The distinct disease phenotypes of the common and yellow vein strains of Tomato golden mosaic virus are determined by nucleotide differences in the 3'-terminal region of the gene encoding the movement protein

VIGS Goes Viral: How VIGS Transforms Our Understanding of Plant Science

Virus-induced gene silencing (VIGS) has developed into an indispensable approach to gene function analysis in a wide array of species, many of which are not amenable to stable genetic transformation. VIGS utilizes the posttranscriptional gene silencing (PTGS) machinery of plants to restrain viral infections systemically and is used to downregulate the plant's endogenous genes. Here, we review the molecular mechanisms of DNA- and RNA-virus-based VIGS, its inherent connection to PTGS, and what is known about the systemic spread of silencing. Recently, VIGS-based technologies have been expanded to enable not only gene silencing but also overexpression [virus-induced overexpression (VOX)], genome editing [virus-induced genome editing (VIGE)], and host-induced gene silencing (HIGS). These techniques expand the genetic toolbox for nonmodel organisms even more. Further, we illustrate the versatility of VIGS and the methods derived from it in elucidating molecular mechanisms, using tomato fruit ripening and programmed cell death as examples. Finally, we discuss challenges of and future perspectives on the use of VIGS to advance gene function analysis in nonmodel plants in the postgenomic era.

Virus-induced gene silencing: empowering genetics in non-model organisms

Virus-induced gene silencing (VIGS) is an RNA interference-based technology used to transiently knock down target gene expression by utilizing modified plant viral genomes. VIGS can be adapted to many angiosperm species that cover large phylogenetic distances, allowing the analysis of gene functions in species that are not amenable to stable genetic transformation. With a vast amount of sequence information already available and even more likely to become available in the future, VIGS provides a means to analyze the functions of candidate genes identified in large genomic or transcriptomic screens. Here, we provide a comprehensive overview of target species and VIGS vector systems, assess recent key publications in the field, and explain how plant viruses are modified to serve as VIGS vectors. As many reports on the VIGS technique are being published, we also propose minimal reporting guidelines for carrying out these experiments, with the aim of increasing comparability between experiments. Finally, we propose methods for the statistical evaluation of phenotypic results obtained with VIGS-treated plants, as analysis is challenging due to the predominantly transient nature of the silencing effect.

Severe stunting in blackgram caused by the Mungbean yellow mosaic virus (MYMV) KA27 DNA B component is ameliorated by co-infection or post-infection with the KA22 DNA B: MYMV nuclear shuttle protein is the symptom determinant

Mungbean yellow mosaic virus-[India:Vigna] (MYMV-[IN:Vig]), a blackgram isolate of MYMV, has five variable and infective DNA B components of which KA22 and KA27 DNA Bs share only 72% nucleotide sequence identity between them. Agroinoculation of blackgram with partial dimers of DNA A and KA27 DNA B caused severe stunting and an inordinate delay in flowering. Interestingly, co-agroinoculation of KA27+KA22 DNA B components along with DNA A ameliorated severe stunting, rescued from the delay in flowering and caused the appearance of yellow mosaic symptom characteristic of KA22 DNA B. Post-agroinoculation of KA27 DNA B-infected blackgram plants with KA22 DNA B also resulted in the amelioration from severe stunting and in the alleviation from the delay in flowering. Alleviation from KA27 DNA B-type of symptom by co-infection or post-infection with KA22 DNA B did not result in a corresponding reduction in KA27 DNA B levels. Swapping of KA27 DNA B with the nuclear shuttle protein gene (NSP) of KA22 DNA B abolished severe stunting and caused the appearance of mild yellow symptom, suggesting that the NSP is the major symptom determinant in MYMV DNA B.

Cell-free construction of disarmed Abutilon mosaic virus-based gene silencing vectors

The bipartite Abutilon mosaic virus (AbMV) was engineered as a versatile silencing vector in which the coat protein gene of DNA A was deleted and replaced by sequences of interest. Plants transgenic for the dimeric AbMV DNA B component were used as test hosts to minimize the risk of unintended release of the recombinant DNA. The vector construct was stable genetically upon systemic infection and, in common with the parental virus, the vector remained phloem-limited. For virus-induced gene silencing (VIGS), a phytoene desaturase gene fragment was isolated from Nicotiana benthamiana (NbPDS) and inserted into the vector. After agroinfection, phytoene desaturase silencing was triggered efficiently in all leaf tissues without interference by viral symptoms. In order to facilitate further the use of the system, a technique for cell-free construction of recombinants was established using rolling circle amplification and biolistic inoculation of DNA B-transgenic plants. This novel procedure provides a convenient and safe way for delivering VIGS constructs for functional genomics.

Geminivirus C4 protein alters Arabidopsis development

The C4 protein of beet curly top virus [BCTV-B (US:Log:76)] induces hyperplasia in infected phloem tissue and tumorigenic growths in transgenic plants. The protein offers an excellent model for studying cell cycle control, cell differentiation, and plant development. To investigate the role of the C4 protein in plant development, transgenic Arabidopsis thaliana plants were generated in which the C4 transgene was expressed under the control of an inducible promoter. A detailed analysis of the developmental changes that occur in cotyledons and hypocotyls of seedlings expressing the C4 transgene showed extensive cell division in all tissues types examined, radically altered tissue layer organization, and the absence of a clearly defined vascular system. Induced seedlings failed to develop true leaves, lateral roots, and shoot and root apical meristems, as well as vascular tissue. Specialized epidermis structures, such as stomata and root hairs, were either absent or developmentally impaired in seedlings that expressed C4 protein. Exogenous application of brassinosteroid and abscisic acid weakly rescued the C4-induced phenotype, while induced seedlings were hypersensitive to gibberellic acid and kinetin. These results indicate that ectopic expression of the BCTV C4 protein in A. thaliana drastically alters plant development, possibly through the disruption of multiple hormonal pathways.

Genetic determinants of symptoms on viral DNA satellites

Begomovirus-DNA-beta disease complexes induce different symptom phenotypes in their hosts. To investigate the genetic determinants of the phenotypic differences, Nicotiana spp. and tomato plants were inoculated with infectious clones of Tobacco curly shoot virus (TbCSV)/TbCSV DNA-beta (TbCSB) and Tomato yellow leaf curl China virus (TYLCCNV)/TYLCCNV DNA-beta (TYLCCNB) pseudorecombinants and showed that TYLCCNB induced characteristic vein-thickening and enation symptoms, while TbCSB only slightly exacerbated the leaf-curling symptoms, regardless of the helper virus being used. The roles of DNA-beta-encoded betaC1 and a 430-nucleotide fragment containing the A-rich region and the putative betaC1 promoter region of the betaC1 gene (referred to as AP) in symptom development were further investigated by constructing hybrid satellites in which the betaC1 coding region or AP was exchanged between the two satellite molecules. A TYLCCNB hybrid with TbCSB betaC1 lost the ability to elicit the vein-thickening and enation phenotypes. TbCSB hybrids containing the TYLCCNB betaC1 or AP fragment failed to induce the characteristic vein thickening and enations. A TYLCCNB hybrid having the TbCSB AP fragment produced the enations, but the number of enations was less and their sizes were reduced. Differently from the phloem-specific pattern of the TYLCCNB promoter, a full-length fragment upstream of the TbCSB betaC1 gene confers a constitutive beta-glucuronidase expression pattern in transgenic tobacco plants. The above results indicate that the DNA-beta-encoded betaC1 protein is the symptom determinant, but the promoter of the betaC1 gene has influence on symptom production.

Three C-terminal phosphorylation sites in the Abutilon mosaic virus movement protein affect symptom development and viral DNA accumulation

The Abutilon mosaic virus (AbMV, Geminiviridae) DNA B component encodes a movement protein (MP), which facilitates viral transport within plants and affects pathogenicity. The presence of phosphorylated serine and threonine residues was confirmed for MP expressed in yeast and Nicotiana benthamiana by comparative Western blot analysis using phospho-amino acid- and MP-specific immunodetection. Mass spectrometry of yeast-derived MP identified three phosphorylation sites located in the C-terminal domain (Thr-221, Ser-223 and Ser-250). To assess their functional relevance in plants, several point mutations were generated in the MP gene of DNA B, which replace Thr-221, Ser-223 and Ser-250, either singly or in combinations, with either an uncharged alanine or a phosphorylation-mimicking aspartate residue. When co-inoculated with DNA A, all mutants were infectious. In systemically infected plants the symptoms and/or viral DNA accumulation were significantly altered for several of the mutants.

Geminiviruses

Plant pathogenic geminiviruses have been proliferating worldwide and have, therefore, attracted considerable scientific interest during the past three decades. Current knowledge concerning their virion and genome structure, their molecular biology of replication, recombination, transcription, and silencing, as well as their transport through plants and dynamic competition with host responses are summarized. The topics are chosen to provide a comprehensive introduction for animal virologists, emphasizing similarities and differences to the closest functional relatives, polyomaviruses and circoviruses.

Post-translational modifications of Abutilon mosaic virus movement protein (BC1) in fission yeast

The movement protein (MP) of Abutilon mosaic virus (AbMV, Geminiviridae) exhibited a complex band pattern upon gel electrophoresis indicating its post-translational modification when expressed in AbMV-infected plants or, ectopically, in fission yeasts. High-resolution separation according to charge and molecular weight in acetic acid/urea polyacrylamide or sodium dodecyl sulphate polyacrylamide gels followed by western blot analysis revealed a pattern of AbMV MP from infected plants more related to that from fission yeast than from bacteria. For this reason, expression in fission yeast was established as an experimental system to study post-translational modifications of AbMV MP. Metabolic labelling with 32P-orthophosphate confirmed a phosphorylation of all MP variants suggesting multiple phosphorylation sites. Treatment with calf intestinal alkaline phosphatase removed this label completely, but was unable to eliminate all protein bands with lower electrophoretic mobility. Thus, multiple phosphorylations contribute to the complex migration behaviour of MP, but additional post-translational modifications may occur as well.

Abutilon mosaic virus DNA B component supports mechanical virus transmission, but does not counteract begomoviral phloem limitation in transgenic plants

Different Nicotiana benthamiana lines stably transformed with Abutilon mosaic virus (AbMV) dimeric DNA B were capable of systemically spreading complete bipartite AbMV genomes, following agroinoculation of DNA A alone. Constitutively expressed viral movement protein (BC1) did not induce any persistent disease phenotype, but plants developed transient morphological abnormalities such as radially symmetric leaves after kanamycin withdrawal. Systemic AbMV infection produced symptoms and virus titers indistinguishable from those in non-transgenic plants. In systemically invaded leaves, the begomovirus remained phloem-limited, whereas the plants' susceptibility to mechanical transmission of AbMV was enhanced by a factor of three to five, as compared to non-transgenic controls. Hence, DNA B-encoded movement functions can complement local movement to the phloem after mechanical transmission, but fail to support viral invasion of non-phloem cells in systemically infected organs, indicating that the phloem restriction of AbMV does not result predominantly from a lack of transport competence in mesophyll tissues.

Tissue and cell tropism of Indian cassava mosaic virus (ICMV) and its AV2 (precoat) gene product

In order to establish defined viruses for challenging plants in resistance breeding programmes, Indian cassava mosaic virus (ICMV; family Geminiviridae) DNA clones were modified to monitor viral spread in plants by replacing the coat protein gene with the green fluorescent protein (GFP) reporter gene. Comparative in situ hybridization experiments showed that ICMV was restricted to the phloem in cassava and tobacco. GFP-tagged virus spread similarly, resulting in homogeneous fluorescence within nuclei and cytoplasm of infected cells. To analyze viral intercellular transport in further detail, GFP was fused to AV2, a protein that has been implicated in viral movement. Expressed from replicating viruses or from plasmids, AV2:GFP became associated with the cell periphery in punctate spots, formed cytoplasmic as well as nuclear inclusion bodies, the latter as conspicuous paired globules. Upon particle bombardment of expression plasmids, AV2:GFP was transported into neighboring cells of epidermal tissues showing that the intercellular transport of the AV2 protein is not restricted to the phloem. The results are consistent with a redundant function of ICMV AV2 acting as a movement protein, presumably as an evolutionary relic of a monopartite geminivirus that may still increase virus fitness but is no longer necessary in a bipartite genome. The fusion of ICMV ORF AV2 to the GFP gene is the first example of a reporter construct that follows the whole track of viral DNA from inside the nucleus to the cell periphery and to the next cell.

Arabidopsis mutants that suppress the phenotype induced by transgene-mediated expression of cauliflower mosaic virus (CaMV) gene VI are less susceptible to CaMV-infection and show reduced ethylene sensitivity

Protein P6 is the main symptom determinant of cauliflower mosaic virus (CaMV), and transgene-mediated expression in Arabidopsis induces a symptom-like phenotype in the absence of infection. Seeds of a P6-transgenic line, A7, were mutagenized by gamma-irradiation and M2 seedlings were screened for mutants that suppressed the phenotype of chlorosis and stunting. We identified four mutants that were larger and less chlorotic than the A7 parent but which contained an intact and transcriptionally active transgene. The two mutants with the strongest suppression phenotype, were recessive and allelic. The transgene was eliminated by back-crossing with wild-type Arabidopsis. In progeny lines that were homozygous for the putative suppressor mutation the proportion of plants becoming infected following inoculation with CaMV was 40% that of wild-type, although in plants that did become infected, levels of virus DNA in mutants and wild-type did not differ significantly. Symptoms in the mutants were milder and delayed although this was somewhat dependent on the virus isolate. This phenotype was inherited stably. Both mutant alleles showed a partially ethylene-insensitive phenotype in an ethylene triple response assay. P6-transgenic plants were also almost completely insensitive to ethylene in the triple response assay. We suggest that the chlorosis and stunting in P6-transgenic and CaMV-infected plants are dependent on interactions between P6 and components involved in ethylene signalling, and that the suppressor gene product may function to augment these interactions.

Genetic analysis of bipartite geminivirus tissue tropism

The bipartite geminiviruses bean golden mosaic virus (BGMV), cabbage leaf curl virus (CabLCV), and tomato golden mosaic virus (TGMV) exhibit differential tissue tropism in Nicotiana benthamiana. In systemically infected leaves, BGMV remains largely confined to vascular-associated cells (phloem-limited), whereas CabLCV and TGMV can escape into the surrounding mesophyll. Previous work established that TGMV BRi, the noncoding region upstream from the BR1 open reading frame (ORF), is required for mesophyll invasion, but the virus must also contain the TGMV AL23 or BL1/BR1 ORFs. Here we show that, in a BGMV-based hybrid virus, CabLCV AL23 also directed efficient mesophyll invasion in conjunction with TGMV BRi, which suggests that host-adaptation of AL23 is important for the phenotype. Cis-acting elements required for mesophyll invasion were delineated by analyzing BGMV-based hybrid viruses in which various parts of BRi were exchanged with those of TGMV. Interestingly, mesophyll invasion efficiency of hybrid viruses was not correlated with the extent of viral DNA accumulation. In conjunction with TGMV AL23, a 52-bp region of TGMV BRi with sequence homology to DNA A was sufficient for mesophyll invasion. This 52-bp sequence also directed mesophyll invasion in combination with the TGMV BL1/BR1 ORFs. Overall, these results are consistent with a model for mesophyll invasion in which AL2 protein, in association with host factors, acts through the 52-bp region in TGMV BRi to affect expression of the BR1 gene.