Post-transcriptional silencing of chalcone synthase in petunia using a geminivirus-based episomal vector

MAP30 transgenic tobacco lines: from silencing to inducing

BACKGROUND

DNA methylation is one of the most important epigenetic event that regulates gene expression. In addition to DNA methylation, transgene copy number may induce gene silencing. Therefore, the study of these cases is useful for understanding of gene silencing regulation.

METHODS AND RESULTS

In this study, the methylation pattern of 35S promoter was investigated in the second generation of MAP30 transgenic tobacco lines. Therefore, the genomic DNA melting curve changes were investigated before and after bisulfite treatment by real time PCR. To determine the exact position of methylation, the samples were sequenced after bisulfite treatment. Observation of decrease in DNA melting curve of expressing line in comparison with silenced line confirmed the presence of DNA methylation in silenced line. In order to induce the MAP30 expression, the silenced line was treated using different concentrations of Azacytidine and green tea extracts. The results showed that all concentrations of green tea extracts for 6 days and the concentrations of 3 and 10 μM Azacytidine for 10 and 3 days could induce the expression of MAP30 in silenced line respectively. Finally, the transgene copy number was estimated using real time PCR, as silenced line contained more than two copies while the lines expressing MAP30 contained only one or two copies.

CONCLUSIONS

Finally, we found that the presence of DNA methylation and also multiple gene copy numbers in silenced line have been led to gene silencing. Moreover, the effect of green tea extract on DNA methylation showed incredible results for the first time.

Localization of Tobacco Yellow Dwarf Virus Replication Using the In Plant Activation (INPACT) Expression Platform

Geminiviruses and their diseases are a considerable economic threat to a vast number of crops worldwide. Investigating how and where these viruses replicate and accumulate in their hosts may lead to novel molecular resistance strategies. In this study, we used the Rep-inducible In Plant Activation (INPACT) expression platform, based on the genome of tobacco yellow dwarf virus (TYDV), to determine where this model mastrevirus replicates in its host tobacco. By developing an infectious clone of TYDV and optimizing its delivery by agroinfiltration, we first established an efficient artificial infection process. When delivered into transgenic tobacco plants containing a TYDV-based INPACT cassette encoding the β-glucuronidase (GUS) reporter, we showed the virus activates GUS expression. Histology revealed that reporter gene expression was limited to phloem-associated cell types suggesting TYDV replication has a restricted tissue tropism.

The activities of four constitutively expressed promoters in single-copy transgenic rice plants for two homozygous generations

We have characterized four novel constitutive promoters ARP1, H3F3, HSP and H2BF3 that are active in all tissues/stages of transgenic plants and stable over two homozygous generations. Gene promoters that are active and stable over several generations in transgenic plants are valuable tools for plant research and biotechnology. In this study, we characterized four putative constitutive promoters (ARP1, H3F3, HSP and H2BF3) in transgenic rice plants. Promoter regions were fused to the green fluorescence protein (GFP) reporter gene and transformed into rice. Single-copy transgenic lines were then selected and promoter activity was analyzed in various organs and tissues of two successive homozygous generations. All four promoters showed a broad expression profile in most tissues and developmental stages, and indeed the expression of the ARP1 and H3F3 promoters was even greater than that of the PGD1 promoter, a previously described constitutive promoter that has been used in transgenic rice. This observation was based on expression levels in leaves, roots, dry seeds and flowers in both the T2 and T3 generations. Each promoter exhibited comparable levels of activity over two homozygous generations with no sign of transgene silencing, which is an important characteristic of promoters to be used in crop biotechnology applications. These promoters therefore have considerable potential value for the stable and constitutive expression of transgenes in monocotyledonous crops.

Virus-induced gene silencing (VIGS) in plants: an overview of target species and the virus-derived vector systems

The analysis of gene functions in non-model plant species is often hampered by the fact that stable genetic transformation to downregulate gene expression is laborious and time-consuming, or, for some species, even not achievable. Virus-induced gene silencing (VIGS) can serve as an alternative to mutant collections or stable transgenic plants to allow the characterization of gene functions in a wide range of angiosperm species, albeit in a transient way. VIGS vector systems have been developed from both RNA and DNA plant viral sources to specifically silence target genes in plants. VIGS is nowadays widely used in plant genetics for gene knockdown due to its ease of use and the short time required to generating phenotypes. Here, we summarize successfully targeted eudicot and monocot plant species along with their specific VIGS vector systems which are already available for researchers.

Characterization of the stress-inducible OsNCED3 promoter in different transgenic rice organs and over three homozygous generations

To be effective in crop biotechnology applications, gene promoters need to be stably active over sequential generations in a population of single-copy transgenic lines. Most of the stress-inducible promoters characterized in plants thus far have been analyzed at early (T₀, T₁ or T₂) generations and/or by testing only a small number of transgenic lines. In our current study, we report our analysis of OsNCED3, a stress-inducible rice promoter involved in ABA biosynthesis, in various organs and tissues of transgenic rice plants over the T(2-4) homozygous generations. The transgene copy numbers in the lines harboring the OsNCED3:gfp construct were determined and six single- and two double-copy transgenic lines were analyzed for promoter activity in comparison with the Wsi18, a stress-inducible promoter previously characterized. The exogenous promoter activities were found to be significantly enhanced in the roots and leaves, whereas zero or low levels of activity were evident in grains and flowers, under drought and high-salinity conditions. The highest induction levels of gfp transcripts in the OsNCED3:gfp plants upon drought treatments were 161- and 93-fold in leaves and roots, respectively, and these levels were comparable with those of gfp transcripts in the Wsi18:gfp plants. A comparison of the promoter activities between the T₂-T₄ plants revealed that comparable activity levels were maintained over these three homozygous generations with no evidence of silencing. Thus, our results provide the OsNCED3 promoter that is stress-inducible in a whole rice plant except for in the aleurones and endosperm and stably active over three generations.

Analysis of the APX, PGD1 and R1G1B constitutive gene promoters in various organs over three homozygous generations of transgenic rice plants

We have previously characterized the constitutively active promoters of the APX, PGD1 and R1G1B genes in rice (Park et al. 2010 in J Exp Bot 61:2459-2467). To have potential crop biotechnology applications, gene promoters must be stably active over many generations. In our current study, we report our further detailed analysis of the APX, PGD1 and R1G1B gene promoters in various organs and tissues of transgenic rice plants for three (T₃₋₅) homozygous generations. The copy numbers in 37 transgenic lines that harbor promoter:gfp constructs were determined and promoter activities were measured by real-time qPCR. Analysis of the 37 lines revealed that 15 contained a single copy of one of the three promoter:gfp chimeric constructs. The promoter activity levels were generally higher in multi-copy lines, whereas variations in these levels over the T₃₋₅ generations studied were observed to be smaller in single-copy than in multi-copy lines. The three promoters were further found to be highly active in the whole plant body at both the vegetative and reproductive stages of plant growth, with the exception of the APX in the ovary and R1G1B in the pistil and filaments where zero or very low levels of activity were detected. Of note, the spatial activities of the PGD1 promoter were found to be strikingly similar to those of the ZmUbi1, a widely used constitutive promoter. Our comparison of promoter activities between T₃, T₄ and T₅ plants revealed that the APX, PGD1 and R1G1B promoters maintained their activities at comparable levels in leaves and roots over three homozygous generations and are therefore potentially viable alternative promoters for crop biotechnology applications.

[Virus-induced gene silencing as a tool for analysis of gene functions in plants]

Virus-induced gene silencing (VIGS) is a technology that exploits an RNA-mediated antivirus defense mechanism in plants and has been shown to have great potential in plant reverse genetics. When the virus vector carries sequences of plant genes, virus infection triggers VIGS that results in the degradation of endogenous mRNAs homologous to the plant genes. The system is well established in Nicotiana benthamiana and several reliable VIGS vectors have been developed for other plant species including important agricultural crops. Here, we describe the use of VIGS technology to determine gene function and plant virus vectors for induction of VIGS in plants.

Efficient and stable expression of GFP through Wheat streak mosaic virus-based vectors in cereal hosts using a range of cleavage sites: formation of dense fluorescent aggregates for sensitive virus tracking

A series of Wheat streak mosaic virus (WSMV)-based expression vectors were developed by engineering a cycle 3 GFP (GFP) cistron between P1 and HC-Pro cistrons with several catalytic/cleavage peptides at the C-terminus of GFP. WSMV-GFP vectors with the Foot-and-mouth disease virus 1D/2A or 2A catalytic peptides cleaved GFP from HC-Pro but expressed GFP inefficiently. WSMV-GFP vectors with homologous NIa-Pro heptapeptide cleavage sites did not release GFP from HC-Pro, but efficiently expressed GFP as dense fluorescent aggregates. However, insertion of one or two spacer amino acids on either side of NIb/CP heptapeptide cleavage site or deletion in HC-Pro cistron improved processing by NIa-Pro. WSMV-GFP vectors were remarkably stable in wheat for seven serial passages and for 120 days postinoculation. Mite transmission efficiencies of WSMV-GFP vectors correlated with the amount of free GFP produced. WSMV-GFP vectors infected the same range of cereal hosts as wild-type virus, and GFP fluorescence was detected in most wheat tissues.

Grapevine virusA-mediated gene silencing in Nicotiana benthamiana and Vitis vinifera

Virus-induced gene silencing (VIGS) is an attractive approach for studying gene function. Although the number of virus vectors available for use in VIGS experiments has increased in recent years, most of these vectors are applied in annual or herbaceous plants. The aim of this work was to develop a VIGS vector based on the Grapevine virus A (GVA), which is a member of the genus Vitivirus, family Flexiviridae. The GVA vector was used to silence the endogenous phytoene desaturase (PDS) gene in Nicotiana benthamiana plants. In addition, an Agrobacterium-mediated method for inoculating micropropagated Vitis vinifera cv. Prime plantlets via their roots was developed. Using this method, it was possible to silence the endogenous PDS gene in V. vinifera plantlets. The GVA-derived VIGS vector may constitute an important tool for improving functional genomics in V. vinifera.

Coat protein gene sequence analysis of potato virus X and potato virus Y: conserved regions to design gene silencing cassette

Potato virus X(PVX) and Potato virus Y(PVY) are two of the three most prevalent viruses that cause significant yield declines in potato. Twenty-seven PVX and thirty-seven PVY accessions were analyzed for nucleotide sequence variation of the coat protein gene. The average and variance of genetic distance for PVX were estimated at 0.118 and 0.004 and 0.118 and 0.005 for PVY using the neighbour joining method. Results of phylogenetic trees and their certification via stepwise discriminant analysis led us to classify of PVX sequences in four groups and PVY sequences in three groups. One purpose of this project was to determine suitable conserved regions to make of gene silencing constructs. Length of identified conserved regions were enough to silence of the virus coat protein genes on infected plants, many of which were located consequently with short gap spacers. In this term, some of groups were divided into subgroups to obtain conserved regions under minimum length of25 nt, enough length to design specific diagnostic-primers.

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.

A stable RNA virus-based vector for citrus trees

Virus-based vectors are important tools in plant molecular biology and plant genomics. A number of vectors based on viruses that infect herbaceous plants are in use for expression or silencing of genes in plants as well as screening unknown sequences for function. Yet there is a need for useful virus-based vectors for woody plants, which demand much greater stability because of the longer time required for systemic infection and analysis. We examined several strategies to develop a Citrus tristeza virus (CTV)-based vector for transient expression of foreign genes in citrus trees using a green fluorescent protein (GFP) as a reporter. These strategies included substitution of the p13 open reading frame (ORF) by the ORF of GFP, construction of a self-processing fusion of GFP in-frame with the major coat protein (CP), or expression of the GFP ORF as an extra gene from a subgenomic (sg) mRNA controlled either by a duplicated CTV CP sgRNA controller element (CE) or an introduced heterologous CE of Beet yellows virus. Engineered vector constructs were examined for replication, encapsidation, GFP expression during multiple passages in protoplasts, and for their ability to infect, move, express GFP, and be maintained in citrus plants. The most successful vectors based on the 'add-a-gene' strategy have been unusually stable, continuing to produce GFP fluorescence after more than 4 years in citrus trees.

Improved expression of recombinant GFP using a replicating vector based on Beet curly top virus in leaf-disks and infiltrated Nicotiana benthamiana leaves

Recombinant green fluorescent protein (GFP) with a molecular mass of 29 kDa was transiently expressed in Agrobacterium-inoculated leaf-disks prepared from Nicotiana benthamiana plants. Expression of GFP from the Cauliflower mosaic virus (CaMV) 35 S promoter within a replicating vector based on the geminivirus Beet curly top virus (BCTV) was more than 3 times higher than from a control, non-replicating vector. Use of the Cassava vein mosaic virus (CsVMV) promoter in the BCTV replicating vector increased the expression of recombinant GFP 320% at the transcript level, compared to use of the control CaMV 35 S promoter. Expression of recombinant GFP from Agrobacterium-inoculated leaf-disks of N. benthamiana was further enhanced up to 240% in the presence of post-transcriptional gene silencing suppressor p19.

Agrobacterium-mediated viral vector-amplified transient gene expression in Nicotiana glutinosa plant tissue culture

A viral vector based on the bean yellow dwarf virus was investigated for its potential to increase transient gene expression. An intron-containing GUS reporter gene and the cis-acting viral regulatory elements were incorporated in the viral vector and could be complemented by the viral replication-associated proteins provided on a secondary vector. All vectors were delivered to Nicotiana glutinosa plant cell suspension or hairy root cultures via auxotrophic Agrobacterium tumefaciens. Cell culture generated greater yield of reporter gene expression than did root culture, as a result of the limitation imposed on roots to express the protein only in surface tissue containing actively dividing cells. Reporter gene expression increased for cell culture when the reporter gene construct was co-delivered with the construct supplying both viral replication associated proteins (REP and REPA); gene expression decreased when the construct supplying only the viral REP protein was co-delivered. Reporter protein expression increased from 0.091% for the reporter construct alone to 0.22% total soluble protein (% TSP) when the viral Rep-supplying vector was co-delivered with the reporter gene construct. Reporter protein was generated 3 days after the initiation of bacterial co-culture, providing for rapid generation of heterologous protein in cell culture.

Analysis of transitive RNA silencing after grafting in transgenic plants with the coat protein gene of Sweet potato feathery mottle virus

We have previously reported the graft transmission of target specificity for RNA silencing using transgenic Nicotiana benthamiana plants expressing the coat protein gene (CP, including the 3' non-translated region) of Sweet potato feathery mottle virus. Transgenic plants carrying the 5' 200 and 400 bp regions of CP were newly produced. From these plants, two silenced and two non-silenced lines were selected to investigate the manifestation of transitive RNA silencing by graft experiments. Non-silenced scions carrying the entire transgene were grafted onto either 5' or 3' silencing inducer rootstocks. When non-silenced scions were grafted onto 5' silencing inducer rootstocks, RNA silencing was induced in the non-silenced scions and spread toward the 3' region of the transgene mRNA. Similarly, when non-silenced scions were grafted onto 3' silencing inducer rootstocks, RNA silencing was induced in the non-silenced scions, but was restricted to the 3' region of the transgene and did not spread to the 5' region. In addition, results from crossing experiments, involving non-silenced and 3' silencing inducer plants, confirmed the above finding. This indicates that RNA silencing spreads in the 5'-3' direction, not in the 3'-5' direction, along the transgene mRNA.

Analysis of silencing escape of tomato leaf curl virus: an evaluation of the role of DNA methylation

RNA silencing is a sequence-specific mechanism regulating gene expression and has been used successfully for antiviral defense against RNA viruses. Similar strategies to develop resistance against DNA containing Tomato leaf curl virus (TLCV) and some other geminiviruses have been unsuccessful. To analyze this silencing escape, we transformed tomato plants with a hairpin construct from the TLCV C2 open reading frame (ORF). The transgenic plants showed a strong RNA silencing response, and following TLCV inoculation, their infection was delayed. However, the viral infection was not prevented and TLCV DNA accumulated to the levels found in nontransgenic plants. To determine the fate of a transgene carrying homology to the virus, we used transgenic plants carrying the TLCV C4 gene, which induces a distinct phenotype. Upon TLCV infection, the phenotype was abolished and C4 transcript disappeared. Concurrently, TLCV-specific small interfering RNAs were produced. In situ hybridization showed abundant levels of TLCV DNA in phloem cells of TLCV-infected C4 transgenic plants. However, the C4 transcripts were no longer detectable in nonvascular cells. Analysis of the transgene by methylation sequencing revealed a high level of de novo methylation of asymmetric cytosines in both the C4 ORF and its 35S promoter. A high level of methylation also was found at both symmetric and asymmetric cytosines of the complementary-sense strand of TLCV double-stranded DNA. Given the previous finding that methylated geminiviral DNA is not competent for replication, we provide a model whereby TLCV evades host defense through a population of de novo synthesized unmethylated DNA.

Bean Yellow Dwarf Virus replicons for high-level transgene expression in transgenic plants and cell cultures

A novel stable transgenic plant expression system was developed using elements of the replication machinery of Bean Yellow Dwarf Virus (BeYDV). The system contains two transgenes: 1) The BeYDV replicon vector with an expression cassette flanked by cis-acting DNA elements of BeYDV, and 2) The viral replication initiator protein (Rep) controlled by an alcohol-inducible promoter. When Rep expression was triggered by treatment with ethanol, it induced release of the BeYDV replicon from stably integrated T-DNA and episomal replication to high copy number. Replicon amplification resulted in substantially increased transgene mRNA levels (up to 80-fold) and translation products (up to 10-fold) after induction of Rep expression by ethanol treatment in tobacco NT1 cells and leaves of whole potato plants. Thus, the BeYDV stable transformant replicon system is a powerful tool for plant-based production of recombinant proteins.

A versatile transreplication-based system to identify cellular proteins involved in geminivirus replication

A versatile green fluorescent protein (GFP) expression cassette containing the replication origins of the monopartite begomovirus Tomato yellow leaf curl Sardinia virus (TYLCSV) is described. Transgenic Nicotiana benthamiana plants containing one copy of the cassette stably integrated into their genome were superinfected with TYLCSV, which mobilized and replicated the cassette as an episomal replicon. The expression of the reporter gene (the GFP gene) was thereby modified. Whereas GFP fluorescence was dimmed in the intercostal areas, an increase of green fluorescence in veins of all leaves placed above the inoculation site, as well as in transport tissues of roots and stems, was observed. The release of episomal trans replicons from the transgene and the increase in GFP expression were dependent on the cognate geminiviral replication-associated protein (Rep) and required interaction between Rep and the intergenic region of TYLCSV. This expression system is able to monitor the replication status of TYLCSV in plants, as induction of GFP expression is only produced in those tissues where Rep is present. To further confirm this notion, the expression of a host factor required for geminivirus replication, the proliferating cellular nuclear antigen (PCNA) was transiently silenced. Inhibition of PCNA prevented GFP induction in veins and reduced viral DNA. We propose that these plants could be widely used to easily identify host factors required for geminivirus replication by virus-induced gene silencing.

Silencing suppression by geminivirus proteins

RNA silencing is an RNA-directed gene regulatory system that is present in a wide range of eukaryotes, and which functions as an antiviral defense in plants. Silencing pathways are complex and partially overlapping, but at least three basic classes can be distinguished: cytoplasmic RNA silencing (or post-transcriptional gene silencing; PTGS) mediated by small interfering RNAs (siRNAs), silencing mediated by microRNAs (miRNAs), and transcriptional gene silencing (TGS) mediated by siRNA-directed methylation of DNA and histone proteins. Recent advances in our understanding of different geminivirus silencing suppressors indicate that they can affect all three pathways, suggesting that multiple aspects of silencing impact geminivirus replication.

Engineering the genome of Grapevine virus A into a vector for expression of proteins in herbaceous plants

Grapevine virus A (GVA), a species of the genus Vitivirus, consists of a approximately 7.4 kb single-stranded RNA genome of positive polarity, organized into five open reading frames (ORFs). In addition to grape varieties, GVA infects Nicotiana benthamiana plants and protoplasts. We engineered the genome of GVA as a vector that includes duplication of homologous sequences that contain the promoter of the movement protein (MP) sgRNA, supplemented by enzymatic restriction sites to be used as a convenient tool for transient expression of foreign genes from an individual sgRNA. The resulting vector was able to infect and to move in N. benthamiana plants in a manner similar to the wild-type GVA, but it was not stable and the inserted sequence was lost from the genome. Replacing the duplicated promoter with a GVA-MP promoter derived from a distantly related isolate of GVA improved the stability of the inserted sequence. The resulting vector was successfully used to express the reporter gene beta-glucuronidase (GUS) and the coat protein gene of Citrus tristeza virus in inoculated N. benthamiana plants. Development of a useful GVA vector is expected to find a use as a biotechnological tool for improvement of grapevines and it may enable vine breeders to bypass obstacles involved in genetic manipulation of perennial and fruiting plants.

Exploiting chinks in the plant's armor: evolution and emergence of geminiviruses

The majority of plant-infecting viruses utilize an RNA genome, suggesting that plants have imposed strict constraints on the evolution of DNA viruses. The geminiviruses represent a family of DNA viruses that has circumvented these impediments to emerge as one of the most successful viral pathogens, causing severe economic losses to agricultural production worldwide. The genetic diversity reflected in present-day geminiviruses provides important insights into the evolution and biology of these pathogens. To maximize replication of their DNA genome, these viruses acquired and evolved mechanisms to manipulate the plant cell cycle machinery for DNA replication, and to optimize the number of cells available for infection. In addition, several strategies for cell-to-cell and long-distance movement of the infectious viral DNA were evolved and refined to be compatible with the constraints imposed by the host endogenous macromolecular trafficking machinery. Mechanisms also evolved to circumvent the host antiviral defense systems. Effectively combatting diseases caused by geminiviruses represents a major challenge and opportunity for biotechnology.

Chalcone synthase as a reporter in virus-induced gene silencing studies of flower senescence

Agrobacterium-mediated infection of petunia (Petunia hybrida) plants with tobacco rattle virus (TRV) bearing fragments of Petunia genes resulted in systemic infection and virus-induced gene silencing (VIGS) of the homologous host genes. Infection with TRV containing a phytoene desaturase (PDS) fragment resulted in reduced abundance of PDS transcripts and typical photobleaching of photosynthetic tissues. Infection with TRV containing a chalcone synthase (CHS) fragment resulted in silencing of anthocyanin production in infected flowers. The silencing phenotype ranged from scattered white spots on the normal purple background to entirely white flowers. Symptoms in the V26 cultivar were a diffuse mosaic, but infection of some purple-flowered commercial cultivars resulted in large white sectors and even entirely white flowers. Abundance of CHS transcripts in the white flowers was less than 4% of that in purple flowers on the same plant. Infection with TRV containing a tandem construct of PDS and CHS resulted in leaf photobleaching and white patterns on the flowers. Transcripts of CHS and PDS were reduced both in leaves and in flowers confirming simultaneous silencing of both genes by the tandem construct. We tested the effects of infection with TRV containing CHS and a fragment of a petunia gene encoding for 1-aminocyclopropane-1-carboxylate oxidase (ACO4) Abundance of transcripts encoding ACO4 and ACO1 were reduced (by 5% and 20%, respectively) in infected flowers. Whether the flowers were treated with ACC or pollinated, the white (silenced) flowers or flower sectors produced less ethylene and senesced later than purple (non-silenced) tissues. These results indicate the value of VIGS with tandem constructs containing CHS as reporter and a target gene as a tool for examining the function of floral-associated genes.

Geminivirus VIGS of endogenous genes requires SGS2/SDE1 and SGS3 and defines a new branch in the genetic pathway for silencing in plants

Virus-induced gene silencing (VIGS) is a sequence-specific RNA degradation process that can be used to downregulate plant gene expression. Both RNA and DNA viruses have been used for VIGS, but they differ in their mode of replication, gene expression, and cellular location. This study examined silencing mediated by a DNA virus, cabbage leaf curl virus (CaLCuV), in several silencing-deficient Arabidopsis mutants. A DNA VIGS vector derived from CaLCuV, which silenced chlorata42 (ChlI) needed for chlorophyll formation, was used to test endogenous gene silencing responses in suppressor of gene silencing (sgs)1, sgs2, sgs3, and Argonaute (ago)1 mutants defective in sense transgene-mediated post-transcriptional silencing (S-PTGS). SGS2/silencing defective (SDE)1, SGS3, and AGO1 are each dispensable for silencing mediated by transgenes containing inverted repeats (IR-PTGS), and SGS2/SDE1 is dispensable for RNA VIGS. We show that DNA VIGS requires both SGS2/SDE1 and SGS3, regardless of the orientation of 362 nt ChlI transcripts produced from the viral DNA promoter. Viral DNA accumulation is slightly higher, and viral symptoms increase in sgs2 and sgs3, whereas overexpression of SGS2/SDE1 mRNA results in decreased viral symptoms. Mutants affected in SGS1 and AGO1 function are only delayed in the onset of silencing, and have a small effect on chlorophyll accumulation. DNA VIGS is unaffected in defective DNA methylation (ddm)1/somniferous (som)8 and maintenance of methylation (mom)1 mutants, impaired for TGS. These results demonstrate that SGS2/SDE1 and SGS3 are needed for endogenous gene silencing from DNA viruses, and suggest that SGS2/SDE1 may reduce geminivirus symptoms by targeting viral mRNAs.

High throughput virus-induced gene silencing implicates heat shock protein 90 in plant disease resistance

Virus-induced gene silencing was used to assess the function of random Nicotiana benthamiana cDNAs in disease resistance. Out of 4992 cDNAs tested from a normalized library, there were 79 that suppressed a hypersensitive response (HR) associated with Pto-mediated resistance against Pseudomonas syringae. However, only six of these clones blocked the Pto-mediated suppression of P.syringae growth. The three clones giving the strongest loss of Pto resistance had inserts corresponding to HSP90 and also caused loss of Rx-mediated resistance against potato virus X and N-mediated tobacco mosaic virus resistance. The role of HSP90 as a cofactor of disease resistance is associated with stabilization of Rx protein levels and could be accounted for in part by SGT1 and other cofactors of disease resistance acting as co-chaperones. This approach illustrates the potential benefits and limitations of RNA silencing in forward screens of gene function in plants.

Geminivirus vectors for high-level expression of foreign proteins in plant cells

Bean yellow dwarf virus (BeYDV) is a monopartite geminivirus that can infect dicotyledonous plants. We have developed a high-level expression system that utilizes elements of the replication machinery of this single-stranded DNA virus. The replication initiator protein (Rep) mediates release and replication of a replicon from a DNA construct ("LSL vector") that contains an expression cassette for a gene of interest flanked by cis-acting elements of the virus. We used tobacco NT1 cells and biolistic delivery of plasmid DNA for evaluation of replication and expression of reporter genes contained within an LSL vector. By codelivery of a GUS reporter-LSL vector and a Rep-supplying vector, we obtained up to 40-fold increase in expression levels compared to delivery of the reporter-LSL vectors alone. High-copy replication of the LSL vector was correlated with enhanced expression of GUS. Rep expression using a whole BeYDV clone, a cauliflower mosaic virus 35S promoter driving either genomic rep or an intron-deleted rep gene, or 35S-rep contained in the LSL vector all achieved efficient replication and enhancement of GUS expression. We anticipate that this system can be adapted for use in transgenic plants or plant cell cultures with appropriately regulated expression of Rep, with the potential to greatly increase yield of recombinant proteins.

Exploring plant genomes by RNA-induced gene silencing

The nucleotide sequences of several animal, plant and bacterial genomes are now known, but the functions of many of the proteins that they are predicted to encode remain unclear. RNA interference is a gene-silencing technology that is being used successfully to investigate gene function in several organisms--for example, Caenorhabditis elegans. We discuss here that RNA-induced gene silencing approaches are also likely to be effective for investigating plant gene function in a high-throughput, genome-wide manner.

Progression of geminivirus-induced transgene silencing is associated with transgene methylation

•  The association of viral-induced gene silencing (VIGS) elicited by a DNA virus with DNA methylation of the silenced transgene was studied. •  35S-Green fluorescent protein (GFP) transgenic Nicotiana benthamiana were treated with an inhibitor of DNA methylation, 5-azacytidine (5-Aza-C), and VIGS of the transgene was observed upon inoculation with tomato golden mosaic virus carrying the GFP coding sequence. •  The onset of VIGS of the 35S-GFP transgene occurred 14-16 d after inoculation in both control and 5-Aza-C-treated plants. At this stage, the silencing was observed in localized regions. Silencing was uniform by 30 d after inoculation in plants that had methylated GFP-DNA, whereas plants that continued to display the same phenotype as seen at 14-15 d after inoculation had hypomethylated GFP-DNA. Viral expression of GFP persisted in pockets throughout the life of infected plants. •  This is the first demonstration of a correlation between post transcriptional gene silencing induced by a DNA virus, and transgene methylation. The results suggest that, while DNA methylation is not necessary for the initiation of silencing, the progression of silencing is affected by inhibition of DNA methylation.

Evidence for gene silencing in Haemophilus influenzae

Evidence for gene silencing of Haemophilus influenzae involved a beta-subunit of RNA polymerase. The gene presumed silenced was rifampin resistance. The evidence that it was silencing, rather than dominance of a rifampin-sensitive marker, was that it took place when the rifampin resistance marker was on both a plasmid and the chromosome, without the presence of a rifampin-sensitive marker, as judged by lack of transformation of a rifampin-resistant cell to rifampin sensitivity by the plasmid. In addition, three compounds that are known to decrease gene silencing in eukaryotes (trichostatin A, sodium butyrate and 5-azacytidine) also decreased the presumed silencing in H. influenzae. Silencing of rifampin-resistant Escherichia coli did not take place with the plasmid from H. influenzae.

Transposon-mediated single-copy gene delivery leads to increased transgene expression stability in barley

Instability of transgene expression in plants is often associated with complex multicopy patterns of transgene integration at the same locus, as well as position effects due to random integration. Based on maize transposable elements Activator (Ac) and Dissociation (Ds), we developed a method to generate large numbers of transgenic barley (Hordeum vulgare var Golden Promise) plants, each carrying a single transgene copy at different locations. Plants expressing Ac transposase (AcTPase) were crossed with plants containing one or more copies of bar, a selectable herbicide (Basta) resistance gene, located between inverted-repeat Ds ends (Ds-bar). F(1) plants were self-pollinated and the F(2) generation was analyzed to identify plants segregating for transposed Ds-bar elements. Of Ds-bar transpositions, 25% were in unlinked sites that segregated from vector sequences, other Ds-bar copies, and the AcTPase gene, resulting in numerous single-copy Ds-bar plants carrying the transgene at different locations. Transgene expression in F(2) plants with transposed Ds-bar was 100% stable, whereas only 23% of F(2) plants carrying Ds-bar at the original site expressed the transgene product stably. In F(3) and F(4) populations, transgene expression in 81.5% of plants from progeny of F(2) plants with single-copy, transposed Ds-bar remained completely stable. Analysis of the integration site in single-copy plants showed that transposed Ds-bar inserted into single- or low-copy regions of the genome, whereas silenced Ds-bar elements at their original location were inserted into redundant or highly repetitive genomic regions. Methylation of the non-transposed transgene and its promoter, as well as a higher condensation of the chromatin around the original integration site, was associated with plants exhibiting transgene silencing.

Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants

In transgenic and nontransgenic plants, viruses are both initiators and targets of a defense mechanism that is similar to posttranscriptional gene silencing (PTGS). Recently, it was found that potyviruses and cucumoviruses encode pathogenicity determinants that suppress this defense mechanism. Here, we test diverse virus types for the ability to suppress PTGS. Nicotiana benthamiana exhibiting PTGS of a green fluorescent protein transgene were infected with a range of unrelated viruses and various potato virus X vectors producing viral pathogenicity factors. Upon infection, suppression of PTGS was assessed in planta through reactivation of green fluorescence and confirmed by molecular analysis. These experiments led to the identification of three suppressors of PTGS and showed that suppression of PTGS is widely used as a counter-defense strategy by DNA and RNA viruses. However, the spatial pattern and degree of suppression varied extensively between viruses. At one extreme, there are viruses that suppress in all tissues of all infected leaves, whereas others are able to suppress only in the veins of new emerging leaves. This variation existed even between closely related members of the potexvirus group. Collectively, these results suggest that virus-encoded suppressors of gene silencing have distinct modes of action, are targeted against distinct components of the host gene-silencing machinery, and that there is dynamic evolution of the host and viral components associated with the gene-silencing mechanism.

Single-copy transgenic wheat generated through the resolution of complex integration patterns

Genetic transformation of plants often results in multiple copies of the introduced DNA at a single locus. To ensure that only a single copy of a foreign gene resides in the plant genome, we used a strategy based on site-specific recombination. The transformation vector consists of a transgene flanked by recombination sites in an inverted orientation. Regardless of the number of copies integrated between the outermost transgenes, recombination between the outermost sites resolves the integrated molecules into a single copy. An example of this strategy has been demonstrated with wheat transformation, where four of four multiple-copy loci were resolved successfully into single-copy transgenes.