Plant viral suppressors of post-transcriptional silencing do not suppress transcriptional silencing

Structural features of T-DNA that induce transcriptional gene silencing during agroinfiltration

Agrobacterium tumefaciens (Rhizobium radiobacter) is used for the transient expression of foreign genes by the agroinfiltration method, but the introduction of foreign genes often induces transcriptional and/or post-transcriptional gene silencing (TGS and/or PTGS). In this study, we characterized the structural features of T-DNA that induce TGS during agroinfiltration. When A. tumefaciens cells harboring an empty T-DNA plasmid containing the cauliflower mosaic virus (CaMV) 35S promoter were infiltrated into the leaves of Nicotiana benthamiana line 16c with a GFP gene over-expressed under the control of the same promoter, no small interfering RNAs (siRNAs) were derived from the GFP sequence. However, siRNAs derived from the CaMV 35S promoter were detected, indicating that TGS against the GFP gene was induced. When the GFP gene was inserted into the T-DNA plasmid, PTGS against the GFP gene was induced whereas TGS against the CaMV 35S promoter was suppressed. We also showed the importance of terminator sequences in T-DNA for gene silencing. Therefore, depending on the combination of promoter, terminator and coding sequences on T-DNA and the host nuclear genome, either or both TGS and/or PTGS could be induced by agroinfiltration. Furthermore, we showed the possible involvement of three siRNA-producing Dicers (DCL2, DCL3 and DCL4) in the induction of TGS by the co-agroinfiltration method. Especially, DCL2 was probably the most important among them in the initial step of TGS induction. These results are valuable for controlling gene expression by agroinfiltration.

Two plant viral suppressors of silencing require the ethylene-inducible host transcription factor RAV2 to block RNA silencing

RNA silencing is a highly conserved pathway in the network of interconnected defense responses that are activated during viral infection. As a counter-defense, many plant viruses encode proteins that block silencing, often also interfering with endogenous small RNA pathways. However, the mechanism of action of viral suppressors is not well understood and the role of host factors in the process is just beginning to emerge. Here we report that the ethylene-inducible transcription factor RAV2 is required for suppression of RNA silencing by two unrelated plant viral proteins, potyvirus HC-Pro and carmovirus P38. Using a hairpin transgene silencing system, we find that both viral suppressors require RAV2 to block the activity of primary siRNAs, whereas suppression of transitive silencing is RAV2-independent. RAV2 is also required for many HC-Pro-mediated morphological anomalies in transgenic plants, but not for the associated defects in the microRNA pathway. Whole genome tiling microarray experiments demonstrate that expression of genes known to be required for silencing is unchanged in HC-Pro plants, whereas a striking number of genes involved in other biotic and abiotic stress responses are induced, many in a RAV2-dependent manner. Among the genes that require RAV2 for induction by HC-Pro are FRY1 and CML38, genes implicated as endogenous suppressors of silencing. These findings raise the intriguing possibility that HC-Pro-suppression of silencing is not caused by decreased expression of genes that are required for silencing, but instead, by induction of stress and defense responses, some components of which interfere with antiviral silencing. Furthermore, the observation that two unrelated viral suppressors require the activity of the same factor to block silencing suggests that RAV2 represents a control point that can be readily subverted by viruses to block antiviral silencing.

RNA silencing is an important antiviral defense in plants, and many plant viruses encode proteins that block RNA silencing. However, the mechanism of action of the viral suppressors is complex, and little is known about the role of host plant proteins in the process. Here we report the first example of a host protein that plays a required role in viral suppression of silencing—a transcription factor called RAV2 that is required for suppression of silencing by two different and unrelated viral proteins. Analysis of plant gene expression patterns shows that RAV2 is required for induction of many genes involved in other stress and defense pathways, including genes implicated as plant suppressors of silencing. Overall, the results suggest that RAV2 is an important factor in viral suppression of silencing and that the role of RAV2 is to divert host defenses toward responses that interfere with antiviral silencing.

The Role of Nuclear Matrix Attachment Regions in Plants

Regions of DNA that bind to the nuclear matrix, or nucleoskeleton, are known as Matrix Attachment Regions (MARs). MARs are thought to play an important role in higher-order structure and chromatin organization within the nucleus. MARs are also thought to act as boundaries of chromosomal domains that act to separate regions of gene-rich, decondensed euchromatin from highly repetitive, condensed heterochromatin. Herein I will present evidence that MARs do indeed act as domain boundaries and can prevent the spread of silencing into active genes. Many fundamental questions remain unanswered about how MARs function in the nucleus. New findings in epigenetics indicate that MARs may also play an important role in the organization of genes and the eventual transport of their mRNAs through the nuclear pore.

P19-dependent and P19-independent reversion of F1-V gene silencing in tomato

As a part of a project to develop a plant-made plague vaccine, we expressed the Yersinia pestis F1-V antigen fusion protein in tomato. We discovered that in some of these plants the expression of the f1-v gene was undetectable in leaves and fruit by ELISA, even though they had multiple copies of f1-v according to Southern-blot analysis. A likely explanation of these results is the phenomenon of RNA silencing, a group of RNA-based processes that produces sequence-specific inhibition of gene expression and may result in transgene silencing in plants. Here we report the reversion of the f1-v gene silencing in transgenic tomato plants through two different mechanisms. In the P19-dependent Reversion or Type I, the viral suppressor of gene silencing, P19, induces the reversion of gene silencing. In the P19-independent Reversion or Type II, the f1-v gene expression is restored after the substantial loss of gene copies as a consequence of transgene segregation in the progeny. The transient and stable expression of the p19 gene driven by a constitutive promoter as well as an ethanol inducible promoter induced a P19-dependent reversion of f1-v gene silencing. In particular, the second generation plant 3D1.6 had the highest P19 protein levels and correlated with the highest F1-V protein accumulation, almost a three-fold increase of F1-V protein levels in fruit than that previously reported for the non-silenced F1-V elite tomato lines. These results confirm the potential exploitation of P19 to substantially increase the expression of value-added proteins in plants.

Transient expression of HPV16 E7 peptide (aa 44-60) and HPV16 L2 peptide (aa 108-120) on chimeric potyvirus-like particles using Potato virus X-based vector

The optimized expression of recombinant Potato virus A coat protein (ACP) carrying two different epitopes from Human papillomavirus type 16 (HPV16) was developed. Epitope derived from minor capsid protein L2 was expressed as N-terminal fusion with ACP while an epitope derived from E7 oncoprotein was fused to its C-terminus. The construct was cloned into Potato X potexvirus (PVX) based vector and transiently expressed in plants using Agrobacterium tumefaciens mediated inoculation. To increase the level of expressed protein the transgenic Nicotiana benthamiana plants expressing Potato virus A HC-Pro gene and transgenic Nicotiana tabacum, cv. Petit Havana SR1 carrying Potato virus A P3 protein gene were tested. Synergistic infection of host plants with PVX carrying the construct and Potato virus Y(O) (PVY(O)) increased the expression of L2ACPE7 in N. tabacum and in transgenic N. benthamiana carrying potyviral HC-Pro gene as compared to control plants infected with L2ACPE7 only.

Amplicon-plus targeting technology (APTT) for rapid production of a highly unstable vaccine protein in tobacco plants

High-level expression of transgenes is essential for cost-effective production of valuable pharmaceutical proteins in plants. However, transgenic proteins often accumulate in plants at low levels. Low levels of protein accumulation can be caused by many factors including post-transcriptional gene silencing (PTGS) and/or rapid turnover of the transgenic proteins. We have developed an Amplicon-plus Targeting Technology (APTT), by using novel combination of known techniques that appears to overcome both of these factors. By using this technology, we have successfully expressed the highly-labile L1 protein of canine oral papillomavirus (COPV L1) by infecting transgenic tobacco plants expressing a suppressor of post-transcriptional gene silencing (PTGS) with a PVX amplicon carrying a gene encoding L1, and targeting the vaccine protein into the chloroplasts. Further, a scalable "wound-and-agrospray" inoculation method has been developed that will permit high-throughput Agrobacterium inoculation of Nicotiana tabacum, and a spray-only method (named "agrospray") for use with N. benthamiana to allow large-scale application of this technology. The good yield and short interval from inoculation to harvest characteristic of APTT, combined with the potential for high-throughput achieved by use of the agrospray inoculation protocol, make this system a very promising technology for producing high value recombinant proteins, especially those known to be highly labile, in plants for a wide range of applications including producing vaccines against rapidly evolving pathogens and for the rapid response needed to meet bio-defense emergencies.

A single transgene locus triggers both transcriptional and post-transcriptional silencing through double-stranded RNA production

Silencing of a target locus by an unlinked silencing locus can result from transcription inhibition (transcriptional gene silencing; TGS) or mRNA degradation (post-transcriptional gene silencing; PTGS), owing to the production of double-stranded RNA (dsRNA) corresponding to promoter or transcribed sequences, respectively. The involvement of distinct cellular components in each process suggests that dsRNA-induced TGS and PTGS likely result from the diversification of an ancient common mechanism. However, a strict comparison of TGS and PTGS has been difficult to achieve because it generally relies on the analysis of distinct silencing loci. We describe a single transgene locus that triggers both TGS and PTGS, owing to the production of dsRNA corresponding to promoter and transcribed sequences of different target genes. We describe mutants and epigenetic variants derived from this locus and propose a model for the production of dsRNA. Also, we show that PTGS, but not TGS, is graft-transmissible, which together with the sensitivity of PTGS, but not TGS, to RNA viruses that replicate in the cytoplasm, suggest that the nuclear compartmentalization of TGS is responsible for cell-autonomy. In contrast, we contribute local and systemic trafficking of silencing signals and sensitivity to viruses to the cytoplasmic steps of PTGS and to amplification steps that require high levels of target mRNAs.

Systematic silencing of a tobacco nitrate reductase transgene in lettuce (Lactuca sativa L.)

A population of 50 independent transgenic lettuces transformed with a nitrate reductase coding sequence under the control of the 35S promoter was studied. None of them showed significantly lower nitrate levels when compared with the untransformed plants, despite the presence of nitrate reductase (NR) activity that derives from the transgene in at least four of the transformants. No repercussion on total NR activity (endogenous+transgenic) was detected in these plants. Nevertheless, 28% of the transformants showed phenotypes characteristic of a general silencing of the NR genes as already described in tobacco and potato, i.e. bleaching of the leaves leading to the death of the plant. By northern blots, it was shown that the transgene was silenced in these chlorotic plants and also in the plants that did not show symptoms of chlorosis. Thus a silencing process specifically directed against the NR mRNA derived from the transgene occurred very early in the development of all the plants studied, whatever homologous endogenous NR mRNA is present in the plant. In some cases this transgene-specific silencing was shown subsequently to extend to the homologous endogenous NR mRNA. These results suggest that, in lettuce, the level of nitrate reductase mRNA is under tight expression control and this is able specifically to target transgenic transcripts by a post-transcriptional gene silencing (PTGS) mechanism during the first stage of development of the plantlet.

Pathogen-derived resistance in potato to Potato virus Y—aspects of stability and biosafety under field conditions

Plants of three different potato cultivars/lines were transformed via Agrobacterium tumefaciens with a truncated NIb gene of a necrotic strain of Potato virus Y (PVY(N)) which had been C-terminally fused to enhanced blue-fluorescing protein. Resistance of the resulting transgenic clones was evaluated under glass house conditions using an NTN-strain of PVY. Four clones with the highest levels of resistance were chosen for further experiments. Their type of resistance was either recovery or extreme resistance. These clones and their resistance types were also characterised at the molecular level. Mechanisms other than post-transcriptional gene silencing seemed to be involved in the resistance which was not dependent on sequence homology between transgene and challenging virus. Stability of resistance was tested under field conditions. The plants usually became infected with PVY. Tubers of the clone with extreme resistance did not recover from infection whereas those from clones with the recovery type did. No influence of transgenic potatoes was apparent on aphid population numbers in test plots. Recombination events could not be detected at the RNA level between transgene and challenging virus.

Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance

In animals, double-stranded short interfering RNA (siRNA) and single-stranded microRNA (miRNA) regulate gene expression by targeting homologous mRNA for cleavage or by interfering with their translation, respectively. siRNAs are processed from injected or transgene-derived, long, perfect double-stranded RNA (dsRNA), while miRNAs are processed from short, imperfect dsRNA precursors transcribed from endogenous intergenic regions. In plants, both siRNAs and miRNAs activate cleavage of homologous RNA targets, but little is known about the genes controlling their production or action. The SGS2/SDE1 protein contributes to produce transgene siRNA, while DCL1 and HEN1 contribute to endogenous miRNA accumulation. Here, we show that: i) SGS2, SGS3, AGO1, and HEN1 contribute to produce transgene siRNA involved in sense posttranscriptional gene silencing (S-PTGS); ii) HEN1, but not SGS2, SGS3, or AGO1, contributes to the accumulation of the endogenous miR171 miRNA and to the cleavage of Scarecrow target mRNA by miR171; iii) SGS2, SGS3, AGO1, and HEN1 contribute to resistance against cucumber mosaic virus, but not to siRNA and IR-PTGS triggered by hairpin transgenes directly producing perfect dsRNA; and iv) the actions of HEN1 in miRNA/development and siRNA/S-PTGS can be uncoupled by single-point mutations at different positions in the protein.

Gene silencing in transgenic soybean plants transformed via particle bombardment

Transgenes are susceptible to silencing in plants especially when multiple copies of the gene of interest are introduced. Transgenic plants derived by particle bombardment, which is the common method for transforming soybean, have a tendency to have multiple integration events. Three independent transgenic soybean plants obtained via particle bombardment were analyzed for transgene silencing. A GUS transgenic soybean line had at least 100 copies of the GUS gene while there were approximately 60 copies of the transgene in the two soybean lines transformed with a 15-kDa zein storage protein gene from maize. Soybean plants transformed with the GUS gene showed variable GUS expression. The coding region and promoter of the GUS gene in the plants with low expression of GUS were heavily methylated. Variability in GUS expression was observed in the progeny of the high expressors in the T(2) and T(3) generations as well. Expression level of the 15-kDa zein gene in transgenic soybean plants showed correlation with the level of transgene methylation. The helper component-proteinase from potyviruses is known to suppress post-transcriptional gene silencing. Transgenic plants were inoculated with the soybean mosaic potyvirus (SMV) to test possible effects on transgene silencing in soybean. Infection with SMV did not suppress transgene silencing in these plants and suggests that the silencing in these plants may not be due to post-transcriptional gene silencing.

Generation of siRNAs by T-DNA sequences does not require active transcription or homology to sequences in the plant

Delivery into plants of T-DNAs containing promoter, terminator, or coding sequences generated small interfering RNAs (siRNAs) specific to each type of sequence. When both promoter and transcribed sequences were simultaneously present in the T-DNA, accumulation of siRNAs to transcribed sequences was favored over accumulation of siRNAs to the nontranscribed upstream promoter sequences. The generation of specific siRNA sequences occurred even in the absence of T-DNA homology to sequences in the plant. Delivery of T-DNA, with homology to the transgene limited to the nontranscribed cauliflower mosaic virus 35S promoter (35SP) and the transcribed nopaline synthase transcription termination (NosT)signal sequences, into transgenic plants expressing the green fluorescent protein (GFP), generated siRNAs in infiltrated tissues to both 35SP (35SsiRNAs) and NosT (NosTsiRNAs), but not to the GFP sequence (GFPsiRNAs). In infiltrated tissues, the 35SsiRNAs failed to trigger the transcriptional silencing of the transgene, accumulation of 35SsiRNAs could be prevented by the potyviral HC-Pro, and the NosTsiRNAs required an initial amplification to trigger efficient transgene silencing, which is mediated by transcripts from the exogenous T-DNA, and not from the transgene. In upper leaves, silencing correlated with the presence of GFPsiRNAs and the absence of 35SsiRNAs, confirming that its spread was posttranscriptionally mediated by the transgene mRNA.

Developing arbovirus resistance in mosquitoes

Diseases caused by arthropod-borne viruses are increasingly significant public health problems, and novel methods are needed to control pathogen transmission. The hypothesis underlying the research described here is that genetic manipulation of Aedes aegypti mosquitoes can profoundly and permanently reduce their competence to transmit dengue viruses to human hosts. Recent key findings now allow us to test the genetic control hypothesis. We have identified viral genome-derived RNA segments that can be expressed in mosquito midguts and salivary glands to ablate homologous virus replication and transmission. We have demonstrated that both transient and heritable expression of virus-derived effector RNAs in cultured mosquito cells can silence virus replication, and have characterized the mechanism of RNA-mediated resistance. We are now developing virus-resistant mosquito lines by transformation with transposable elements that express effector RNAs from mosquito-active promoters.

Transgenic plants expressing HC-Pro show enhanced virus sensitivity while silencing of the transgene results in resistance

Nicotiana benthamiana plants were engineered to express sequences of the helper component-proteinase (HC-Pro) of Cowpea aphid-borne mosaic potyvirus (CABMV). The sensitivity of the transgenic plants to infection with parental and heterologous viruses was studied. The lines expressing HC-Pro showed enhanced symptoms after infection with the parental CABMV isolate and also after infection with a heterologous potyvirus, Potato virus Y (PVY) and a comovirus, Cowpea mosaic virus (CPMV). On the other hand, transgenic lines expressing nontranslatable HC-Pro or translatable HC-Pro with a deletion of the central domain showed wild type symptoms after infection with the parental CABMV isolate and heterologous viruses. These results showed that CABMV HC-Pro is a pathogenicity determinant that conditions enhanced sensitivity to virus infection in plants, and that the central domain of the protein is essential for this. The severe symptoms in CABMV-infected HC-Pro expressing lines were remarkably followed by brief recovery and subsequent re-establishment of infection, possibly indicating counteracting effects of HC-Pro expression and a host defense response. One of the HC-Pro expressing lines (h48) was found to contain low levels of transgenic HC-Pro RNA and to be resistant to CABMV and to recombinant CPMV expressing HC-Pro. This indicated that h48 was (partially) posttranscriptionally silenced for the HC-Pro transgene inspite of the established role of HC-Pro as a suppressor of posttranscriptional gene silencing. Line h48 was not resistant to PVY, but instead showed enhanced symptoms compared to nontransgenic plants. This may be due to relief of silencing of the HC-Pro transgene by HC-Pro expressed by PVY.

Making an ally from an enemy: plant virology and the new agriculture

Historically, the study of plant viruses has contributed greatly to the elucidation of eukaryotic biology. Recently, concurrent with the development of viruses into expression vectors, the biotechnology industry has developed an increasing number of disease therapies utilizing recombinant proteins. Plant virus vectors are viewed as a viable option for recombinant protein production. Employing pathogens in the process of creating added value to agriculture is, in effect, making an ally from an enemy. This review discusses the development and use of viruses as expression vectors, with special emphasis on (+) strand RNA virus systems. Further, the use of virus expression vectors in large-scale agricultural settings to produce recombinant proteins is described, and the technical challenges that need to be addressed by agriculturists and molecular virologists to fully realize the potential of this latest evolution of plant science are outlined.

Resistance of RNA-mediated TGS to HC-Pro, a viral suppressor of PTGS, suggests alternative pathways for dsRNA processing

In plants, double-stranded (ds) RNA that is degraded to small (sm) RNAs that are approximately 23 nucleotides in length can trigger the degradation of homologous RNAs in the cytoplasm (posttranscriptional gene silencing or PTGS) and de novo methylation of homologous DNA in the nucleus [1]. PTGS is similar to quelling in fungi [2] and RNAi in animals [3]. RNA-directed DNA methylation (RdDM) can lead to transcriptional gene silencing (TGS) and the methylation of homologous target promoters if dsRNAs containing promoter sequences are involved [4]. HC-Pro is a plant viral suppressor of PTGS that acts by preventing the accumulation of smRNAs [5, 6] that provide the specificity determinant for homologous RNA degradation [7-10]. Here, we show that HC-Pro does not suppress TGS induced by promoter dsRNA. Moreover, the amount of promoter smRNAs is elevated 5-fold in the presence of HC-Pro, and target promoter methylation is slightly increased without a concomitant rise in the level of promoter dsRNA. The promoter dsRNA, which is not polyadenylated, failed to trigger substantial degradation of polyadenylated, single-stranded promoter RNA. The differential effects of HC-Pro on smRNA accumulation associated with dsRNA-mediated TGS and at least some cases of PTGS suggest that dsRNA processing can occur by alternative pathways, and they support the idea that RdDM is triggered by smRNAs.

Gene silencing as an adaptive defence against viruses

Gene silencing was perceived initially as an unpredictable and inconvenient side effect of introducing transgenes into plants. It now seems that it is the consequence of accidentally triggering the plant's adaptive defence mechanism against viruses and transposable elements. This recently discovered mechanism, although mechanistically different, has a number of parallels with the immune system of mammals.

Gene silencing and DNA methylation processes

Epigenetic gene silencing results from the inhibition of transcription or from posttranscriptional RNA degradation. DNA methylation is one of the most central and frequently discussed elements of gene silencing in both plants and mammals. Because DNA methylation has not been detected in yeast, Drosophila or Caenorhabditis elegans, the standard genetic workhorses, plants are important models for revealing the role of DNA methylation in the epigenetic regulation of genes in vivo.

RNA-based silencing strategies in plants

In plants, double-stranded RNA can silence genes by triggering degradation of homologous RNA in the cytoplasm and by directing methylation of homologous nuclear DNA sequences. Analyses of Arabidopsis mutants and plant viral suppressors of silencing are unraveling RNA-silencing mechanisms, which require common proteins in diverse organisms, and are assessing the role of methylation in transcriptional and posttranscriptional gene silencing.

Viral suppressors of RNA silencing

The suppression of RNA silencing by plant viruses represents a viral adaptation to a novel host antiviral defense. Three types of viral suppressors have been identified through the use of a variety of silencing suppression assays. The first two types of suppressor are capable of a complete or partial reversal of pre-existing RNA silencing; the third type does not reverse RNA silencing but can instead prevent its systemic signaling.