Transgenes and gene suppression: telling us something new?

Increased ascorbic acid synthesis by overexpression of AcGGP3 ameliorates copper toxicity in kiwifruit

The widespread application of copper (Cu) -based fertilizers and pesticides could increase the accumulation of Cu in kiwifruit. According to a global survey, red- and yellow-fleshed kiwifruit contained more elevated amounts of Cu than green-fleshed kiwifruit due to weaker disease resistance and higher use of Cu pesticides. Intriguingly, our research revealed that external and endogenous ascorbic acid (AsA) reduced the phenotypic and physiological injury of Cu toxicity in kiwifruit. Cu stress assays and transcriptional analysis have shown that Cu treatment for 12 h significantly increased the AsA content in kiwifruit leaves and up-regulated key genes involved in AsA biosynthesis, such as GDP-L-galactose phosphorylase3 (GGP3) and GDP-mannose-3',5'-epimerase (GME). Overexpressing GGP3 in transgenic kiwifruit significantly increased the endogenous AsA content of kiwifruit, which was beneficial in mitigating Cu toxicity by decreasing levels of reactive oxygen species, malondialdehyde, and electrolyte leakage, as well as reducing damage to the chloroplast structure and photosystem II. This study presented a novel strategy to ameliorate plant Cu stress by increasing the endogenous antioxidant (AsA) content through transgenesis.

Targeting of genomic and negative-sense strands of viral RNA contributes to antiviral resistance mediated by artificial miRNAs and promotes the emergence of complex viral populations

Technology based on artificial small RNAs, including artificial microRNAs (amiRNAs), exploits natural RNA silencing mechanisms to achieve silencing of endogenous genes or pathogens. This technology has been successfully employed to generate resistance against different eukaryotic viruses. However, information about viral RNA molecules effectively targeted by these small RNAs is rather conflicting, and factors contributing to the selection of virus mutants escaping the antiviral activity of virus-specific small RNAs have not been studied in detail. In this work, we transformed Nicotiana benthamiana plants with amiRNA constructs designed against the potyvirus plum pox virus (PPV), a positive-sense RNA virus, and obtained lines highly resistant to PPV infection and others showing partial resistance. These lines have allowed us to verify that amiRNA directed against genomic RNA is more efficient than amiRNA targeting its complementary strand. However, we also provide evidence that the negative-sense RNA strand is cleaved by the amiRNA-guided RNA silencing machinery. Our results show that the selection pressure posed by the amiRNA action on both viral RNA strands causes an evolutionary explosion that results in the emergence of a broad range of virus variants, which can further expand in the presence, and even in the absence, of antiviral challenges.

RNA silencing: From discovery and elucidation to application and perspectives

RNA silencing (or RNA interference, RNAi) is a conserved mechanism for regulating gene expression in eukaryotes. The discovery of natural trans-kingdom RNAi indicated that small RNAs act as signaling molecules and enable communication between organisms in different kingdoms. The phenomenon and potential mechanisms of trans-kingdom RNAi are among the most exciting research topics. To better understand trans-kingdom RNAi, we review the history of the discovery and elucidation of RNAi mechanisms. Based on canonical RNAi mechanisms, we summarize the major points of divergence around RNAi pathways in the main eukaryotes' kingdoms, including plants, animals, and fungi. We review the representative incidents associated with the mechanisms and applications of trans-kingdom RNAi in crop protection, and discuss the critical factors that should be considered to develop successful trans-kingdom RNAi-based crop protection strategies.

Mathematical Linear Programming to Model MicroRNAs-Mediated Gene Regulation Using Gurobi Optimizer

Genes are transcribed into various RNA molecules, and a portion of them called messenger RNA (mRNA) is then translated into proteins in the process known as gene expression. Gene expression is a high-energy demanding process, and aberrant expression changes often manifest into pathophysiology. Therefore, gene expression is tightly regulated by several factors at different levels. MicroRNAs (miRNAs) are one of the powerful post-transcriptional regulators involved in key biological processes and diseases. They inhibit the translation of their mRNA targets or degrade them in a sequence-specific manner, and hence control the rate of protein synthesis. In recent years, in response to experimental limitations, several computational methods have been proposed to predict miRNA target genes based on sequence complementarity and structural features. However, these predictions yield a large number of false positives. Integration of gene and miRNA expression data drastically alleviates this problem. Here, I describe a mathematical linear modeling approach to identify miRNA targets at the genome scale using gene and miRNA expression data. Mathematical modeling is faster and more scalable to genome-level compared to conventional statistical modeling approaches.

An Overview of Current Research in Plant Epigenetic and Epigenomic Phenomena

Biological phenomena defined as having an "epigenetic" component (according to various definitions) have been extensively studied in plant systems and illuminated many mechanisms by which gene expression is regulated and patterns of expression inherited through cell divisions. This second volume of Plant Epigenetics and Epigenomics: Methods in Molecular Biology builds on the work of its predecessor to describe cutting-edge tools for plant epigenetic and epigenomic research, and embrace crop and forestry species as well as natural populations and further insights from model species. In this chapter, the historical background to plant epigenetic and epigenomic research is summarized, and key considerations for the interpretation of current data are outlined.

Amount of Escape Estimation Based on Bayesian and MCMC Approaches for RNA Interference

The amount of short interfering RNA (siRNA) escaping from the endosome has a significant impact on the efficiency of RNAi. In general, the initial injected amount of siRNAs during the experiment is known, and also the amount of siRNAs after the experiment can be revealed by the level of mRNA measured. However, it is impossible to measure the amount of siRNAs that escape from the endosome and really take part in the chemical reaction of RNAi by detecting the biological organism and its tissues. Inspired by the bottleneck effect in the virus, we introduce the Bayesian approach to infer the amount of escape based on a single type and multiple types of siRNA, respectively. With the consideration of the large calculation quantity of the accurate posterior distribution and the unavailable analytic expression of the likelihood function, our article proposes to take samples by the improved Markov chain Monte Carlo (MCMC) method. The article takes the silencing gene of the synthesis of chitin and the interfering multiple target oncogene as numerical examples to show that our improved MCMC method has higher operation efficiency compared to the Bayesian approach. Our research models siRNA endosome escape using statistical methods for the first time. It perhaps provides a theoretical basis to decrease the cost of a biotic experiment for the future and the standardized statistical approaches for the amount of escape estimation.

An efficient method for multigene co-interference by recombinant Bombyx mori nucleopolyhedrovirus

Bombyx mori Nucleopolyhedrovirus (BmNPV), which is a member of the Baculoviridae family, is a significant pathogen of the silkworm. The infection of BmNPV is often lethal and causes about 20% loss of cocoon in the silk industry annually. To explore the effects of different gene inhibition strategies on the replication cycle of baculovirus, we constructed the mutant virus to infect BmN cells directly and further identified ie0, ie1, and gp64 as the essential viral genes of BmNPV. To elucidate the significance of the inhibition effect of different interference strategies, we characterized and constructed the recombinant BmNPV that carried a single or multigene-interfering cassette. The results showed that the inhibition effect of dsie1 on target gene expression, virus titer, and silkworm mortality was significantly better than that of dsie0 and dsgp64. It also showed that the dsie1 interference produced fewer progeny virions and was less lethal, which indicates that ie1 played a more critical role in the BmNPV replication cycle. Furthermore, the inhibitory effect of the virus titer and mortality indicated that the multigene co-interference constructed by the baculovirus expression system was significantly better than the interference of any single-gene (p < 0.05). In summary, the strategy of multigene synergy can achieve the function of continuous interference and provide a new platform for the breeding of silkworm disease resistant. In addition, this strategy improves the various traits of the silkworm.

RNA Interference Mechanisms and Applications in Plant Pathology

The origin of RNA interference (RNAi), the cell sentinel system widely shared among eukaryotes that recognizes RNAs and specifically degrades or prevents their translation in cells, is suggested to predate the last eukaryote common ancestor ( 138 ). Of particular relevance to plant pathology is that in plants, but also in some fungi, insects, and lower eukaryotes, RNAi is a primary and effective antiviral defense, and recent studies have revealed that small RNAs (sRNAs) involved in RNAi play important roles in other plant diseases, including those caused by cellular plant pathogens. Because of this, and because RNAi can be manipulated to interfere with the expression of endogenous genes in an intra- or interspecific manner, RNAi has been used as a tool in studies of gene function but also for plant protection. Here, we review the discovery of RNAi, canonical mechanisms, experimental and translational applications, and new RNA-based technologies of importance to plant pathology.

The Impact of "Coat Protein-Mediated Virus Resistance" in Applied Plant Pathology and Basic Research

Worldwide, plant viruses cause serious reductions in marketable crop yield and in some cases even plant death. In most cases, the most effective way to control virus diseases is through genetically controlled resistance. However, developing virus-resistant (VR) crops through traditional breeding can take many years, and in some cases is not even possible. Because of this, the demonstration of the first VR transgenic plants in 1985 generated much attention. This seminal report served as an inflection point for research in both basic and applied plant pathology, the results of which have dramatically changed both basic research and in a few cases, commercial crop production. The typical review article on this topic has focused on only basic or only applied research results stemming from this seminal discovery. This can make it difficult for the reader to appreciate the full impact of research on transgenic virus resistance, and the contributions from fundamental research that led to translational applications of this technology. In this review, we take a global view of this topic highlighting the significant changes to both basic and applied plant pathology research and commercial food production that have accumulated in the last 30 plus years. We present these milestones in the historical context of some of the scientific, economic, and environmental drivers for developing specific VR crops. The intent of this review is to provide a single document that adequately records the significant accomplishments of researchers in both basic and applied plant pathology research on this topic and how they relate to each other. We hope this review therefore serves as both an instructional tool for students new to the topic, as well as a source of conversation and discussion for how the technology of engineered virus resistance could be applied in the future.

Epigenetic silencing in transgenic plants

Epigenetic silencing is a natural phenomenon in which the expression of genes is regulated through modifications of DNA, RNA, or histone proteins. It is a mechanism for defending host genomes against the effects of transposable elements and viral infection, and acts as a modulator of expression of duplicated gene family members and as a silencer of transgenes. A major breakthrough in understanding the mechanism of epigenetic silencing was the discovery of silencing in transgenic tobacco plants due to the interaction between two homologous promoters. The molecular mechanism of epigenetic mechanism is highly complicated and it is not completely understood yet. Two different molecular routes have been proposed for this, that is, transcriptional gene silencing, which is associated with heavy methylation of promoter regions and blocks the transcription of transgenes, and post-transcriptional gene silencing (PTGS), the basic mechanism is degradation of the cytosolic mRNA of transgenes or endogenous genes. Undesired transgene silencing is of major concern in the transgenic technologies used in crop improvement. A complete understanding of this phenomenon will be very useful for transgenic applications, where silencing of specific genes is required. The current status of epigenetic silencing in transgenic technology is discussed and summarized in this mini-review.

Current status of viral expression systems in plants and perspectives for oral vaccines development

During the last 25 years, the technology to produce recombinant vaccines in plant cells has evolved from modest proofs of the concept to viable technologies adopted by some companies due to significant improvements in the field. Viral-based expression strategies have importantly contributed to this success owing to high yields, short production time (which is in most cases free of tissue culture steps), and the implementation of confined processes for production under GMPs. Herein the distinct expression systems based on viral elements are analyzed. This review also presents the outlook on how these technologies have been successfully applied to the development of plant-based vaccines, some of them being in advanced stages of development. Perspectives on how viral expression systems could allow for the development of innovative oral vaccines constituted by minimally-processed plant biomass are discussed.

Engineered plant virus resistance

Virus diseases are among the key limiting factors that cause significant yield loss and continuously threaten crop production. Resistant cultivars coupled with pesticide application are commonly used to circumvent these threats. One of the limitations of the reliance on resistant cultivars is the inevitable breakdown of resistance due to the multitude of variable virus populations. Similarly, chemical applications to control virus transmitting insect vectors are costly to the farmers, cause adverse health and environmental consequences, and often result in the emergence of resistant vector strains. Thus, exploiting strategies that provide durable and broad-spectrum resistance over diverse environments are of paramount importance. The development of plant gene transfer systems has allowed for the introgression of alien genes into plant genomes for novel disease control strategies, thus providing a mechanism for broadening the genetic resources available to plant breeders. Genetic engineering offers various options for introducing transgenic virus resistance into crop plants to provide a wide range of resistance to viral pathogens. This review examines the current strategies of developing virus resistant transgenic plants.

Landscaping plant epigenetics

The understanding of epigenetic mechanisms is necessary for assessing the potential impacts of epigenetics on plant growth, development and reproduction, and ultimately for the response of these factors to evolutionary pressures and crop breeding programs. This volume highlights the latest in laboratory and bioinformatic techniques used for the investigation of epigenetic phenomena in plants. Such techniques now allow genome-wide analyses of epigenetic regulation and help to advance our understanding of how epigenetic regulatory mechanisms affect cellular and genome function. To set the scene, we begin with a short background of how the field of epigenetics has evolved, with a particular focus on plant epigenetics. We consider what has historically been understood by the term "epigenetics" before turning to the advances in biochemistry, molecular biology, and genetics which have led to current-day definitions of the term. Following this, we pay attention to key discoveries in the field of epigenetics that have emerged from the study of unusual and enigmatic phenomena in plants. Many of these phenomena have involved cases of non-Mendelian inheritance and have often been dismissed as mere curiosities prior to the elucidation of their molecular mechanisms. In the penultimate section, consideration is given to how advances in molecular techniques are opening the doors to a more comprehensive understanding of epigenetic phenomena in plants. We conclude by assessing some opportunities, challenges, and techniques for epigenetic research in both model and non-model plants, in particular for advancing understanding of the regulation of genome function by epigenetic mechanisms.

Improved silencing suppression and enhanced heterologous protein expression are achieved using an engineered viral helper component proteinase

RNA silencing limits transient expression of heterologous proteins in plants. Co-expression of viral silencing suppressor proteins can increase and prolong protein expression, but highly efficient silencing suppressors may stress plant tissue and be detrimental to protein yields. Little is known whether silencing suppression could be improved without harm to plant tissues. This study reports development of enhanced silencing suppressors by engineering the helper component proteinase (HCpro) of Potato virus A (PVA). Mutations were introduced to a short region of HCpro (positions 330-335 in PVA HCpro), which is hypervariable among potyviruses. Three out of the four HCpro mutants suppressed RNA silencing more efficiently and sustained expression of co-expressed jellyfish green fluorescent protein for a longer time than wild-type HCpro in agroinfiltrated leaves of Nicotiana benthamiana. Leaf tissues remained healthy-looking without any visible signs of stress.

Insulin-like peptides (AmILP1 and AmILP2) differentially affect female caste development in the honey bee (Apis mellifera L.)

The food a honey bee female larva receives determines whether she develops into a large long-lived fertile queen or a short-lived sterile worker. Through well-established nutrient-sensing and growth-promoting functions in metazoans, the insulin/insulin-like growth factor 1 signaling (IIS) pathway has become a focal topic in investigations on how differences in food environment can be translated into internal signals responsible for queen-worker determination. However, low expression levels of two insulin receptors (AmInRs) in honey bee larvae and the failure of one AmInR to influence caste differentiation are in potential conflict with such a classical growth-promoting role of IIS in queen-worker development. In view of such an apparent contradiction, and the fact that binding partners and affinities of these two AmInRs have not been worked out, we performed a functional study on insulin-like peptide genes (AmILP1 and AmILP2) in honey bee larvae by using a double-stranded RNA (dsRNA)-mediated gene knockdown approach. We found that juvenile hormone (JH) levels were diminished by AmILP1 dsRNA treatment, while the AmILP2 knockdown caused a reduction in ovary size. Blood sugar titers were not significantly affected by the treatments. From these results we conclude that AmILP2 transcript levels may influence specific organ development, such as the ovary and body mass, while more general traits of caste differentiation, such as mandibles, may require additional regulators. In addition, JH production may be regulated by AmILP1 expressed locally in the brain, similar to the function of certain ILPs in Drosophila.

Molecular analysis of transgenic melon plants showing virus resistance conferred by direct repeat of movement gene of Cucumber green mottle mosaic virus

Cucumber green mottle mosaic virus (CGMMV) is a major limiting factor in the production of melon plants worldwide. For effective control of this virus using the transgenic approach, the direct repeat of the movement protein gene of CGMMV was used for transforming melon plants by Agrobacterium tumefaciens. PCR and Southern blot analyses of T₃ confirmed that they carried the transgene. Northern blot analysis with total RNA showed that transgene transcript RNA as well as siRNA was observed in all plants tested. Separate leaves or individual plants were inoculated with CGMMV and subjected to ELISA and RNA blot analysis using the coat protein gene probe of the virus. Compared to nontransgenic control, these plants were shown to have high virus resistance. Furthermore, cytosine of the transgene DNA in the plants was methylated. Thus, these results reveal that the transgenic lines were highly resistant to the virus through RNA silencing. Key message High virus resistance was obtained in transgenic melon plants with direct repeat of movement protein gene of Cucumber green mottle mosaic tobamovirus through RNA silencing.

Delay in virus accumulation and low virus transmission from transgenic rice plants expressing Rice tungro spherical virus RNA

Rice tungro, a devastating viral disease of rice in South and Southeast Asia, is caused by the joint infection of a DNA virus, Rice tungro bacilliform virus (RTBV) and an RNA virus Rice tungro spherical virus (RTSV). RTBV and RTSV are transmitted exclusively by the insect vector Green leafhopper (GLH). RTSV is necessary for the transmission of RTBV. To obtain transgenic resistance against RTSV, indica rice plants were transformed using DNA constructs designed to express an untranslatable sense or anti-sense RTSV RNA. Progeny of primary transformants showing low copies of the integrated transgenes and accumulating the corresponding transcripts at low levels were challenged with viruliferous GLH. Three out of four transgenic plant lines expressing untranslatable RTSV RNA in the sense orientation and two out of the four lines expressing an RTSV gene in the anti-sense orientation showed delayed buildup of RTSV RNA over time. Transmission of RTBV from the above lines was reduced significantly.

Vector-initiated transitive RNA interference in the filamentous fungus Aspergillus oryzae

RNA interference (RNAi), modulates gene expression via cleavage of double-stranded RNA (dsRNA) by Dicer, producing 21-25 nucleotide silence-inducing RNAs (siRNAs). In association with Argonaute containing complexes, these siRNAs target sequence-specific degradation of the homologous single-stranded messenger RNA. In the majority of eukaryotes, degradation occurs within the boundaries of the dsRNA target. In Arabidopsis thaliana and Caenorhabditis elegans, gene silencing can also take place transitively, impacting transcripts from coding sequences that are adjacent to the intended target gene. Here we demonstrate effective transitive RNAi in the ascomycete Aspergillus oryzae. Fragments of 174 bp and 499 bp derived from the A. oryzae wA gene involved in spore color development, were inserted immediately upstream of an inverted repeat derived from the Escherichia coli gene encoding for Hygromycin Phosphotransferase B (hph), which provided a double-stranded hph RNAi trigger. Introduction of this construct into A. oryzae host cells produced transformants with spores that were lighter in color than those of wild type. Real-time RT-qPCR analysis demonstrated a direct correspondence of steady-state wA mRNA level to spore color. An A. oryzae strain deficient in RNA-dependent RNA Polymerase (RdRP) produced exclusively wild type colored spores when transformed with a wA transitive RNAi construct. Conversely, increased expression of RdRP enhanced the incidence of wA gene silencing via transitive RNAi.

A historical overview of RNAi in plants

RNA interference, or RNAi, is arguably one of the most significant discoveries in biology in the last several decades. First recognized in plants (where it was called post-transcriptional gene silencing, PTGS) RNAi is a gene down-regulation mechanism since demonstrated to exist in all eukaryotes. In RNAi, small RNAs (of about 21-24 nucleotides) function to guide specific effector proteins (members of the Argonaute protein family) to a target nucleotide sequence by complementary base pairing. The effector protein complex then down-regulates the expression of the targeted RNA or DNA. Small RNA-directed gene regulation systems were independently discovered (and named) in plants, fungi, worms, flies, and mammalian cells. Collectively, PTGS, RNA silencing, and co-suppression (in plants); quelling (in fungi and algae); and RNAi (in Caenorhabditis elegans, Drosophila, and mammalian cells) are all examples of small RNA-based gene regulation systems. From the very beginning, plant research has had a major impact on our understanding of RNAi. The purpose of this chapter is to provide an historical perspective and overview on the discovery, characterization, and applications of RNAi in plants.

Field testing, gene flow assessment and pre-commercial studies on transgenic Solanum tuberosum spp. tuberosum (cv. Spunta) selected for PVY resistance in Argentina

Solanum tuberosum ssp. tuberosum (cv. Spunta) was transformed with a chimeric transgene containing the Potato virus Y (PVY) coat protein (CP) sequence. Screening for PVY resistance under greenhouse conditions yielded over 100 independent candidate lines. Successive field testing of selected lines allowed the identification of two genetically stable PVY-resistant lines, SY230 and SY233, which were further evaluated in field trials at different potato-producing regions in Argentina. In total, more than 2,000 individuals from each line were tested along a 6-year period. While no or negligible PVY infection was observed in the transgenic lines, infection rates of control plants were consistently high and reached levels of up to 70-80%. Parallel field studies were performed in virus-free environments to assess the agronomical performance of the selected lines. Tubers collected from these assays exhibited agronomical traits and biochemical compositions indistinguishable from those of the non-transformed Spunta cultivar. In addition, an interspecific out-crossing trial to determine the magnitude of possible natural gene flow between transgenic line SY233 and its wild relative Solanum chacoense was performed. This trial yielded negative results, suggesting an extremely low probability for such an event to occur.

Transient co-expression of post-transcriptional gene silencing suppressors for increased in planta expression of a recombinant anthrax receptor fusion protein

Potential epidemics of infectious diseases and the constant threat of bioterrorism demand rapid, scalable, and cost-efficient manufacturing of therapeutic proteins. Molecular farming of tobacco plants provides an alternative for the recombinant production of therapeutics. We have developed a transient production platform that uses Agrobacterium infiltration of Nicotiana benthamiana plants to express a novel anthrax receptor decoy protein (immunoadhesin), CMG2-Fc. This chimeric fusion protein, designed to protect against the deadly anthrax toxins, is composed of the von Willebrand factor A (VWA) domain of human capillary morphogenesis 2 (CMG2), an effective anthrax toxin receptor, and the Fc region of human immunoglobulin G (IgG). We evaluated, in N. benthamiana intact plants and detached leaves, the expression of CMG2-Fc under the control of the constitutive CaMV 35S promoter, and the co-expression of CMG2-Fc with nine different viral suppressors of post-transcriptional gene silencing (PTGS): p1, p10, p19, p21, p24, p25, p38, 2b, and HCPro. Overall, transient CMG2-Fc expression was higher on intact plants than detached leaves. Maximum expression was observed with p1 co-expression at 3.5 days post-infiltration (DPI), with a level of 0.56 g CMG2-Fc per kg of leaf fresh weight and 1.5% of the total soluble protein, a ten-fold increase in expression when compared to absence of suppression. Co-expression with the p25 PTGS suppressor also significantly increased the CMG2-Fc expression level after just 3.5 DPI.

EGO-1, a C. elegans RdRP, modulates gene expression via production of mRNA-templated short antisense RNAs

BACKGROUND

The development of the germline in Caenorhabditis elegans is a complex process involving the regulation of thousands of genes in a coordinated manner. Several genes required for small RNA biogenesis and function are among those required for the proper organization of the germline. EGO-1 is a putative RNA-directed RNA polymerase (RdRP) that is required for multiple aspects of C. elegans germline development and efficient RNA interference (RNAi) of germline-expressed genes. RdRPs have been proposed to act through a variety of mechanisms, including the posttranscriptional targeting of specific mRNAs, as well as through a direct interaction with chromatin. Despite extensive investigation, the molecular role of EGO-1 has remained enigmatic.

RESULTS

Here we use high-throughput small RNA and messenger RNA sequencing to investigate EGO-1 function. We found that EGO-1 is required to produce a distinct pool of small RNAs antisense to a number of germline-expressed mRNAs through several developmental stages. These potential mRNA targets fall into distinct classes, including genes required for kinetochore and nuclear pore assembly, histone-modifying activities, and centromeric proteins. We also found several RNAi-related genes to be targets of EGO-1. Finally, we show a strong association between the loss of small RNAs and the rise of mRNA levels in ego-1(-) animals.

CONCLUSIONS

Our data support the conclusion that EGO-1 produces triphosphorylated small RNAs derived from mRNA templates and that these small RNAs modulate gene expression through the targeting of their cognate mRNAs.

Antiviral strategies in plants based on RNA silencing

One of the challenges being faced in the twenty-first century is the biological control of plant viral infections. Among the different strategies to combat virus infections, those based on pathogen-derived resistance (PDR) are probably the most powerful approaches to confer virus resistance in plants. The application of the PDR concept not only revealed the existence of a previously unknown sequence-specific RNA-degradation mechanism in plants, but has also helped to design antiviral strategies to engineer viral resistant plants in the last 25 years. In this article, we review the different platforms related to RNA silencing that have been developed during this time to obtain plants resistant to viruses and illustrate examples of current applications of RNA silencing to protect crop plants against viral diseases of agronomic relevance. This article is part of a Special Issue entitled: MicroRNAs in viral gene regulation.

Tapping RNA silencing pathways for plant biotechnology

Plants have evolved a variety of gene silencing pathways mediated by small RNAs. Mostly 21 or 24 nt in size, these small RNAs repress the expression of sequence homologous genes at the transcriptional, post-transcriptional and translational levels. These pathways, also referred as RNA silencing pathways, play important roles in regulating growth and development as well as in response to both biotic and abiotic stress. Although the molecular basis of these complicated and interconnected pathways has become clear only in recent years, RNA silencing effects were observed and utilized in transgenic plants early in the plant biotechnology era, more than two decades ago. Today, with a better understanding of the pathways, various genetic engineering approaches have been developed to apply RNA silencing more effectively and broadly. In addition to summarizing the current models of RNA silencing, this review discusses examples of its potential uses and related issues concerning its application in plant biotechnology.

A viral suppressor P1/HC-pro increases the GFP gene expression in agrobacterium-mediated transient assay

More than 20 post-transcriptional gene silencing (PTGS) suppressors have been found since HC-Pro, the first gene silencing suppressor, was found in 1998. The silencing suppressor strongly suggested that gene silencing functions as natural defense mechanisms against viruses. It also represented a valuable tool for the dissection of the gene silencing pathway. We have used P1/HC-Pro RNA silencing suppressor activity to increase green fluorescent protein (GFP) expression in tobacco using an Agrobacterium-mediated transient expression system. P1/HC-Pro stimulated GFP-gene expression but not dsGFP-gene expression was shown by RT-PCR, Northern and Western blot analysis. Expression of the gene silencing suppressor and the target gene provided a new strategy of heterogeneous gene expressing in plants. It may be of commercial significance to produce foreign proteins using plant bioreactors.

Molecular therapy and prevention of liver diseases

Molecular analyses have become an integral part of biomedical research as well as clinical medicine. The definition of the molecular and genetic basis of many human diseases has led to a better understanding of their pathogenesis and has in addition offered new perspectives for their diagnosis, therapy and prevention. Genetically, liver diseases can be classified as hereditary monogenic, acquired monogenic, complex genetic and diseases. Based on this classification, gene therapy is based on six concepts: gene repair, gene substitution, cell therapy, block of gene expression or function, DNA vaccination as well as gene augmentation. While recent developments are promising, various delivery, targeting and safety issues need to be addressed before gene therapy will enter clinical practice. In the future, molecular diagnosis and therapy liver diseases will be part of our patient management and complement existing diagnostic, therapeutic and preventive strategies.

Cytosine methylation is associated with RNA silencing in silenced plants but not with systemic and transitive RNA silencing through grafting

RNA silencing is often associated with methylation of the target gene. The DNA methylation level of transgenes was investigated in post-transcriptionally silenced or non-silenced Nicotiana benthamiana carrying either the 5' region (200 or 400 bp) or the entire region of the coat protein gene (CP, including the 3' non-translated region) of Sweet potato feathery mottle virus. Higher levels of transgene cytosine methylation were observed in both symmetrical (CpG, CpNpG) and non-symmetrical (CpHpH) contexts (CpG>CpNpG>CpHpH) in silenced lines, but there was very lower levels or no transgene methylation in non-silenced lines. RNA silencing was induced in non-silenced scions from silenced rootstocks and spread to the 3' region of the transgene mRNA (Haque et al., Plant Mol. Biol. 2007; 63: 35-47). In this system, transgene methylation levels were analyzed in scions at different time intervals after being grafted onto silenced or non-silenced rootstocks to investigate if transgene methylation was associated with induction or transitivity of RNA silencing. We observed that, there was no change of transgene methylation level in the initial target or in extended regions in scions. These results showed that transgene methylation was associated with RNA silencing in individual transformants, but it was not associated with systemic RNA silencing and/or transitive RNA silencing through grafting.

VPg of Potato virus A alone does not suppress RNA silencing but affects virulence of a heterologous virus

The viral genome-linked protein (VPg) is a well-known virulence factor in potyviruses (genus Potyvirus), including Potato virus A (PVA). Its ability to suppress onset and signalling of transgene-mediated RNA silencing and accumulation of small interfering RNA (siRNA) was studied using cross-protection and Agrobacterium infiltration assays and green fluorescent protein (GFP) and PVA VPg protein-expressing transgenic Nicotiana benthamiana plants. N. benthamiana plants were also transformed with a transgene comprising the cylindrical inclusion protein (CI), nuclear inclusion protein a (NIa) and coat protein (CP) encoding regions of PVA. This transgene mRNA was expressed in the T1 progeny of the transgenic lines but all were susceptible to PVA. This result contrasted the plants transformed with the PVA P1, VPg (N-proximal part of NIa) or CP encoding regions that expressed various forms of resistance. There was little evidence for direct involvement of VPg in suppression of silencing, while other mechanisms by which VPg might interfere with transgenic resistance could not be excluded. Expression of the wild-type PVA VPg from the genome of Potato virus X (PVX, genus Potexvirus) increased symptom severity in N. benthamiana, whereas a single point mutation introduced to the VPg enhanced accumulation of the PVX chimera. These data demonstrated previously unknown virulence functions controlled by the VPg of a potyvirus.

Distinct populations of primary and secondary effectors during RNAi in C. elegans

RNA interference (RNAi) is a phylogenetically widespread gene-silencing process triggered by double-stranded RNA. In plants and Caenorhabditis elegans, two distinct populations of small RNAs have been proposed to participate in RNAi: "Primary siRNAs" (derived from DICER nuclease-mediated cleavage of the original trigger) and "secondary siRNAs" [additional small RNAs whose synthesis requires an RNA-directed RNA polymerase (RdRP)]. Analyzing small RNAs associated with ongoing RNAi in C. elegans, we found that secondary siRNAs constitute the vast majority. The bulk of secondary siRNAs exhibited structure and sequence indicative of a biosynthetic mode whereby each molecule derives from an independent de novo initiation by RdRP. Analysis of endogenous small RNAs indicated that a fraction derive from a biosynthetic mechanism that is similar to that of secondary siRNAs formed during RNAi, suggesting that small antisense transcripts derived from cellular messenger RNAs by RdRP activity may have key roles in cellular regulation.

Development of resistant transgenic soybeans with inverted repeat-coat protein genes of soybean dwarf virus

In an attempt to generate soybean plants resistant to soybean dwarf virus (SbDV), we transformed a construct containing inverted repeat-SbDV coat protein (CP) genes spaced by beta-glucuronidase (GUS) sequences into soybean somatic embryos via microprojectile bombardment. Three T(0) plants with an introduced CP gene were obtained, and one generated T(1) seeds. The presence of the transgene in T(1) plants was confirmed by PCR and Southern blot hybridization analysis, but expression of CP was not detected by northern blot hybridization analysis. Two months after inoculation of SbDV by aphid, T(2) plants contained little SbDV-specific RNA and remained symptomless. These plants contained SbDV-CP-specific siRNA. These results suggest that the T(2) plants achieved resistance to SbDV by an RNA-silencing-mediated process.

Synergistic Disease in Pepper Caused by the Mixed Infection of Cucumber mosaic virus and Pepper mottle virus

ABSTRACT The occurrence of more than one virus species in a single plant is not uncommon in cultivated and native plant species. A mixed virus infection may lead to greater disease severity than individual viral components and this is sometimes referred to as a synergistic disease. Although, in some cases, synergism has been demonstrated for various plant growth parameters such as plant height, weight, and yield, proof of synergy typically has not been demonstrated for symptom severity when the mixed virus infection was not lethal. We demonstrated synergy in bell pepper plants co-infected with Cucumber mosaic virus (CMV) and Pepper mottle virus (PepMoV) relative to each virus alone for stem height (two of three trials) and aboveground fresh weight (one of three trials) using factorial analysis and Abbott's equation for synergy. This approach allowed affirmation of the type of response (i.e., synergistic rather than antagonistic) and statistical proof of synergy. A detailed evaluation of symptom severity for each viral treatment revealed three phases associated with host plant developmental stages. A numerical symptom severity rating scale was developed and used in each of two equations to demonstrate statistical proof for synergy based on symptom severity for co-infected plants. Virus accumulation in noninoculated leaves was determined by enzyme-linked immunosorbent assay. In singly infected plants, CMV titers declined in mildly symptomatic leaves representing later stages of plant development, but titers increased in similar leaves of co-infected plants. In contrast, PepMoV titers did not differ in singly or co-infected plants.

Antiviral applications of RNAi for coronavirus

Until the appearance of severe acute respiratory syndrome (SARS), caused by the SARS coronavirus (SARS-CoV) in early 2003, coronavirus infection was not considered to be serious enough to be controlled by either vaccination or specific antiviral therapy. It is now believed that the availability of antiviral drugs effective against SARS-CoV will be crucial for the control of future SARS outbreaks. Recently, RNA interference has been successfully used as a more specific and efficient method for gene silencing. RNA interference induced by small interfering RNA can inhibit the expression of viral antigens and so provides a new approach to the therapy of pathogenic viruses. This review provides an overview of current information on coronavirus and the application of small interfering RNA in viral therapeutics, with particular reference to SARS-CoV.

Plant pathology and RNAi: a brief history

This article describes the discovery of RNA-activated sequence-specific RNA degradation, a phenomenon now referred to as RNA silencing or RNA interference (RNAi). From 1992 to 1996, a series of articles were published on virus resistant transgenic plants expressing either translatable or nontranslatable versions of the coat protein gene of Tobacco etch virus (TEV). Certain transgenic plant lines were resistant to TEV but not to closely related viruses. In these plants a surprising correlation was observed: Transgenic plant lines with the highest degree of TEV resistance had actively transcribed transgenes but low steady-state levels of transgene RNA. Molecular analysis of these transgenic plants demonstrated the existence of a cellular-based, sequence-specific, posttranscriptional RNA-degradation system that was programmed by the transgene-encoded RNA sequence. This RNA-degradation activity specifically targeted both the transgene RNA and TEV (viral) RNA for degradation and was the first description of RNA-mediated gene silencing.

Revealing the world of RNA interference

The recent discoveries of RNA interference and related RNA silencing pathways have revolutionized our understanding of gene regulation. RNA interference has been used as a research tool to control the expression of specific genes in numerous experimental organisms and has potential as a therapeutic strategy to reduce the expression of problem genes. At the heart of RNA interference lies a remarkable RNA processing mechanism that is now known to underlie many distinct biological phenomena.

Human influenza virus NS1 protein enhances viral pathogenicity and acts as an RNA silencing suppressor in plants

RNA silencing has a well-established function as an antiviral defence mechanism in plants and insects. Using an Agrobacterium-mediated transient assay, we report here that NS1 protein from human influenza A virus suppresses RNA silencing in plants in a manner similar to P1/HC-Pro protein of Tobacco etch potyvirus, a well-characterized plant virus silencing suppressor. Moreover, we have shown that NS1 protein expression strongly enhances the symptoms of Potato virus X in three different plant hosts, suggesting that NS1 protein could be inhibiting defence mechanisms activated in the plant on infection. These data provide further evidence that an RNA silencing pathway could also be activated as a defence response in mammals.

Identification of a mitochondrial external NADPH dehydrogenase by overexpression in transgenic Nicotiana sylvestris

The plant respiratory chain contains a complex setup of non-energy conserving NAD(P)H dehydrogenases, the physiological consequences of which are highly unclear. An expression construct for the potato (Solanum tuberosum L., cv. Desiree) ndb1 gene, a homologue of bacterial and fungal type II NAD(P)H dehydrogenases, was introduced into Nicotiana sylvestris. Transgenic lines with high transcript and protein levels for St-NDB1 had up to threefold increased activity of external NADPH dehydrogenase in isolated mitochondria as compared to the wild type (WT). In two lines, the external NADPH dehydrogenase activity was instead 10-fold decreased, indicating that the corresponding N. sylvestris gene had been suppressed. Activities of external and internal rotenone-insensitive NADH dehydrogenases were unchanged in the transgenic lines. The results demonstrate that the St-ndb1 encodes an external dehydrogenase specific for NADPH and dependent on calcium for activity. Transgenic lines overexpressing St-ndb1 had specifically increased protein levels for alternative oxidase and uncoupling protein, as compared to the WT and one co-suppressing line. This indicates cross-talk in the expressional control, or metabolic conditions influencing it, for the different categories of energy-dissipating proteins that bypass oxidative phosphorylation. The potential effects of external NADPH oxidation on other cellular processes are discussed.

Translation start sequences affect the efficiency of silencing of Agrobacterium tumefaciens T-DNA oncogenes

Agrobacterium tumefaciens oncogenes cause transformed plant cells to overproduce auxin and cytokinin. Two oncogenes encode enzymes that convert tryptophan to indole-3-acetic acid (auxin): iaaM (tryptophan mono-oxygenase) and iaaH (indole-3-acetamide hydrolase). A third oncogene (ipt) encodes AMP isopentenyl transferase, which produces cytokinin (isopentenyl-AMP). Inactivation of ipt and iaaM (or iaaH) abolishes tumorigenesis. Because adequate means do not exist to control crown gall, we created resistant plants by introducing transgenes designed to elicit posttranscriptional gene silencing (PTGS) of iaaM and ipt. Transgenes that elicit silencing trigger sequence-specific destruction of the inducing RNA and messenger RNAs with related sequences. Although PTGS has proven effective against a variety of target genes, we found that a much higher percentage of transgenic lines silenced iaaM than ipt, suggesting that transgene sequences influenced the effectiveness of PTGS. Sequences required for oncogene silencing included a translation start site. A transgene encoding a translatable sense-strand RNA from the 5' end of iaaM silenced the iaaM oncogene, but deletion of the translation start site abolished the ability of the transgene to silence iaaM. Silencing A. tumefaciens T-DNA oncogenes is a new and effective method to produce plants resistant to crown gall disease.

Cucumber mosaic virus infection transiently breaks dsRNA-induced transgenic immunity to Potato virus Y in tobacco

Post-transcriptional gene silencing (PTGS), an intrinsic plant defense mechanism, can be efficiently triggered by double stranded (ds)RNA-producing transgenes and can provide high level virus resistance by specific targeting of cognate viral RNA. The discovery of virus-encoded suppressors of PTGS led to concerns about the stability of such resistance. Here, we show that Cucumber mosaic virus (CMV) is able to suppress dsRNA-induced PTGS and the associated Potato virus Y (PVY) immunity in tobacco. CMV suppression supported only a transient PVY accumulation and did not prevent recovery of the transgenic plants from PVY infection. CMV inoculation resulted in strongly increased transgene mRNA levels due to suppression of PTGS, but accumulation of PVY-specific small interfering (si)RNA was unaffected. However, PVY accumulation in previously immune plants resulted in increased PVY siRNA levels and transgene mRNA was no longer detected, despite the presence of CMV. Transgene mRNA returned to high levels once PVY was no longer detected in CMV-infected plants. Recovered and chronically CMV-infected tissues were immune to further PVY infection.

Double-stranded RNA-mediated gene silencing in fission yeast

Double-stranded RNA (dsRNA) can specifically inhibit gene expression in a variety of organisms by invoking post-transcriptional degradation of homologous mRNA. Here we show that dsRNA-mediated gene regulation also occurs in the fission yeast Schizosaccharomyces pombe. We present evidence that: (i) reporter gene silencing is significantly enhanced when additional non-coding sense RNA is co-expressed with antisense RNA; (ii) expression of a panhandle RNA also silences target gene expression; (iii) expression of dsRNA is associated with siRNAs; (iv) a novel host-encoded factor which enhances antisense RNA gene silencing also enhances panhandle RNA-mediated gene inhibition. Both the exogenously introduced lacZ and c-myc genes are shown to be susceptible to dsRNA- mediated gene silencing in this model. Taken together, these data indicate that RNA-mediated gene silencing can occur through a RNAi-like mechanism in fission yeast.

RNA silencing bridging the gaps in wheat extracts

In plants, RNA silencing plays important roles in antiviral defence, genome integrity and development. This process involves nucleotide sequence-specific interactions that are mediated by small RNA molecules of 21-25 nucleotides. Although the core biochemical reactions of RNA silencing have been well characterized in animals, such information was crucially missing in plants. Recent work now addresses this question and reveals an overall similarity between the plant and animal RNA-silencing pathways, as well as some intriguing plant-specific aspects.

Gene silencing

Gene silencing has evolved in a broad range of organisms probably as defense mechanisms against invasive nucleic acids. Two major strategies are utilized. Transcriptional gene silencing (TGS) acts to prevent RNA synthesis and posttranscriptional gene silencing (PTGS) acts to degrade existing RNA. Although the final effects are similar, the mechanisms of TGS and PTGS are species specific. In most eukaryotes, gene silencing is associated with de novo DNA methylation. However, Caenorhabditis elegans shows an efficient PTGS-like mechanism but lacks a DNA methylation system. Additionally, key enzymes involved in plant and nematode PTGS, the cellular RNA-directed RNA polymerases, appear to be missing in Drosophila melanogaster. In this review, we discuss common features of TGS and PTGS that have been identified across species but for TGS we will concentrate only on methylation-mediated gene inactivation. This effort is complicated by the vague borders between gene silencing and normal gene regulation. Mechanisms that are involved in gene silencing are also used to regulate controlled expression of endogenous genes. To outline the general aspects, gene silencing will be defined as narrowly as possible. The intention behind this review is to stimulate discussion and we seek to facilitate this by introducing speculative concepts that could lead to some reappraisal of the literature.

An active role for endogenous beta-1,3-glucanase genes in transgene-mediated co-suppression in tobacco

Post-transcriptional gene silencing (PTGS) is characterized by the accumulation of short interfering RNAs that are proposed to mediate sequence-specific degradation of cognate and secondary target mRNAs. In plants, it is unclear to what extent endogenous genes contribute to this process. Here, we address the role of the endogenous target genes in transgene-mediated PTGS of beta-1,3-glucanases in tobacco. We found that mRNA sequences of the endogenous glucanase glb gene with varying degrees of homology to the Nicotiana plumbaginifolia gn1 transgene are targeted by the silencing machinery, although less efficiently than corresponding transgene regions. Importantly, we show that endogene-specific nucleotides in the glb sequence provide specificity to the silencing process. Consistent with this finding, small sense and antisense 21- to 23-nucleotide RNAs homologous to the endogenous glb gene were detected. Combined, these data demonstrate that a co-suppressed endogenous glucan ase gene is involved in signal amplification and selection of homologous targets, and show that endogenous genes can actively participate in PTGS in plants. The findings are introduced as a further sophistication of the post-transciptional silencing model.