Infectious in vitro transcripts from cloned cDNA of a potyvirus, tobacco vein mottling virus

Development and application of sugarcane streak mosaic virus vectors

Sugarcane streak mosaic virus (SCSMV) is one of the major pathogens of sugarcane in the world. Molecular studies and disease management of SCSMV are hindered by the lack of efficient infectious clones. In this study, we successfully constructed Agrobacterium infiltration based infectious clone of SCSMV with different variants. Infectious clones of wild type SCSMV could efficiently infect Nicotiana benthamiana and sugarcane plants resulting in streak and mosaic symptoms on systemic leaves which were further confirmed with RT-PCR and serological assays. SCSMV variants of less adenylation displayed attenuated pathogenicity on N.benthamiana. SCSMV-based recombinant heterologous EGFP protein vector was also developed. The EGFP-tagged recombinant SCSMV could highly expressed in vegetative organs including roots. These infectious clones of SCSMV could be further developed for platform tools for both biotechnological studies and management of SCSMV disease.

Complete genome sequencing and construction of full-length infectious cDNA clone of papaya ringspot virus-HYD isolate and its efficient in planta expression

Papaya ringspot virus (PRSV) is a devastating Potyvirus that causes papaya ringspot disease in Carica papaya plantations globally. In this study, the complete genome sequence of a PRSV isolate from Shankarpalli, Telangana, India, was reported and designated as PRSV-HYD (KP743981.1). The genome is a single-stranded positive-sense RNA comprising 10,341 nucleotides. Phylogenetic analysis revealed that PRSV-HYD is closely related to PRSV Pune (Aundh) isolate with 92 and 95% nucleotide and amino acid sequence identity, respectively. To develop infectious cDNA (icDNA), the complete nucleotide sequence of PRSV-HYD was cloned between the right and left borders in the binary vector pCB301 using BglII and XmaI restriction sites. Cauliflower mosaic virus (CaMV) double promoter (35S) was fused at the 5'-end and Avocado sunblotch viroid (ASBVd) ribozyme (RZ) sequence was fused to the 3' end to generate an authentic 3' viral end in the transcribed mRNAs. The icDNA generated was mobilized into the Agrobacterium tumefaciens EHA 105, and the agrobacterial cultures were infiltrated into the natural host C. papaya and a non-host Nicotiana benthamiana plants; both did not show any symptoms. In RT-PCR analysis of RNAs isolated from N. benthamiana, we could detect viral genes as early as 3 days and continued up to 28 days post infiltration. Alternatively, virion particles were purified from agroinfiltrated N. benthamiana plants and introduced into C. papaya by mechanical inoculation as well as by pinprick method. In both cases, we could see visible systemic symptoms similar to that of wild type by 40 days. Additionally, we studied the expression patterns of the genes related to plant defense, transcription factors (TFs), and developmental aspects from both C. papaya and N. benthamiana.

OUP accepted manuscript

Potyviridae, the largest family of known RNA viruses (realm Riboviria), belongs to the picorna-like supergroup and has important agricultural and ecological impacts. Potyvirid genomes are translated into polyproteins, which are in turn hydrolyzed to release mature products. Recent sequencing efforts revealed an unprecedented number of potyvirids with a rich variability in gene content and genomic layouts. Here, we review the heterogeneity of non-core modules that expand the structural and functional diversity of the potyvirid proteomes. We provide a family-wide classification of P1 proteinases into the functional Types A and B, and discuss pretty interesting sweet potato potyviral ORF (PISPO), putative zinc fingers, and alkylation B (AlkB)—non-core modules found within P1 cistrons. The atypical inosine triphosphate pyrophosphatase (ITPase/HAM1), as well as the pseudo tobacco mosaic virus-like coat protein (TMV-like CP) are discussed alongside homologs of unrelated virus taxa. Family-wide abundance of the multitasking helper component proteinase (HC-pro) is revised. Functional connections between non-core modules are highlighted to support host niche adaptation and immune evasion as main drivers of the Potyviridae evolutionary radiation. Potential biotechnological and synthetic biology applications of potyvirid leader proteinases and non-core modules are finally explored.

Complete Genome Sequencing and Infectious cDNA Clone Construction of Soybean Mosaic Virus Isolated from Shanxi

Soybean mosaic virus (SMV) is the predominant viral pathogen that affects the yield and quality of soybean. The natural host range for SMV is very narrow, and generally limited to Leguminosae. However, we found that SMV can naturally infect Pinellia ternata and Atractylodes macrocephala. In order to clarify the molecular mechanisms underlying the crossfamily infection of SMV, we used double-stranded RNA extraction, rapid amplification of cDNA ends polymerase chain reaction and Gibson assembly techniques to carry out SMV full-length genome amplification from susceptible soybeans and constructed an infectious cDNA clone for SMV. The genome of the SMV Shanxi isolate (SMV-SX) consists of 9,587 nt and encodes a polyprotein consisting of 3,067 aa. SMV-SX and SMV-XFQ008 had the highest nucleotide and amino acid sequence identities of 97.03% and 98.50%, respectively. A phylogenetic tree indicated that SMV-SX and SMV-XFQ018 were clustered together, sharing the closest relationship. We then constructed a pSMV-SX infectious cDNA clone by Gibson assembly technology and used this clone to inoculate soybean and Ailanthus altissima; the symptoms of these hosts were similar to those caused by the virus isolated from natural infected plant tissue. This method of construction not only makes up for the time-consuming and laborious defect of traditional methods used to construct infectious cDNA clones, but also avoids the toxicity of the Potyvirus special sequence to Escherichia coli, thus providing a useful cloning strategy for the construction of infectious cDNA clones for other viruses and laying down a foundation for the further investigation of SMV cross-family infection mechanisms.

Home-made enzymatic premix and Illumina sequencing allow for one-step Gibson assembly and verification of virus infectious clones

An unprecedented number of viruses have been discovered by leveraging advances in high-throughput sequencing. Infectious clone technology is a universal approach that facilitates the study of biology and role in disease of viruses. In recent years homology-based cloning methods such as Gibson assembly have been used to generate virus infectious clones. We detail herein the preparation of home-made cloning materials for Gibson assembly. The home-made materials were used in one-step generation of the infectious cDNA clone of a plant RNA virus into a T-DNA binary vector. The clone was verified by a single Illumina reaction and a de novo read assembly approach that required no primer walking, custom primers or reference sequences. Clone infectivity was finally confirmed by Agrobacterium-mediated delivery to host plants. We anticipate that the convenient home-made materials, one-step cloning and Illumina verification strategies described herein will accelerate characterization of viruses and their role in disease development.

Construction of stable infectious full-length and eGFP-tagged cDNA clones of Mirabilis crinkle mosaic virus via In-Fusion cloning

Mirabilis crinkle mosaic virus (MiCMV) was tentatively classified as a new member of the genus Potyvirus in the family Potyviridae in 2019. However, it was considered to be basella rugose mosaic virus based on the sequence similarity of the coat protein (CP) region. In this study, infectious MiCMV cDNA clones under the control of the 35S promoter were constructed with an In-Fusion cloning method. Systemically infected leaves of Mirabilis jalapa and Nicotiana benthamiana plants inoculated with pMiCMV and pMiCMV-NIb/eGFP had mosaic symptoms by 5 dpi. Infections were confirmed by a western blot analysis, electron microscopy, RT-PCR, and the inoculation of N. benthamiana seedlings with progeny virions. Systemic infections were not observed after Nicotiana glutinosa leaves were similarly inoculated, with eGFP fluorescence detected only in the inoculated leaves. Interestingly, the symptoms induced by pMiCMV and pMiCMV-NIb/eGFP were not similar to those caused by the wild-type MiCMV in Basella rubra plants. Moreover, RT-PCR analyses of B. rubra plants with virus-specific primers (MicpF and MicpR) indicated that a non-target fragment corresponding to the MiCMV CP coding region was amplified. This is the first report of the construction of a biologically active, full-length cDNA copy of the MiCMV RNA genome.

Construction of Full-length Infectious cDNA Clones of Apple chlorotic leaf spot virus and Their Agroinoculation to Woody Plants by a Novel Method of Vacuum Infiltration

Construction and agroinoculation of full-length infectious cDNA clones of plant RNA viruses have been used in plant virology to prove Koch's postulates and for development of viruses as vectors for expressing foreign genes in plants. Four full-length cDNA clones (pIF3-12, pIF3-14, pIF3-15, and pIF3-19) of Apple chlorotic leaf spot virus (ACLSV) isolate 38/85 were produced. Two of the four full-length cDNA clones (pIF3-15 and pIF3-19) proved to be infectious on Nicotiana occidentalis 37B test plants by agroinoculation and were then mechanically transmissible to healthy N. occidentalis 37B. The genomic cDNAs of ACLSV pIF3-15 and pIF3-19 shared nucleotide identity of 77.5%, demonstrating mixed infections of multiple strains of ACLSV in the source tree of isolate 38/85. The two full-length cDNA clones were agroinoculated to apple seedlings by a newly developed vacuum infiltration method. The success rate of agroinoculation was greater than 78%, defined as the number of PCR positive seedlings to the number of apple seedlings that survived. ACLSV was transmissible from agroinoculated seedlings by cleft grafting. The results of this study will be useful for construction of infectious cDNA clones of plant viruses from full-length PCR fragments and agroinoculating woody host plants using the vacuum infiltration method outlined here.

Sequence analysis of six full-length bean yellow mosaic virus genomes reveals phylogenetic diversity in India strains, suggesting subdivision of phylogenetic group-IV

We report the complete genome sequence of five bean yellow mosaic virus (BYMV) isolates (CK-GL1, CK-GL3, CK-GL4, CK-GL5 and Vfaba2) that share 74.6-98.9% (nucleotide) and 81.5-99.1% (amino acid) identity with globally available BYMV sequences. Phylogenetic analysis clustered them specifically in BYMV phylogenetic group-IV within the existing nine groups. The CK-GL1, CK-GL2, CK-GL4 and CK-GL5 isolates formed a discrete cluster within group-IV. The present study suggests subdivision of group-IV into subgroup-IVa and IVb. Moreover, infectivity assays using in vitro RNA transcripts from subgroup-IVa (CK-GL3 isolate) and IVb (CK-GL1 isolate) showed distinct biological differences between the isolates supporting subdivision.

Recombination-based generation of the agroinfectious clones of Peanut stunt virus

Full-length cDNA clones of Peanut stunt virus strain P (PSV-P) were constructed and introduced into Nicotiana benthamiana plants via Agrobacterium tumefaciens. The cDNA fragments corresponding to three PSV genomic RNAs and satellite RNA were cloned into pGreen binary vector between Cauliflower mosaic virus (CaMV) 35S promoter and nopaline synthase (NOS) terminator employing seamless recombinational cloning system. The plasmids were delivered into A. tumefaciens, followed by infiltration of hosts plants. The typical symptoms on systemic leaves of infected plants similar to those of wild-type PSV-P were observed. The presence of the virus was confirmed by means of RT-PCR and Western blotting. Re-inoculation to N. benthamiana, Phaseolus vulgaris, and Pisum sativum resulted in analogous results. Generation of infectious clones of PSV-P enables studies on virus-host interaction as well as revealing viral genes functions.

Construction of an infectious clone of a plant RNA virus in a binary vector using one-step Gibson Assembly

The construction of full-length infectious clones of RNA viruses is often laborious due to the many cloning steps required and the DNA exclusion within the plasmid during Escherichia coli transformation. We demonstrate single-step cloning procedure of an infectious cDNA of the tomato blistering mosaic virus (ToBMV) using Gibson Assembly (GA), which drastically reduces the number of cloning steps. By agro-inoculation with the construct obtained by this procedure, ToBMV was recovered six days post-inoculation in Nicotiana benthamiana plants. The symptoms induced by the recovered virus were indistinguishable from those caused by the wild-type virus. We conclude that the GA is very useful method particularly to construct a full-length cDNA clone of a plant RNA virus in a binary vector.

Construction of infectious cDNA clones derived from the potyviruses clover yellow vein virus and bean yellow mosaic virus

Infectious cDNA clones are now indispensible tools for the genetic analysis of viral factors involved in viral virulence and host resistance. In addition, infectious cDNA-derived virus vectors that express foreign genes in infected plants enable the production of useful proteins at low cost and can confer novel crop traits. We constructed infectious cDNA clones derived from two potyviruses, Clover yellow vein virus and Bean yellow mosaic virus, which infect legume plants and cause disease. Here, we present our procedure for constructing these potyvirus infectious clones.

Multiple loci condition seed transmission of soybean mosaic virus (SMV) and SMV-induced seed coat mottling in soybean

Infection of soybean plants with Soybean mosaic virus (SMV), which is transmitted by aphids and through seed, can cause significant reductions in seed production and quality. Because seedborne infections are the primary sources of inoculum for SMV infections in North America, host-plant resistance to seed transmission can limit the pool of plants that can serve as sources of inoculum. To examine the inheritance of SMV seed transmission in soybean, crosses were made between plant introductions (PIs) with high (PI88799), moderate (PI60279), and low (PI548391) rates of transmission of SMV through seed. In four F(2) populations, SMV seed transmission segregated as if conditioned by two or more genes. Consequently, a recombinant inbred line population was derived from a cross between PIs 88799 and 548391 and evaluated for segregation of SMV seed transmission, seed coat mottling, and simple sequence repeat markers. Chromosomal regions on linkage groups C1 and C2 were significantly associated with both transmission of isolate SMV 413 through seed and SMV-induced seed coat mottling, and explained ≈42.8 and 46.4% of the variability in these two traits, respectively. Chromosomal regions associated with seed transmission and seed coat mottling contained homologues of Arabidopsis genes DCL3 and RDR6, which encode enzymes involved in RNA-mediated transcriptional and posttranscriptional gene silencing.

P1 peptidase--a mysterious protein of family Potyviridae

The Potyviridae family, named after its type member, Potato virus Y (PVY), is the largest of the 65 plant virus groups and families currently recognized. The coding region for P1 peptidase is located at the very beginning of the viral genome of the family Potyviridae. Until recently P1 was thought of as serine peptidase with RNA-binding activity and with possible influence in cell-to-cell viral spreading. This N-terminal protein, among all of the potyviruses, is the most divergent protein: varying in length and in its amino acid sequence. Nevertheless, P1 peptidase in many ways is still a mysterious viral protein. In this review, we would like to offer a comprehensive overview, discussing the proteomic, biochemical and phylogenetic views of the P1 protein.

Development of infectious transcripts from full-length and GFP-tagged cDNA clones of Pepper mottle virus and stable systemic expression of GFP in tobacco and pepper

A full-length cDNA clone (pSP6PepMoV-Vb1) of the genomic RNA of a Korean isolate of Pepper mottle virus (PepMoV-Vb1) was constructed downstream of a bacteriophage SP6 RNA polymerase promoter in the plasmid. In vitro RNA transcripts generated from pSP6PepMoV-Vb1 corresponded to PepMoV-Vb1 RNA (9641nt) with an extra guanosine residue at the 5' terminus and a 15-nt, poly (A) tract at the 3' end. The RNAs synthesized from the pSP6PepMoV-Vb1 clone, by in vitro run-off transcription in the presence of the 5' cap analog m(7)GpppG, were highly infectious in Nicotiana benthamiana and Capsicum annuum cv. Early Calwonder. Visible symptoms appeared at 4-5 days post-inoculation, at essentially the same time as occurred on these host plant species inoculated with wild-type PepMoV-Vb. Symptoms induced by progeny virus of the transcripts were indistinguishable from wild-type PepMoV-Vb on their experimental and natural hosts. The gene encoding the green fluorescent protein (GFP), turboGFP, was inserted between the coding regions for NIb and CP in the pSP6PepMoV-Vb1 clone. RNA transcripts of the resulting GFP-tagged clone, designated SP6PepMoV-Vb1/GFP, were highly infectious and symptoms were not different from those induced by either transcripts of pSP6PepMoV-Vb1 or wild-type PepMoV-Vb. However, GFP expression could be detected earlier than virus-induced symptom in plants infected by SP6PepMoV-Vb1/GFP. This study is the first report of the construction of a biologically active, full-length cDNA copy of the Pepper mottle virus RNA genome and the stable expression of a foreign gene within the modified virus.

Efficiency of VIGS and gene expression in a novel bipartite potexvirus vector delivery system as a function of strength of TGB1 silencing suppression

We have developed plant virus-based vectors for virus-induced gene silencing (VIGS) and protein expression, based on Alternanthera mosaic virus (AltMV), for infection of a wide range of host plants including Nicotiana benthamiana and Arabidopsis thaliana by either mechanical inoculation of in vitro transcripts or via agroinfiltration. In vivo transcripts produced by co-agroinfiltration of bacteriophage T7 RNA polymerase resulted in T7-driven AltMV infection from a binary vector in the absence of the Cauliflower mosaic virus 35S promoter. An artificial bipartite viral vector delivery system was created by separating the AltMV RNA-dependent RNA polymerase and Triple Gene Block (TGB)123-Coat protein (CP) coding regions into two constructs each bearing the AltMV 5' and 3' non-coding regions, which recombined in planta to generate a full-length AltMV genome. Substitution of TGB1 L(88)P, and equivalent changes in other potexvirus TGB1 proteins, affected RNA silencing suppression efficacy and suitability of the vectors from protein expression to VIGS.

Host-specific effect of P1 exchange between two potyviruses

The potyviruses Plum pox virus (PPV) and Tobacco vein mottling virus (TVMV) have distinct host ranges and induce different symptoms in their common herbaceous hosts. To test the relevance of the P1 protein in host compatibility and pathogenicity, hybrid viruses were constructed in which the P1 coding sequence of PPV was completely or partially replaced by the corresponding sequences from TVMV. Infections induced by these chimeric viruses revealed that the TVMV P1 and a PPV/TVMV hybrid P1 proteins are functionally equivalent in herbaceous plants to the P1 protein of a PPV isolate adapted to these hosts, in spite of having high sequence divergence. Moreover, the presence of TVMV P1 sequences enhanced the competence of a low-infectivity PPV-D-derived chimera in Nicotiana clevelandii. Conversely, all PPV/TVMV hybrids were unable to infect Prunus persicae, a specific host for PPV, suggesting that TVMV P1 is not functionally competent in this plant. Together, these data highlight the importance of the P1 protein in defining the virus host range.

Identification of a plum pox virus CI-interacting protein from chloroplast that has a negative effect in virus infection

The cylindrical inclusion (CI) protein of potyviruses is involved in virus replication and cell-to-cell movement. These two processes should rely on multiple plant-virus interactions; however, little is known about the host factors that are involved in, or that may interfere with, CI functions. By using a yeast two-hybrid system, the CI protein from Plum pox virus (PPV) was found to interact with the photosystem I PSI-K protein, the product of the gene psaK, of Nicotiana benthamiana. Coexpression of PPV CI was shown to cause a decrease in the accumulation level of PSI-K transiently expressed in N. benthamiana leaves. To test the biological relevance of this interaction, we have analyzed the infection of PPV in N. benthamiana plants in which psaK gene expression has been silenced by RNA interference, as well as in Arabidopsis thaliana psaK knockout plants. Our results show that downregulation of the psaK gene leads to higher PPV accumulation, suggesting a role for the CI-PSI-K interaction in PPV infection.

Construction of a stable and highly infectious intron-containing cDNA clone of plum pox potyvirus and its use to infect plants by particle bombardment

An infectious plum pox potyvirus cDNA clone was constructed placing a copy of the full-length sequence of the virus genome between an enhanced cauliflower mosaic virus 35S promoter and a nopaline synthase termination signal. Stabilization of the clone and faster growth of bacteria, in addition to higher plasmid yield, followed a modification consisting of the insertion of an intron which interrupted the viral open reading frame at the P3 region. This intron-containing clone was infectious when inoculated into plants after undergoing in vivo transcription and splicing. Particle bombardment delivery of the cDNA greatly increased the efficiency of plant infection.

Identification of a novel plant virus promoter using a potyvirus infectious clone

A putative promoter from the strawberry vein banding caulimovirus (SVBV) genome was identified by its ability to drive infection with full-length cDNA of the zucchini yellow mosaic RNA potyvirus (ZYMV). A high rate of infection was obtained with the cDNA under control of the SVBV promoter using particle bombardment technology. The SVBV promoter shows 60% homology to the cauliflower mosaic virus 35S promoter in the domain spanning the conserved motifs of CCACT (at -83) and the TATA box (at -31), to the transcription start. The 3'-end one-third of the putative promoter (328 bp) was sufficient to invoke full infectivity with the ZYMV clone, and drove transient reporter gene expression in Solanaceae and Cucurbitaceae transformed with a binary plant transformation vector. Stable expression of a reporter gene (GUS) under control of the truncated SVBV promoter was shown in transformed tobacco shoots in roots, leaves and stems.

Fully biologically active in vitro transcripts of the eriophyid mite-transmitted wheat streak mosaic tritimovirus

ABSTRACT Infectious RNA of wheat streak mosaic virus (WSMV) has been produced using a full-length cDNA clone as a template for in vitro transcription with SP6 RNA polymerase. Infectivity was dependent on the use of template plasmid DNA that had not undergone spontaneous rearrangement during amplification in Escherichia coli. The presence of WSMV in systemically infected wheat plants inoculated with in vitro transcripts was confirmed by reverse-transcription polymerase chain reaction of the WSMV P3 gene and by accumulation of WSMV coat protein as detected by immunoblotting. Maintenance of the full-length WSMV cDNA in the high copy number plasmid pUC18 was problematic because of spontaneous rearrangement of WSMV sequences during growth in liquid media for more than 8 h or if the clone was subcultured. Stability of the WSMV cDNA clone was improved by the use of the low copy number plasmid pACYC177, and it could be grown in large scale volumes (up to 1 liter) of liquid culture for 14 h without noticeable rearrangements. Both the original WSMV culture and the progeny virus derived from infectious in vitro transcripts were efficiently transmitted by the natural eriophyid mite vector Aceria tosichella. This is the first report of infectious in vitro transcripts for any eriophyid mite-transmitted plant virus and represents the only monopartite member of the family Potyviridae infecting monocotyledonous hosts for which infectious in vitro transcripts are available.

Context of the coat protein DAG motif affects potyvirus transmissibility by aphids

Previous work with tobacco vein mottling virus (TVMV) has established that a highly conserved three amino acid motif, asp-ala-gly (DAG), located near the N terminus of the coat protein (CP), is important for aphid transmission. However, several other potyviruses which have motifs other than DAG are aphid-transmissible. Creation of these motifs in TVMV through site-directed mutagenesis failed to render TVMV aphid-transmissible from infected plants, and the creation of a putative complementary motif in the helper component did not restore transmissibility. In an isolate of tobacco etch virus (TEV) that contains two consecutive DAG motifs separated by a single ala, transmissibility was abolished or reduced by mutations affecting the first motif, whereas mutations in the second motif had little or no effect. In a TEV mutant made non-transmissible due to an altered first motif, substitution of val for ala in the position immediately before the second DAG restored transmissibility, whereas changing val to ala in the location prior to the first DAG resulted in reduced TEV transmissibility. In contrast, a val to ala change in the position preceding the single DAG motif of TVMV did not affect transmission. Creation of another DAG motif at the beginning of the TVMV CP core, in a position where certain other potyviruses have a second DAG motif, did not restore transmissibility. Our results suggest that the mere presence of a DAG motif does not guarantee transmissibility and that the context in which the DAG or equivalent motif is found plays a role in the process.

Infectious virus in transgenic plants inoculated with a nonviable, P1-proteinase defective mutant of a potyvirus

A mutant (P1-616) of the tobacco vein mottling potyvirus that contains a four-codon insertion in the P1 protein coding region of the viral RNA is unable to infect the normal host plant of the virus. Processing of the P1/HC-Pro cleavage site does not occur during in vitro translation of the mutant viral RNA. When plants transformed with the P1/HC-Pro/P3 coding region of tobacco vein mottling potyvirus RNA were inoculated with P1-616, some of them became infected, although there was a delay in the production of disease symptoms. Virus isolated from these plants was able to infect nontransgenic plants. Two variants of the recovered, infectious virus contained single-nucleotide alterations in the four-codon insertion in the P1-616 genome. In vitro translation of the variant genomic RNAs resulted in partial processing of the P1/HC-Pro cleavage site, although serological analysis of infected tissue showed complete processing in vivo. These results indicate that limited complementation of P1-616 occurs in the transgenic plants and that eventually there arises one or more variants of the mutant sequence that can effect P1/HC-Pro processing and therefore be replicated.

Identification of viral genes required for cell-to-cell movement of southern bean mosaic virus

Inoculation of Vigna unguiculata (cowpea) with transcripts synthesized in vitro from a genome-length cDNA clone of the cowpea strain of southern bean mosaic virus (SBMV-C) resulted in a systemic SBMV-C infection of this host. Capped RNA was about five times more infectious than uncapped RNA as determined by a local lesion assay. The SBMV-C cDNA clone was also used for mutagenesis of the four SBMV-C open reading frames (ORFs). ORF1, ORF3, and coat protein (CP) mutants were not infectious in cowpea. Electroporation of cowpea protoplasts with mutant transcripts demonstrated that the ORF1, ORF3, and CP gene products were not required for SBMV-C RNA synthesis, and the ORF1 and ORF3 gene products were not required for SBMV-C assembly. From these results, it was concluded that the ORF1 and ORF3 proteins and the CP are required for SBMV-C cell-to-cell movement. One of the ORF3 mutants pSBMV2-UAA1833 contained a nonsense codon between the predicted -1 ribosomal frameshift site (SBMV-C nucleotides 1796-1802) and a potential ORF3 translation initiation codon at SBMV-C nucleotide 1895. The lack of infectivity of this mutant suggested that ORF3 was expressed by a -1 ribosomal frameshift in ORF2 rather than by initiation of translation at nucleotide 1895.

Infectivity of turnip mosaic potyvirus cDNA clones and transcripts on the systemic host Arabidopsis thaliana and local lesion hosts

Full-length cDNA clones of turnip mosaic virus were assembled under the control of T7 or 35S promoter. The 35S or nopaline synthase terminator signals were introduced downstream the full length cDNA controlled by 35S promoter. Both the capped in vitro transcripts from T7 controlled template, and the cDNAs from 35S controlled plasmids were infectious on Arabidopis thaliana plants according to systemically induced symptoms and to ELISA assays. The cDNAs from 35S controlled plasmids induced local lesions in Chenopodium amaranticolor and Chenopodium quinoa plants. A spontaneous silent C/T transition, giving rise to an additional SpeI restriction site, not present in the original viral RNA template, was used as a marker of the origin of infection.

A specific interaction between coat protein and helper component correlates with aphid transmission of a potyvirus

Specific binding between the coat protein (CP) and the helper component (HC) of the tobacco vein mottling potyvirus (TVMV) was characterized using a protein blotting-overlay protocol. In this in vitro assay, HC interacted with either virions or CP monomers originating from the aphid-transmissible TVMV-AT but not from the non-aphid-transmissible TVMV-NAT. There was a strong correlation between the aphid transmissibility of a series of TVMV variants having mutations in the DAG motif of the CP and their ability to bind HC. Expression of TVMV CP derivatives in bacteria allowed a precise determination of the minimum domain mediating HC binding. This domain is composed of seven amino acids, including the DAG motif (DTVDAGK), located in the N-terminus of the TVMV CP at amino acid positions 2 to 8.

Construction and analysis of infectious transcripts from a resistance-breaking strain of tobacco vein mottling potyvirus

The Burley tobacco (Nicotiana tabacum) cultivar TN 86 is "resistant" to most strains of tobacco vein mottling potyvirus (TVMV), the virus being restricted to epidermal cells of inoculated leaves. One strain, designated TVMV-S, overcomes this resistance and infects cv TN 86 systemically. To begin our investigation of the molecular basis for the resistance-breaking phenomenon, we have completed the cloning and sequencing of the TVMV-S RNA genome. The complete cDNA clone, under the control of a T7 RNA polymerase promoter, was used to produce infectious transcripts which were tested for their ability to reproduce the characteristics of TVMV-S RNA on three types of tobacco (N. tabacum cv TN 86, N. tabacum cv KY 14, and N. benthamiana). Timing of symptom appearance, symptom type, and titer of virus were identical to those of plants inoculated with TVMV-S RNA. As a step toward mapping the responsible genetic region(s) that contribute(s) to resistance-breaking by TVMV-S, the nucleotide and deduced amino acid sequences were compared to those of wild-type TVMV, a strain that does not overcome cv TN 86 resistance. Variant TVMV-S transcripts containing changes within the VPg cistron exhibited an altered pattern of infectivity on cv TN 86.

Helper-dependent vector transmission of plant viruses

A variety of noncirculatively transmitted viruses have evolved a vector transmission strategy that involves, in addition to virions, virus-encoded proteins that are not constituents of virions. These "helpers" and the genes encoding them have been characterized for viruses in the genera Potyvirus and Caulimovirus. Several lines of evidence support the hypothesis that these helpers act by mediating retention of virions in regions of the vector's alimentary tract from which they subsequently can be egested to initiate an infection. The possible advantage this convergently evolved strategy could confer to noncirculatively transmitted virus quasispecies is discussed.

Expression of multiple eukaryotic genes from a single promoter in Nicotiana

We engineered an expression unit composed of three eukaryotic genes driven by a single plant-active promoter and demonstrated functional expression in planta. The individual genes were linked as translational fusions to produce a polyprotein using spacer sequences encoding specific heptapeptide cleavage recognition sites for NIa protease of tobacco vein mottling virus (TVMV). The NIa gene itself was included as the second gene of the multi-gene unit. The first and third genes, obtained from the TR region of pTi15955, encoded enzymatic functions associated with the mannityl opine biosynthetic pathway. The mannityl opine conjugase gene (mas2) was the first unit of the construct and provided the native plant-active promoter and 5' untranslated regulatory sequence. The third gene (mas1), encoding the mannityl opine reductase, furnished the native 3' untranslated region. Cis-processing of the polyprotein by the NIa protease domain was demonstrated in vitro using rabbit reticulocyte lysate and wheat germ cell-free translation systems. Tobacco plant cells transformed with the multi-gene unit produced detectable levels of mannopine, mannopinic acid, and their biosynthetic intermediates, deoxyfructosyl-glutamate and deoxyfructosyl-glutamine. This indicates that the polygene construct results in a set of functional enzymatic activities that constitute a complete metabolic pathway.

Synthesis of an infectious full-length cDNA clone of rice yellow mottle virus and mutagenesis of the coat protein

A full-length cDNA clone of rice yellow mottle sobemovirus (RYMV) was synthesized and placed adjacent to a bacteriophage T7 RNA polymerase promoter sequence. Capped-RNA transcripts produced in vitro were infectious when mechanically inoculated onto rice plants (Oryza sativa L). Individual full-length clones varied in their degree of infectivity but all were less infectious than native viral RNA. A representative clone, designated RYMV-FL5, caused a disease phenotype identical to that produced by viral RNA except that symptoms were somewhat slower to appear than those induced by viral RNA. The infectivity of RYMV-FL5 was verified by ELISA, Western blot analysis, Northern blot hybridization, RT-PCR, and Southern blot hybridization. Frameshift and deletion mutations introduced into the coat protein cistron demonstrated that the coat protein was dispensable for RNA replication in rice protoplasts. However, the coat protein was required for full infectivity in rice plants, presumably by playing a role in phloem-mediated long-distance movement and possibly in cell-to-cell movement.

Mutational analysis of the helper component-proteinase gene of a potyvirus: effects of amino acid substitutions, deletions, and gene replacement on virulence and aphid transmissibility

We have previously provided evidence that amino acid substitutions within the N-terminal portion of the helper component-proteinase (HC-Pro) from tobacco vein mottling virus (TVMV), in particular at Lys-307, not only affect the aphid transmission activity of HC-Pro but also have a significant effect on TVMV virulence. In the present study amino acids which differ in their charge properties were substituted at position 307. A highly basic residue was required to retain helper component activity and virulence. Deletion and insertion mutagenesis in the 5' terminus of the HC-Pro gene suggested that this RNA domain may be an essential element for TVMV infectivity. Replacement of the TVMV HC-Pro gene with that from another potyvirus, zucchini yellow mosaic virus, maintained infectivity and aphid transmissibility of the chimeric virus, although symptoms were attenuated. Our results suggest that, in addition to its importance in aphid transmission, the HC-Pro gene may be of general importance in regulating virulence of potyviruses, possibly by interaction of these sequences with the host.

A determinant of disease symptom severity is located in the 3'-terminal noncoding region of the RNA of a plant virus

Inoculation of Nicotiana tabacum plants with RNA transcribed in vitro from a variant (pXBS8) of a cloned full-length DNA copy of tobacco vein mottling virus (TVMV) RNA resulted in attenuation of the vein mottling and blotching symptoms typically produced by transcripts of cloned wild-type cDNA (pXBS7). Similar amounts of virus were detected by ELISA (using anti-TVMV coat protein serum) in systemically infected leaves of plants inoculated with pXBS7 or pXBS8 transcripts. pXBS8 was shown to contain a 58-nucleotide segment in the sequence corresponding to the 3'-terminal untranslated region of TVMV RNA that was not present in pXBS7. This segment resulted in the appearance in pXBS8 transcripts of four adjacent direct repeats of a 14-nucleotide sequence, AUAAUUAUAUAUAU, that is present in the 3'-untranslated region of TVMV RNA, with two additional nucleotides (AU) between the first and second repeats. Insertion of restriction fragments containing the segment into pXBS7 and inoculation of plants with transcripts of the chimeric construct (pXBS78) resulted in the attenuated-symptom phenotype and was not accompanied by a reduced accumulation of virus in the plant as determined by ELISA and Northern blot analysis. When the extra nucleotides were removed from the variant clone, symptoms induced by transcripts of the cDNA (pXBS87) resembled those induced by wild-type transcripts. The results indicate that a noncoding region of the genome can have a direct effect on the induction of disease symptoms by an RNA virus.

Amino acid substitutions in the coat protein result in loss of insect transmissibility of a plant virus

Amino acids near the N terminus of the coat protein of tobacco vein mottling virus were deleted or altered by site-directed mutagenesis to determine the effect on aphid transmissibility of the virus. Deletion of a three amino acid sequence Asp-Ala-Gly, which is conserved in aphid-transmissible potyvirus isolates, abolished transmission. The mutation Ala----Thr in this triplet drastically reduced transmission, whereas the mutation Asp----Asn had no effect, and the mutation Asp----Lys consistently reverted to the wild-type residue. The mutation Lys----Glu, in the residue adjacent to the glycine of the triplet, drastically reduced transmission, whereas the mutation Gln----Pro, seven residues downstream from the glycine had no effect. Comparison of the sequences of other potyviruses suggests that the presence of a glycine residue at the third position of the Asp-Ala-Gly triplet is critical for aphid transmissibility and that certain changes in the residues adjacent to this position abolish or greatly reduce aphid transmissibility.

Strategies for expression of foreign genes in plants. Potential use of engineered viruses

Advances in gene transfer techniques for higher plants have already permitted important achievements towards crop protection and improvement using recombinant DNA technology. Besides plant genetic engineering, the possible use of plant viruses to express foreign genes could be of considerable interest to plant biotechnology. However, insuring containment of engineered viruses for environmental use is an important safety issue that must be addressed.

A tyrosine residue in the small nuclear inclusion protein of tobacco vein mottling virus links the VPg to the viral RNA

The identity of the amino acid residue that links the VPg of the potyvirus tobacco vein mottling virus (TVMV) to the viral RNA was determined. 32P-labeled TVMV RNA was digested with RNase A and micrococcal nuclease. The resulting 32P-labeled VPg was isolated and partially hydrolyzed with 6 N HCl at 110 degrees C for 2 h. Analysis by thin-layer electrophoresis revealed the presence of [32P]phosphotyrosine but not [32P]phosphoserine or [32P]phosphothreonine. Another preparation of TVMV RNA was treated with endoproteinase Lys-C, and the resulting peptide-RNA was purified by sodium dodecyl sulfate-sucrose gradient centrifugation. The sequence of the N-terminal 15 amino acid residues of the peptide, when compared with the RNA-derived amino acid sequence of the TVMV polyprotein, demonstrated that the peptide occurs in the small nuclear inclusion protein. These data suggest that Tyr-1860 of the polyprotein is the amino acid residue that links the TVMV VPg to the viral RNA.

Construction of full-length cDNA clones of cucumber mosaic virus RNAs 1, 2 and 3: generation of infectious RNA transcripts

Full-length cDNA copies of cucumber mosaic virus (CMV) RNAs 1 and 2 of the Fny strain were constructed from partial cDNA clones and were cloned downstream of bacteriophage T7 promoters. In one pair of clones, transcription proceeded from an unaltered T7 promoter such that in vitro transcripts representing RNAs 1 and 2 contained an additional 17 nucleotides at their 5' termini. In a second pair of clones, the T7 promoter/cDNA junction was altered by oligonucleotide-directed mutagenesis such that the in vitro transcripts contained only an additional G residue at their 5' ends. In addition, a full-length cDNA copy of Fny-CMV RNA 3 was constructed from two overlapping cDNA clones and was cloned downstream of an altered T7 promoter such that the resultant in vitro transcripts also contained only an additional G residue at their 5' ends. In vitro transcripts derived from all clones contained an additional C residue at their 3' ends. In vitro transcripts representing RNAs 1, 2 and 3 which contained an additional residue at each terminus were shown to be infectious together in several hosts of CMV.

Expression in transgenic plants of a viral gene product that mediates insect transmission of potyviruses

Helper component (HC) is a virus-encoded nonstructural protein that is required for transmission of potyviruses by their aphid vectors. As a prelude to studies on the molecular basis of HC activity, a cDNA clone (pPB-3) was constructed that contained the first three cistrons (34 kDa-HC-42 kDa) of the RNA genome of the potyvirus tobacco vein mottling virus, the first six nucleotides of the adjacent cylindrical inclusion body protein cistron, and a synthetic translation termination codon. This construction was introduced into tobacco cells via a Ti plasmid-based vector. Northern blot analysis of transgenic plants demonstrated the presence of an RNA of the size expected from the construction of pPB-3, and Western blot analysis revealed the presence of a protein that comigrated with authentic HC, indicating that the proteolytic activity necessary to produce mature-sized HC was encoded by pPB-3. The HC produced in the transgenic plants was demonstrated to be active in a virus transmission bioassay with aphids.