking differences can still be discerned between the animal/human-infecting viruses and their plant-infecting counterparts which for the latter relate to their adaptation to plants as hosts. The first one is the capacity to modify plasmodesmata to facilitate systemic spread of infectious viral entities throughout the plant host. The second one is the capacity to counteract RNA interference (RNAi, also referred to as RNA silencing), the innate antiviral defence system of plants and insects. In this review an overview will be presented on the negative-strand RNA plant viruses classified within the families Bunyaviridae, Rhabdoviridae, Ophioviridae and floating genera Tenuivirus and Varicosavirus. Genetic differences with the animal-infecting counterparts and their evolutionary descendants will be described in light of the above processes.

Base-pairing promotes leader selection to prime in vitro influenza genome transcription

The requirements for alignment of capped leader sequences along the viral genome during influenza transcription initiation (cap-snatching) have long been an enigma. In this study, competition experiments using an in vitro transcription assay revealed that influenza virus transcriptase prefers leader sequences with base complementarity to the 3'-ultimate residues of the viral template, 10 or 11 nt from the 5' cap. Internal priming at the 3'-penultimate residue, as well as prime-and-realign was observed. The nucleotide identity immediately 5' of the base-pairing residues also affected cap donor usage. Application to the in vitro system of RNA molecules with increased base complementarity to the viral RNA template showed stronger reduction of globin RNA leader initiated influenza transcription compared to those with a single base-pairing possibility. Altogether the results indicated an optimal cap donor consensus sequence of (7m)G-(N)(7-8)-(A/U/G)-(A/U)-AGC-3'.

Preferential use of RNA leader sequences during influenza A transcription initiation in vivo

In vitro transcription initiation studies revealed a preference of influenza A virus for capped RNA leader sequences with base complementarity to the viral RNA template. Here, these results were verified during an influenza infection in MDCK cells. Alfalfa mosaic virus RNA3 leader sequences mutated in their base complementarity to the viral template, or the nucleotides 5' of potential base-pairing residues, were tested for their use either singly or in competition. These analyses revealed that influenza transcriptase is able to use leaders from an exogenous mRNA source with a preference for leaders harboring base complementarity to the 3'-ultimate residues of the viral template, as previously observed during in vitro studies. Internal priming at the 3'-penultimate residue, as well as "prime-and-realign" was observed. The finding that multiple base-pairing promotes cap donor selection in vivo, and the earlier observed competitiveness of such molecules in vitro, offers new possibilities for antiviral drug design.

Nucleotide sequence of melon yellow spot virus M RNA segment and characterization of non-viral sequences in subgenomic RNA

The nucleotide sequence of melon yellow spot virus (MYSV) M RNA segment was determined. The M RNA segment contains one open reading frame (ORF) encoding 308 amino acids (aa) in the sense orientation and another ORF encoding 1,127 aa in the complementary orientation, which were homologous to the NSm protein and G1/G2 glycoprotein precursor (Gp) protein, respectively. Amino acid sequences identities with the other tospovirus suggested that MYSV is closely related to groundnut bud necrosis virus and watermelon silver mottle virus. To analyze subgenomic RNA of the M RNA segment, RNA transcripts corresponding to the NSm and Gp genes were specifically amplified, and the nucleotide sequence of the 5' terminal region was determined. Sequence analysis of the NSm and Gp transcripts showed that they had a non-viral sequence 12-18 and 10-18 nucleotides long, respectively. Although these sequences varied considerably, in more than half of the cases, a cytosine residue was observed at the 3' end of the non-viral leader sequence, which suggests that the viral transcriptase prefers certain cap-donor sequences harboring a 3'CA dinucleotide.

Tomato spotted wilt virus transcriptase in vitro displays a preference for cap donors with multiple base complementarity to the viral template

Transcription of segmented negative-strand RNA viruses is initiated by cap snatching: a host mRNA is cleaved generally at 10-20 nt from its 5' capped end and the resulting capped leader used to prime viral transcription. For Tomato spotted wilt virus (TSWV), type species of the plant-infecting Tospovirus genus within the Bunyaviridae, cap donors were previously shown to require a single base complementarity to the ultimate or penultimate viral template sequence. More recently, the occurrence in vitro of "re-snatching" of viral mRNAs, i.e., the use of viral mRNAs as cap donors, has been demonstrated for TSWV. To estimate the relative occurrence of re-snatching compared to snatching of host mRNAs, the use of cap donors with either single, double, or multiple complementarity to the viral template was analyzed in pair-wise competition in TSWV in vitro transcription assays. A strong preference was observed for multiple-basepairing donors.

Tomato spotted wilt virus S-segment mRNAs have overlapping 3′-ends containing a predicted stem-loop structure and conserved sequence motif

The Tomato spotted wilt virus ambisense M- and S-RNA segments contain an A/U-rich intergenic region predicted to form a stable hairpin structure. The site of transcription termination of S-segment encoded N and NSs mRNAs synthesised in an in vitro transcription system was roughly mapped to the 3'-end of the intergenic hairpin, i.e. position 1568-1574 for N and position 1852-1839 for NSs, as determined by RT-PCR cloning and size estimation on Northern blots. This suggests that these viral transcripts contain a predicted stem-loop structure at their 3'-end. The potential involvement of the 3'-end structure in transcription termination is discussed.

Tospovirus-thrips interactions

The complex and specific interplay between thrips, tospoviruses, and their shared plant hosts leads to outbreaks of crop disease epidemics of economic and social importance. The precise details of the processes underpinning the vector-virus-host interaction and their coordinated evolution increase our understanding of the general principles underlying pathogen transmission by insects, which in turn can be exploited to develop sustainable strategies for controlling the spread of the virus through plant populations. In this review, we focus primarily on recent progress toward understanding the biological processes and molecular interactions involved in the acquisition and transmission of Tospoviruses by their thrips vectors.

In vitro transcription of Tomato spotted wilt virus is independent of translation

Ongoing transcriptionin vitroofTomato spotted wilt virus(TSWV) has previously been demonstrated to require the presence of reticulocyte lysate. This dependence was further investigated by testing the occurrence of transcription in the presence of two translation inhibitors: edeine, an inhibitor that still allows scanning of nascent mRNAs by the 40S ribosomal subunit, and cycloheximide, an inhibitor that completely blocks translation including ribosome scanning. Neither of these inhibitors blocked TSWV transcription initiation or elongationin vitro, as demonstrated byde novo-synthesized viral mRNAs with globin mRNA-derived leader sequences, suggesting that TSWV transcriptionin vitrorequires the presence of (a component within) reticulocyte lysate, rather than a viral protein resulting from translation.

Expression strategies of ambisense viruses

Among the negative RNA viruses, ambisense RNA viruses or 'ambisense viruses' occupy a distinct niche. Ambisense viruses contain at least one ambisense RNA segment, i.e. an RNA that is in part of positive and in part of negative polarity. Because of this unique gene organization, one might expect ambisense RNA viruses to borrow expression strategies from both positive and negative RNA viruses. However, they have little in common with positive RNA viruses, but possess many features of negative RNA viruses. Transcription and/or replication of their RNAs appear generally to be coupled to translation. Such coupling might be important to ensure temporal control of gene expression, allowing the two genes of an ambisense RNA segment to be differently regulated. Ambisense viruses can infect one host asymptomatically and in certain cases, they can lethally infect two hosts of a different kingdom. A possible model to explain the differential behavior of a given virus in different hosts could be that perturbation of the translation machinery would lead to differences in the severity of symptoms.

Purified tomato spotted wilt virus particles support both genome replication and transcription in vitro

Purified Tomato spotted wilt virus particles were shown to support either genome replication or transcription in vitro, depending on the conditions chosen. Transcriptional activity was observed only upon addition of rabbit reticulocyte lysate, indicating a dependence on translation. Under these conditions RNA molecules of subgenomic length were synthesized that hybridized to strand-specific probes for the N and NSs genes. Cloning of these transcripts demonstrated the presence of nonviral leader sequences at their 5' ends, confirming the occurrence of genuine viral transcription initiation known as "cap snatching." Sequence analyses revealed that both alpha- and beta-globin mRNA, present in the reticulocyte lysate, as well as added Alfalfa mosaic virus (AMV) RNA sequences, were utilized as cap donors. Moreover, an artificially produced N mRNA containing an AMV-derived leader was shown to be used as cap donor, indicating that resnatching of viral mRNAs takes place in vitro.

In vivo analysis of the TSWV cap-snatching mechanism: single base complementarity and primer length requirements

Requirements for capped leader sequences for use during transcription initiation by tomato spotted wilt virus (TSWV) were tested using mutant alfalfa mosaic virus (AMV) RNAs as specific cap donors in transgenic Nicotiana tabacum plants expressing the AMV replicase proteins. Using a series of AMV RNA3 mutants modified in either the 5'-non-translated region or in the subgenomic RNA4 leader, sequence analysis revealed that cleaved leader lengths could vary between 13 and 18 nucleotides. Cleavage occurred preferentially at an A residue, suggesting a requirement for a single base complementarity with the TSWV RNA template, which could be confirmed by analyses of host mRNAs used in vivo as cap donors.

Tomato spotted wilt virus-positive steps towards negative success

Abstract Taxonomy: Tomato spotted wilt virus (TSWV) is the type member of the plant-infecting Tospovirus genus in the family Bunyaviridae, a large group of predominantly vertebrate- and insect-infecting RNA viruses. Physical properties: Virions are 80-120-nm pleomorphic particles with surface projections composed of two viral glycoproteins, G1 and G2 (Fig. 1). Virion composition is 5% nucleic acid, 70% protein, 5% carbohydrate and 20% lipid. The genome consists of three negative or ambisense ssRNAs designated S (2.9 kb), M (4.8 kb) and L (8.9 kb), with partially complementary terminal sequences that allow the RNA to adopt a pseudocircular or panhandle conformation. Each genomic RNA is encapsidated by multiple copies of the viral nucleocapsid (N) protein to form ribonucleoprotein structures also known as nucleocapsids. The nucleocapsids are enclosed in a host-derived membrane bilayer along with an estimated 10-20 copies of the L protein, the putative RNA-dependent RNA polymerase. Hosts: Over 800 plant species, both dicots and monocots, in more than 80 plant families are susceptible to TSWV (Goldbach and Peters, 1994). The Solanaceae and Compositae families contain the largest numbers of susceptible plant species (Prins and Kormelink, 1998). TSWV also replicates in its insect vector, thrips (Thysanoptera: Thripidae) (Ullman et al., 1993; Wijkamp et al., 1993). Useful web site: http://www4.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/11050003.htm.