Journal articles: 'Plant gene silencing'

1

Richards, Kenneth E. "Plant Gene Silencing." Plant Science 162, no. 4 (April 2002): 643. http://dx.doi.org/10.1016/s0168-9452(02)00006-7.

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Unver, Turgay, and Hikmet Budak. "Virus-Induced Gene Silencing, a Post Transcriptional Gene Silencing Method." International Journal of Plant Genomics 2009 (June 15, 2009): 1–8. http://dx.doi.org/10.1155/2009/198680.

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Virus-induced gene silencing (VIGS) is one of the reverse genetics tools for analysis of gene function that uses viral vectors carrying a target gene fragment to produce dsRNA which trigger RNA-mediated gene silencing. There are a number of viruses which have been modified to silence the gene of interest effectively with a sequence-specific manner. Therefore, different types of methodologies have been advanced and modified for VIGS approach. Virus-derived inoculations are performed on host plants using different methods such as agro-infiltration and in vitro transcriptions. VIGS has many advantages compared to other loss-of-gene function approaches. The approach provides the generation of rapid phenotype and no need for plant transformation. The cost of VIGS experiment is relatively low, and large-scale analysis of screening studies can be achieved by the VIGS. However, there are still limitations of VIGS to be overcome. Nowadays, many virus-derived vectors are optimized to silence more than one host plant such as TRV-derived viral vectors which are used for Arabidopsis and Nicothiana benthamiana. By development of viral silencing systems monocot plants can also be targeted as silencing host in addition to dicotyledonous plants. For instance, Barley stripe mosaic virus (BSMV)-mediated VIGS allows silencing of barley and wheat genes. Here we summarize current protocols and recent modified viral systems to lead silencing of genes in different host species.

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Bruening, G. "Plant gene silencing regularized." Proceedings of the National Academy of Sciences 95, no. 23 (November 10, 1998): 13349–51. http://dx.doi.org/10.1073/pnas.95.23.13349.

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Senior, Ian J. "Uses of Plant Gene Silencing." Biotechnology and Genetic Engineering Reviews 15, no. 1 (April 1998): 79–120. http://dx.doi.org/10.1080/02648725.1998.10647953.

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Land, K. "Gene silencing and plant antiviral immunity." Trends in Genetics 17, no. 7 (July 1, 2001): 379. http://dx.doi.org/10.1016/s0168-9525(01)02404-0.

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Bucher, Etienne, Titia Sijen, Peter de Haan, Rob Goldbach, and Marcel Prins. "Negative-Strand Tospoviruses and Tenuiviruses Carry a Gene for a Suppressor of Gene Silencing at Analogous Genomic Positions." Journal of Virology 77, no. 2 (January 15, 2003): 1329–36. http://dx.doi.org/10.1128/jvi.77.2.1329-1336.2003.

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ABSTRACT Posttranscriptional silencing of a green fluorescent protein (GFP) transgene in Nicotiana benthamiana plants was suppressed when these plants were infected with Tomato spotted wilt virus (TSWV), a plant-infecting member of the Bunyaviridae. Infection with TSWV resulted in complete reactivation of GFP expression, similar to the case for Potato virus Y, but distinct from that for Cucumber mosaic virus, two viruses known to carry genes encoding silencing suppressor proteins. Agrobacterium-based leaf injections with individual TSWV genes identified the NSS gene to be responsible for the RNA silencing-suppressing activity displayed by this virus. The absence of short interfering RNAs in NSS-expressing leaf sectors suggests that the tospoviral NSS protein interferes with the intrinsic RNA silencing present in plants. Suppression of RNA silencing was also observed when the NS3 protein of the Rice hoja blanca tenuivirus, a nonenveloped negative-strand virus, was expressed. These results indicate that plant-infecting negative-strand RNA viruses carry a gene for a suppressor of RNA silencing.

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Qiao, Yongli, Rui Xia, Jixian Zhai, Yingnan Hou, Li Feng, Yi Zhai, and Wenbo Ma. "Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens." Annual Review of Phytopathology 59, no. 1 (August 25, 2021): 265–88. http://dx.doi.org/10.1146/annurev-phyto-121520-023514.

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Gene silencing guided by small RNAs governs a broad range of cellular processes in eukaryotes. Small RNAs are important components of plant immunity because they contribute to pathogen-triggered transcription reprogramming and directly target pathogen RNAs. Recent research suggests that silencing of pathogen genes by plant small RNAs occurs not only during viral infection but also in nonviral pathogens through a process termed host-induced gene silencing, which involves trans-species small RNA trafficking. Similarly, small RNAs are also produced by eukaryotic pathogens and regulate virulence. This review summarizes the small RNA pathways in both plants and filamentous pathogens, including fungi and oomycetes, and discusses their role in host–pathogen interactions. We highlight secondarysmall interfering RNAs of plants as regulators of immune receptor gene expression and executors of host-induced gene silencing in invading pathogens. The current status and prospects of trans-species gene silencing at the host–pathogen interface are discussed.

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Zhang, Huan, Gozde S. Demirer, Honglu Zhang, Tianzheng Ye, Natalie S. Goh, Abhishek J. Aditham, Francis J. Cunningham, Chunhai Fan, and Markita P. Landry. "DNA nanostructures coordinate gene silencing in mature plants." Proceedings of the National Academy of Sciences 116, no. 15 (March 25, 2019): 7543–48. http://dx.doi.org/10.1073/pnas.1818290116.

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Delivery of biomolecules to plants relies onAgrobacteriuminfection or biolistic particle delivery, the former of which is amenable only to DNA delivery. The difficulty in delivering functional biomolecules such as RNA to plant cells is due to the plant cell wall, which is absent in mammalian cells and poses the dominant physical barrier to biomolecule delivery in plants. DNA nanostructure-mediated biomolecule delivery is an effective strategy to deliver cargoes across the lipid bilayer of mammalian cells; however, nanoparticle-mediated delivery without external mechanical aid remains unexplored for biomolecule delivery across the cell wall in plants. Herein, we report a systematic assessment of different DNA nanostructures for their ability to internalize into cells of mature plants, deliver siRNAs, and effectively silence a constitutively expressed gene inNicotiana benthamianaleaves. We show that nanostructure internalization into plant cells and corresponding gene silencing efficiency depends on the DNA nanostructure size, shape, compactness, stiffness, and location of the siRNA attachment locus on the nanostructure. We further confirm that the internalization efficiency of DNA nanostructures correlates with their respective gene silencing efficiencies but that the endogenous gene silencing pathway depends on the siRNA attachment locus. Our work establishes the feasibility of biomolecule delivery to plants with DNA nanostructures and both details the design parameters of importance for plant cell internalization and also assesses the impact of DNA nanostructure geometry for gene silencing mechanisms.

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Rodríguez-Negrete, Edgar A., Jimena Carrillo-Tripp, and Rafael F. Rivera-Bustamante. "RNA Silencing against Geminivirus: Complementary Action of Posttranscriptional Gene Silencing and Transcriptional Gene Silencing in Host Recovery." Journal of Virology 83, no. 3 (November 19, 2008): 1332–40. http://dx.doi.org/10.1128/jvi.01474-08.

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ABSTRACT RNA silencing in plants is a natural defense system mechanism against invading nucleic acids such as viruses. Geminiviruses, a family of plant viruses characterized by a circular, single-stranded DNA genome, are thought to be both inducers and targets of RNA silencing. Some natural geminivirus-host interactions lead to symptom remission or host recovery, a process commonly associated with RNA silencing-mediated defense. Pepper golden mosaic virus (PepGMV)-infected pepper plants show a recovery phenotype, which has been associated with the presence of virus-derived small RNAs. The results presented here suggest that PepGMV is targeted by both posttranscriptional and transcriptional gene silencing mechanisms. Two types of virus-related small interfering RNAs (siRNAs) were detected: siRNAs of 21 to 22 nucleotides (nt) in size that are related to the coding regions (Rep, TrAP, REn, and movement protein genes) and a 24-nt population primarily associated to the intergenic regions. Methylation levels of the PepGMV A intergenic and coat protein (CP) coding region were measured by a bisulfite sequencing approach. An inverse correlation was observed between the methylation status of the intergenic region and the concentration of viral DNA and symptom severity. The intergenic region also showed a methylation profile conserved in all times analyzed. The CP region, on the other hand, did not show a defined profile, and its methylation density was significantly lower than the one found on the intergenic region. The participation of both PTGS and TGS mechanisms in host recovery is discussed.

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Schröder, Jens A., and Pauline E. Jullien. "The Diversity of Plant Small RNAs Silencing Mechanisms." CHIMIA International Journal for Chemistry 73, no. 5 (May 29, 2019): 362–67. http://dx.doi.org/10.2533/chimia.2019.362.

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Small RNAs gene regulation was first discovered about 20 years ago. It represents a conserve gene regulation mechanism across eukaryotes and is associated to key regulatory processes. In plants, small RNAs tightly regulate development, but also maintain genome stability and protect the plant against pathogens. Small RNA gene regulation in plants can be divided in two canonical pathways: Post-transcriptional Gene Silencing (PTGS) that results in transcript degradation and/or translational inhibition or Transcriptional Gene Silencing (TGS) that results in DNA methylation. In this review, we will focus on the model plant Arabidopsis thaliana. We will provide a brief overview of the molecular mechanisms involved in canonical small RNA pathways as well as introducing more atypical pathways recently discovered.

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Souza, Amancio José de, Beatriz Madalena Januzzi Mendes, and Francisco de Assis Alves Mourão Filho. "Gene silencing: concepts, applications, and perspectives in woody plants." Scientia Agricola 64, no. 6 (December 2007): 645–56. http://dx.doi.org/10.1590/s0103-90162007000600014.

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RNA interference, transcriptional gene silencing, virus induced gene silencing, and micro RNAs comprise a series of mechanisms capable of suppressing gene expression in plants. These mechanisms reveal similar biochemical pathways and appear to be related in several levels. The ability to manipulate gene silencing has produced transgenic plants able to switch off endogenous genes and invading nucleic acids. This powerful biotechnological tool has provided plant breeders and researchers with great opportunity to accelerate breeding programs and developmental studies in woody plants. This research work reports on gene silencing in woody plants, and discuss applications and future perspectives.

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Pignatta, Daniela, Pavan Kumar, Massimo Turina, Abhaya Dandekar, and Bryce W. Falk. "Quantitative Analysis of Efficient Endogenous Gene Silencing in Nicotiana benthamiana Plants Using Tomato bushy stunt virus Vectors That Retain the Capsid Protein Gene." Molecular Plant-Microbe Interactions® 20, no. 6 (June 2007): 609–18. http://dx.doi.org/10.1094/mpmi-20-6-0609.

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Tomato bushy stunt virus (TBSV) coat protein (CP) replacement vectors have been used previously to silence transgenes (e.g., the green fluorescent protein gene) but have not been effective for silencing endogenous plant genes. New TBSV vectors which retained the CP gene were developed by engineering an XhoI restriction site in three positions (3f, CEB, and CEA) of the pTBSV-100 infectious clone. Magnesium chelatase (ChlH) and phytoene desaturase (PDS) were chosen as targets for endogenous gene silencing. Initial experiments using CP replacement vectors with a 230-bp sense or antisense ChlH insert gave a silencing phenotype prominent only in the first new leaves above those inoculated. No silencing phenotype was apparent beyond these leaves whereas, for PDS, no silencing phenotype was observed. When plants were inoculated with the XhoI insert vectors containing ChlH and PDS sequences, plants showed a silencing phenotype extensively throughout the challenged plant, indicating an improved ability for virus movement and silencing in Nicotiana benthamiana host plants. Silencing efficiencies were quantified using real-time reverse-transcription polymerase chain reaction, indicating specific silencing effects of each individual silencing vector. Only one recombinant vector (pPD-3f5), where the XhoI insert was at the 3′ end of the CP gene, failed to give effective silencing. Here, we show that our new CP-retaining TBSV vectors (CEA-CEB) form typical TBSV virions, retain silencing inserts of variable lengths (110 to 260 nucleotides), and can systemically silence endogenous genes in N. benthamiana.

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Shao, Y., H. L. Zhu, H. Q. Tian, X. G. Wang, X. J. Lin, B. Z. Zhu, Y. H. Xie, and Y. B. Luo. "Virus-induced gene silencing in plant species." Russian Journal of Plant Physiology 55, no. 2 (March 2008): 168–74. http://dx.doi.org/10.1134/s1021443708020027.

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14

Vaucheret, Hervé, Christophe Béclin, and Mathilde Fagard. "Post-transcriptional gene silencing in plants." Journal of Cell Science 114, no. 17 (September 1, 2001): 3083–91. http://dx.doi.org/10.1242/jcs.114.17.3083.

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Post-transcriptional gene silencing (PTGS) in plants is an RNA-degradation mechanism that shows similarities to RNA interference (RNAi) in animals. Indeed, both involve double-stranded RNA (dsRNA), spread within the organism from a localised initiating area, correlate with the accumulation of small interfering RNA (siRNA) and require putative RNA-dependent RNA polymerases, RNA helicases and proteins of unknown functions containing PAZ and Piwi domains. However, some differences are evident. First, PTGS in plants requires at least two genes – SGS3 (which encodes a protein of unknown function containing a coil-coiled domain) and MET1 (which encodes a DNA-methyltransferase) – that are absent in C. elegans and thus are not required for RNAi. Second, all Arabidopsis mutants that exhibit impaired PTGS are hypersusceptible to infection by the cucumovirus CMV, indicating that PTGS participates in a mechanism for plant resistance to viruses. Interestingly, many viruses have developed strategies to counteract PTGS and successfully infect plants – for example, by potentiating endogenous suppressors of PTGS. Whether viruses can counteract RNAi in animals and whether endogenous suppressors of RNAi exist in animals is still unknown.

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Wang, Ming-Bo, and Peter M. Waterhouse. "Application of gene silencing in plants." Current Opinion in Plant Biology 5, no. 2 (April 2002): 146–50. http://dx.doi.org/10.1016/s1369-5266(02)00236-4.

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Patel, R. M., J. A. L. van Kan, A. M. Bailey, and G. D. Foster. "RNA-Mediated Gene Silencing of Superoxide Dismutase (bcsod1) in Botrytis cinerea." Phytopathology® 98, no. 12 (December 2008): 1334–39. http://dx.doi.org/10.1094/phyto-98-12-1334.

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Gene silencing is a powerful tool utilized for identification of gene function and analysis in plants, animals, and fungi. Here, we report the silencing of superoxide dismutase (bcsod1) in Botrytis cinerea through sense and antisense-mediated silencing mechanisms. Because superoxide dismutase (SOD) is a virulence factor, transformants were tested for phenotypic silencing in vitro and reduction in pathogenicity in planta. Plate-based assays with and without paraquat were performed to screen initial silencing efficiency, and a subset of transformants was used for in planta studies of virulence. Transformants exhibiting strongly decreased transcripts levels were recovered with both constructs but none of those exhibited a reduction in virulence in planta. Our investigations may help optimize a high-throughput gene silencing system useful for identifying potential gene targets for future fungal control.

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Furner, Ian J., Mazhar A. Sheikh, and Clare E. Collett. "Gene Silencing and Homology-Dependent Gene Silencing in Arabidopsis: Genetic Modifiers and DNA Methylation." Genetics 149, no. 2 (June 1, 1998): 651–62. http://dx.doi.org/10.1093/genetics/149.2.651.

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Abstract Transgenes inserted into the plant genome can become inactive (gene silencing) or result in silencing of homologous cellular genes [homology-dependent gene silencing (HDG silencing)]. In an earlier study we reported HDG silencing of chalcone synthase (CHS) in Arabidopsis. This study concerns genetic revertants of one of the CHS HDG -silencing transgenic homozygotes. Two monogenic recessive trans-acting mutations (hog1 and ddm1) that impair gene silencing and HDG silencing were identified. These mutations reduce genomic DNA methylation and affect the quantity and size of CHS mRNA. These results imply that DNA methylation is necessary for both gene silencing and HDG silencing. Two further monogenic, trans-acting, recessive mutations (sil1 and sil2) reduce gene silencing but not HDG silencing. The existence of this mutant class shows that gene silencing involves genes that are not necessary for HDG silencing. A further mutant (Catt) was isolated and has an attenuated HDG-silencing T-DNA.

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Vaucheret, Hervé, Christophe Béclin, Taline Elmayan, Frank Feuerbach, Christian Godon, Jean-Benoit Morel, Philippe Mourrain, Jean-Christophe Palauqui, and Samantha Vernhettes. "Transgene-induced gene silencing in plants." Plant Journal 16, no. 6 (December 1998): 651–59. http://dx.doi.org/10.1046/j.1365-313x.1998.00337.x.

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Lahmy, Sylvie, Natacha Bies-Etheve, and Thierry Lagrange. "Plant-specific multisubunit RNA polymerase in gene silencing." Epigenetics 5, no. 1 (January 2010): 4–8. http://dx.doi.org/10.4161/epi.5.1.10435.

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20

Waterhouse, Peter M., and Christopher A. Helliwell. "Exploring plant genomes by RNA-induced gene silencing." Nature Reviews Genetics 4, no. 1 (January 2003): 29–38. http://dx.doi.org/10.1038/nrg982.

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Hedtke, B., and B. Grimm. "Silencing of a plant gene by transcriptional interference." Nucleic Acids Research 37, no. 11 (April 17, 2009): 3739–46. http://dx.doi.org/10.1093/nar/gkp241.

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Paszkowski, J. "Gene silencing and DNA methylation processes." Current Opinion in Plant Biology 4, no. 2 (April 1, 2001): 123–29. http://dx.doi.org/10.1016/s1369-5266(00)00147-3.

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Quốc, Nguyễn Bảo, and Nguyễn Ngọc Bảo Châu. "Perspectives of RNAi studies in plant pathogenic fungi." Vietnam Journal of Biotechnology 14, no. 1 (March 30, 2016): 157–68. http://dx.doi.org/10.15625/1811-4989/14/1/9306.

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RNA silencing, the phenomenon known as RNA interference (RNAi), co-suppression or post-transcriptional gene silencing (PTGS) and quelling, has become more popular in studies of its intrinsic roles and applications in many organisms or of gene functions in a whole genomic scale. Since the discovery of RNA silencing more two decades ago, this powerful technology has demonstrated its applicability in developing RNAi-based drugs for various diseases in human. RNA silencing is also of interest in basic and applied studies in agriculture, especially in plant protection to create crop varieties that are resistant to biotic and abiotic stresses. This review provides an overview of RNA silencing studies in filamentous fungi, the molecular mechanisms of RNA silencing in fungi, and also describes potential applications in plant protection potentially important for the agricultural industry and for global food security.

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Walsh, E., J. M. Elmore, and C. G. Taylor. "Root-Knot Nematode Parasitism Suppresses Host RNA Silencing." Molecular Plant-Microbe Interactions® 30, no. 4 (April 2017): 295–300. http://dx.doi.org/10.1094/mpmi-08-16-0160-r.

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Root-knot nematodes damage crops around the world by developing complex feeding sites from normal root cells of their hosts. The ability to initiate and maintain this feeding site (composed of individual “giant cells”) is essential to their parasitism process. RNA silencing pathways in plants serve a diverse set of functions, from directing growth and development to defending against invading pathogens. Influencing a host’s RNA silencing pathways as a pathogenicity strategy has been well-documented for viral plant pathogens, but recently, it has become clear that silencing pathways also play an important role in other plant pathosystems. To determine if RNA silencing pathways play a role in nematode parasitism, we tested the susceptibility of plants that express a viral suppressor of RNA silencing. We observed an increase in susceptibility to nematode parasitism in plants expressing viral suppressors of RNA silencing. Results from studies utilizing a silenced reporter gene suggest that active suppression of RNA silencing pathways may be occurring during nematode parasitism. With these studies, we provide further evidence to the growing body of plant-biotic interaction research that suppression of RNA silencing is important in the successful interaction between a plant-parasitic animal and its host.

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Cao, Xuesong, Peng Zhou, Xiaoming Zhang, Shifeng Zhu, Xuehua Zhong, Qi Xiao, Biao Ding, and Yi Li. "Identification of an RNA Silencing Suppressor from a Plant Double-Stranded RNA Virus." Journal of Virology 79, no. 20 (October 15, 2005): 13018–27. http://dx.doi.org/10.1128/jvi.79.20.13018-13027.2005.

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ABSTRACT RNA silencing is a mechanism which higher plants and animals have evolved to defend against viral infection in addition to regulation of gene expression for growth and development. As a counterdefense, many plant and some animal viruses studied to date encode RNA silencing suppressors (RSS) that interfere with various steps of the silencing pathway. In this study, we report the first identification of an RSS from a plant double-stranded RNA (dsRNA) virus. Pns10, encoded by S10 of Rice dwarf phytoreovirus (RDV), exhibited RSS activity in coinfiltration assays with the reporter green fluorescent protein (GFP) in transgenic Nicotiana benthamiana line 16c carrying GFP. The other gene segments of the RDV genome did not have such a function. Pns10 suppressed local and systemic silencing induced by sense RNA but did not interfere with local and systemic silencing induced by dsRNA. Expression of Pns10 also increased the expression of β-glucuronidase in transient assays and enhanced Potato virus X pathogenicity in N. benthamiana. Collectively, our results establish Pns10 as an RSS encoded by a plant dsRNA virus and further suggest that Pns10 targets an upstream step of dsRNA formation in the RNA silencing pathway.

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Cooper, Bret, and Kimberly B. Campbell. "Protection Against Common Bean Rust Conferred by a Gene-Silencing Method." Phytopathology® 107, no. 8 (August 2017): 920–27. http://dx.doi.org/10.1094/phyto-03-17-0095-r.

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Rust disease of the dry bean plant, Phaseolus vulgaris, is caused by the fungus Uromyces appendiculatus. The fungus acquires its nutrients and energy from bean leaves using a specialized cell structure, the haustorium, through which it secretes effector proteins that contribute to pathogenicity by defeating the plant immune system. Candidate effectors have been identified by DNA sequencing and motif analysis, and some candidates have been observed in infected leaves by mass spectrometry. To assess their roles in pathogenicity, we have inserted small fragments of genes for five candidates into Bean pod mottle virus. Plants were infected with recombinant virus and then challenged with U. appendiculatus. Virus-infected plants expressing gene fragments for four of five candidate effectors accumulated lower amounts of rust and had dramatically less rust disease. By contrast, controls that included a fungal gene fragment for a septin protein not expressed in the haustorium died from a synergistic reaction between the virus and the fungus. The results imply that RNA generated in the plant moved across the fungal haustorium to silence effector genes important to fungal pathogenicity. This study shows that four bean rust fungal genes encode pathogenicity determinants and that the expression of fungal RNA in the plant can be an effective method for protecting bean plants from rust.

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Dietzgen, R. G., and N. Mitter. "Transgenic gene silencing strategies for virus control." Australasian Plant Pathology 35, no. 6 (2006): 605. http://dx.doi.org/10.1071/ap06064.

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Lenka, Biswajit, Satya Narayan Satapathy, and Manoranjan Senapati. "Engineering Plant Virus Resistance: Gene Silencing to Genome Editing." International Journal of Current Microbiology and Applied Sciences 9, no. 10 (October 10, 2020): 3086–96. http://dx.doi.org/10.20546/ijcmas.2020.910.371.

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Mmeka, Ebelechukwu C., Adenubi Adesoye, Kingsley I. Ubaoji, and Arinze B. Nwokoye. "Gene Silencing Technologies in Creating Resistance to Plant Diseases." International Journal of Plant Breeding and Genetics 8, no. 3 (June 15, 2014): 100–120. http://dx.doi.org/10.3923/ijpbg.2014.100.120.

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Burton, Rachel A., David M. Gibeaut, Antony Bacic, Kim Findlay, Keith Roberts, Andrew Hamilton, David C. Baulcombe, and Geoffrey B. Fincher. "Virus-Induced Silencing of a Plant Cellulose Synthase Gene." Plant Cell 12, no. 5 (May 2000): 691. http://dx.doi.org/10.2307/3870995.

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II, TETSUO. "Effectiveness of plant virus-4 Gene silencing and suppressor." Kagaku To Seibutsu 41, no. 6 (2003): 390–97. http://dx.doi.org/10.1271/kagakutoseibutsu1962.41.390.

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Burton, Rachel A., David M. Gibeaut, Antony Bacic, Kim Findlay, Keith Roberts, Andrew Hamilton, David C. Baulcombe, and Geoffrey B. Fincher. "Virus-Induced Silencing of a Plant Cellulose Synthase Gene." Plant Cell 12, no. 5 (May 2000): 691–705. http://dx.doi.org/10.1105/tpc.12.5.691.

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Kjemtrup, Susanne, Kim S. Sampson, Charles G. Peele, Long V. Nguyen, Mark A. Conkling, William F. Thompson, and Dominique Robertson. "Gene silencing from plant DNA carried by a Geminivirus." Plant Journal 14, no. 1 (April 1998): 91–100. http://dx.doi.org/10.1046/j.1365-313x.1998.00101.x.

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Sarris, Panagiotis F., Shang Gao, Konstantinos Karademiris, Hailing Jin, Kriton Kalantidis, and Nickolas J. Panopoulos. "Phytobacterial Type III Effectors HopX1, HopAB1 and HopF2 Enhance Sense-Post-Transcriptional Gene Silencing Independently of Plant R Gene-Effector Recognition." Molecular Plant-Microbe Interactions® 24, no. 8 (August 2011): 907–17. http://dx.doi.org/10.1094/mpmi-01-11-0010.

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Plant- and animal-pathogenic bacteria deploy a variable arsenal of type III effector proteins (T3EP) to manipulate host defense. Specific biochemical functions and molecular or subcellular targets have been demonstrated or proposed for a growing number of T3EP but remain unknown for the majority of them. Here, we show that transient expression of genes coding certain bacterial T3EP (HopAB1, HopX1, and HopF2), which did not elicit hypersensitive response (HR) in transgenic green fluorescent protein (GFP) Nicotiana benthamiana 16C line, enhanced the sense post-transcriptional gene silencing (S-PTGS) triggered by agrodelivery of a GFP-expressing cassette and the silencing enhancement could be blocked by two well-known viral silencing suppressors. Further analysis using genetic truncations and site-directed mutations showed that the receptor recognition domains of HopAB1 and HopX1 are not involved in enhancing silencing. Our studies provide new evidence that phytobacterial pathogen T3EP manipulate the plant small interfering RNA pathways by enhancing silencing efficiency in the absence of effector-triggered immunity signaling and suggest that phytopathogenic bacterial effectors affect host RNA silencing in yet other ways than previously described.

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Qiu, Wenping, and Karen-Beth G. Scholthof. "Satellite Panicum Mosaic Virus Capsid Protein Elicits Symptoms on a Nonhost Plant and Interferes with a Suppressor of Virus-Induced Gene Silencing." Molecular Plant-Microbe Interactions® 17, no. 3 (March 2004): 263–71. http://dx.doi.org/10.1094/mpmi.2004.17.3.263.

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The capsid protein (CP) of satellite panicum mosaic virus (SPMV) has been implicated as a pathogenicity factor, inducing severe chlorosis on millet plants co-infected with SPMV and its helper virus, Panicum mosaic virus (PMV). In this study, we tested the effects of SPMV CP on Nicotiana benthamiana, a plant that does not support PMV+SPMV infections. SPMV CP expressed from a Potato virus X (PVX) gene vector elicited necrotic lesions on N. benthamiana. Pathogenicity factors often have the additional feature of acting as suppressors of gene silencing; therefore, several assays were developed to test if SPMV CP could act in such a capacity. The results showed that SPMV CP failed to act as a suppressor of posttranscriptional gene silencing when such tests were performed with transgenic N. benthamiana plants silenced for green fluorescent protein (GFP) expression by agroinfiltration or plant virus vectors. However SPMV CP expressed from the PVX gene vector did interfere with suppressor activity associated with PVX p25. This included a rebounded level of GFP silencing along the vascular tissues, including the veins on upper noninoculated leaves. Therefore, the roles of the SPMV CP now include encapsidation of the SPMV RNA, activity as a pathogenicity factor in both host and nonhost plants, and the enigmatic feature of interfering with suppression of gene silencing.

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Lewsey, Mathew G., Alex M. Murphy, Daniel MacLean, Neil Dalchau, Jack H. Westwood, Keith Macaulay, Mark H. Bennett, et al. "Disruption of Two Defensive Signaling Pathways by a Viral RNA Silencing Suppressor." Molecular Plant-Microbe Interactions® 23, no. 7 (July 2010): 835–45. http://dx.doi.org/10.1094/mpmi-23-7-0835.

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The Cucumber mosaic virus (CMV) 2b counter-defense protein disrupts plant antiviral mechanisms mediated by RNA silencing and salicylic acid (SA). We used microarrays to investigate defensive gene expression in 2b-transgenic Arabidopsis thaliana plants. Surprisingly, 2b inhibited expression of few SA-regulated genes and, in some instances, enhanced the effect of SA on certain genes. Strikingly, the 2b protein inhibited changes in the expression of 90% of genes regulated by jasmonic acid (JA). Consistent with this, infection of plants with CMV, but not the 2b gene-deletion mutant CMVΔ2b, strongly inhibited JA-inducible gene expression. JA levels were unaffected by infection with either CMV or CMVΔ2b. Although the CMV–Arabidopsis interaction is a compatible one, SA accumulation, usually considered to be an indicator of plant resistance, was increased in CMV-infected plants but not in CMVΔ2b-infected plants. Thus, the 2b protein inhibits JA signaling at a step downstream of JA biosynthesis but it primes induction of SA biosynthesis by another CMV gene product or by the process of infection itself. Like many plant viruses, CMV is aphid transmitted. JA is important in plant defense against insects. This raises the possibility that disruption of JA-mediated gene expression by the 2b protein may influence CMV transmission by aphids.

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Wang, Changchun, Xinzhong Cai, Xuemin Wang, and Zhong Zheng. "Optimisation of tobacco rattle virus-induced gene silencing in Arabidopsis." Functional Plant Biology 33, no. 4 (2006): 347. http://dx.doi.org/10.1071/fp05096.

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Arabidopsis thaliana (L.) Heynh. is a model plant species in which to study plant gene functions. Recently developed virus-induced gene silencing (VIGS) offers a rapid and high-throughput technique platform for gene function analysis. In this paper we report optimisation of tobacco rattle virus (TRV)-induced gene silencing in Arabidopsis. The parameters potentially affecting the efficiency of VIGS in Arabidopsis were investigated. These included the concentration and pre-incubation of Agrobacterium inocula (agro-inocula), the concentration of acetosyringone included in agro-inocula, the Agrobacterium inoculation (agro-inoculation) method, the ecotypes and the growth stages of Arabidopsis plants for agro-inoculation, and the growth temperature of agro-inoculated plants. The optimised VIGS procedure involves preparing the agro-inocula with OD600 of 2.0, pre-incubating for 2 h in infiltration buffer containing 200 μm acetosyringone, agro-inoculating by vacuum infiltration, and growth of agro-inoculated plants at 22 −24°C. Following this procedure consistent and highly efficient VIGS was achieved for the genes encoding phytoene desaturase (PDS) and actin in Arabidopsis. The silencing phenotype lasts for at least 6 weeks, and is applicable in at least seven ecotypes, including Col-0, Cvi-0, Sd, Nd-1, Ws-0, Bay-0 and Ler. TRV-induced VIGS was expressed not only in leaves, but also in stems, inflorescences and siliques. However, VIGS was not transmissible through seed to the subsequent generation. The optimised procedure of the TRV-induced gene silencing should facilitate high-throughput functional analysis of genes in Arabidopsis.

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Camargo, Roberto A., Guilherme O. Barbosa, Isabella Presotto Possignolo, Lazaro E. P. Peres, Eric Lam, Joni E. Lima, Antonio Figueira, and Henrique Marques-Souza. "RNA interference as a gene silencing tool to controlTuta absolutain tomato (Solanum lycopersicum)." PeerJ 4 (December 15, 2016): e2673. http://dx.doi.org/10.7717/peerj.2673.

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RNA interference (RNAi), a gene-silencing mechanism that involves providing double-stranded RNA molecules that match a specific target gene sequence, is now widely used in functional genetic studies. The potential application of RNAi-mediated control of agricultural insect pests has rapidly become evident. The production of transgenic plants expressing dsRNA molecules that target essential insect genes could provide a means of specific gene silencing in larvae that feed on these plants, resulting in larval phenotypes that range from loss of appetite to death. In this report, we show that the tomato leafminer (Tuta absoluta), a major threat to commercial tomato production, can be targeted by RNAi. We selected two target genes (Vacuolar ATPase-AandArginine kinase) based on the RNAi response reported for these genes in other pest species. In view of the lack of an artificial diet forT. absoluta, we used two approaches to deliver dsRNA into tomato leaflets. The first approach was based on the uptake of dsRNA by leaflets and the second was based on “in planta-induced transient gene silencing” (PITGS), a well-established method for silencing plant genes, used here for the first time to deliverin planta-transcribed dsRNA to target insect genes.Tuta absolutalarvae that fed on leaves containing dsRNA of the target genes showed an ∼60% reduction in target gene transcript accumulation, an increase in larval mortality and less leaf damage. We then generated transgenic ‘Micro-Tom’ tomato plants that expressed hairpin sequences for both genes and observed a reduction in foliar damage byT. absolutain these plants. Our results demonstrate the feasibility of RNAi as an alternative method for controlling this critical tomato pest.

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Bottley, A., G. M. Xia, and R. M. D. Koebner. "Homoeologous gene silencing in hexaploid wheat." Plant Journal 47, no. 6 (September 2006): 897–906. http://dx.doi.org/10.1111/j.1365-313x.2006.02841.x.

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Knizewski, Lukasz, Krzysztof Ginalski, and Andrzej Jerzmanowski. "Snf2 proteins in plants: gene silencing and beyond." Trends in Plant Science 13, no. 10 (October 2008): 557–65. http://dx.doi.org/10.1016/j.tplants.2008.08.004.

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Koch, Aline, and Michael Wassenegger. "Host‐induced gene silencing – mechanisms and applications." New Phytologist 231, no. 1 (May 2, 2021): 54–59. http://dx.doi.org/10.1111/nph.17364.

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Hiriart, Jean-Baptiste, Eva-Mari Aro, and Kirsi Lehto. "Dynamics of the VIGS-Mediated Chimeric Silencing of the Nicotiana benthamiana ChlH Gene and of the Tobacco Mosaic Virus Vector." Molecular Plant-Microbe Interactions® 16, no. 2 (February 2003): 99–106. http://dx.doi.org/10.1094/mpmi.2003.16.2.99.

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The ChlH gene, encoding for the H subunit of the magnesium chelatase enzyme, was silenced in Nicotiana bentahamiana plants by virus-induced gene silencing (VIGS), using tobacco mosaic virus (TMV) expression vector. Strong silencing of the ChlH target gene was initiated only in the apical tissues, in which the endogenous transcription level of the target gene and the level of TMV vector RNA were both very high. The virus vector was also targeted by VIGS, and its suppression was correlated with the silencing of the ChlH mRNA. In the apical tissues, the suppression of both the virus vector and the ChlH mRNA led to a reduction of the silencing pressure and, consequently, to partial recovery of the new growth from the silencing. As the virus vector and the target mRNA levels increased, silencing was reestablished. The feedback regulation system, caused by the transient increase and reduction in levels of the virus vector and ChlH mRNA, led to a fluctuation of the silenced and recovered phenotypes in the plant apex. This TMV-vector mediated silencing system differed from previously analyzed VIGS systems; although the TMV vector was initially targeted by the silencing system, it was not permanently suppressed, indicating that, in this system, TMV was able to effectively escape post-transcriptional gene silencing.

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Wang, Zhiquan, Xiaoyang Xu, Longjie Ni, Jinbo Guo, and Chunsun Gu. "Efficient virus-induced gene silencing in Hibiscus hamabo Sieb. et Zucc. using tobacco rattle virus." PeerJ 7 (August 12, 2019): e7505. http://dx.doi.org/10.7717/peerj.7505.

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Background Hibiscus hamabo Sieb. et Zucc. is a semi-mangrove plant used for the ecological restoration of saline-alkali land, coastal afforestation and urban landscaping. The genetic transformation H. hamabo is currently inefficient and laborious, restricting gene functional studies on this species. In plants, virus-induced gene silencing provides a pathway to rapidly and effectively create targeted gene knockouts for gene functional studies. Methods In this study, we tested the efficiency of a tobacco rattle virus vector in silencing the cloroplastos alterados 1 (CLA1) gene through agroinfiltration. Results The leaves of H. hamabo showed white streaks typical of CLA1 gene silencing three weeks after agroinfiltration. In agroinfiltrated H. hamabo plants, the CLA1 expression levels in leaves with white streaks were all significantly lower than those in leaves from mock-infected and control plants. Conclusions The system presented here can efficiently silence genes in H. hamabo and may be a powerful tool for large-scale reverse-genetic analyses of gene functions in H. hamabo.

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Romero, Irene, Yury Tikunov, and Arnaud Bovy. "Virus-induced gene silencing in detached tomatoes and biochemical effects of phytoene desaturase gene silencing." Journal of Plant Physiology 168, no. 10 (July 2011): 1129–35. http://dx.doi.org/10.1016/j.jplph.2010.12.020.

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Helliwell, Chris A., S. Varsha Wesley, Anna J. Wielopolska, and Peter M. Waterhouse. "High-throughput vectors for efficient gene silencing in plants." Functional Plant Biology 29, no. 10 (2002): 1217. http://dx.doi.org/10.1071/fp02033.

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A major challenge in the post-genome era of plant biology is to determine the functions of all genes in the plant genome. A straightforward approach to this problem is to reduce or knockout expression of a gene with the hope of seeing a phenotype that is suggestive of its function. Insertional mutagenesis is a useful tool for this type of study but is limited by gene redundancy, lethal knockouts, non-tagged mutants, and the inability to target the inserted element to a specific gene. The efficacy of gene silencing in plants using inverted-repeat transgene constructs that encode a hairpin RNA (hpRNA) has been demonstrated by a number of groups, and has several advantages over insertional mutagenesis. In this paper we describe two improved pHellsgate vectors that facilitate rapid generation of hpRNA-encoding constructs. pHellsgate 4 allows the production of an hpRNA construct in a single step from a single polymerase chain reaction product, while pHellsgate 8 requires a two-step process via an intermediate vector. We show that these vectors are effective at silencing three endogenous genes in Arabidopsis, FLOWERING LOCUS C, PHYTOENE DESATURASE and ETHYLENE INSENSITIVE 2. We also show that a construct of sequences from two genes silences both genes.

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Jian, Jiao, and Xu Liang. "One Small RNA of Fusarium graminearum Targets and Silences CEBiP Gene in Common Wheat." Microorganisms 7, no. 10 (October 9, 2019): 425. http://dx.doi.org/10.3390/microorganisms7100425.

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The pathogenic fungus Fusarium graminearum (F. graminearum), causing Fusarium head blight (FHB) or scab, is one of the most important cereal killers worldwide, exerting great economic and agronomic losses on global grain production. To repress pathogen invasion, plants have evolved a sophisticated innate immunity system for pathogen recognition and defense activation. Simultaneously, pathogens continue to evolve more effective means of invasion to conquer plant resistance systems. In the process of co-evolution of plants and pathogens, several small RNAs (sRNAs) have been proved in regulating plant immune response and plant-microbial interaction. In this study, we report that a F. graminearum sRNA (Fg-sRNA1) can suppress wheat defense response by targeting and silencing a resistance-related gene, which codes a Chitin Elicitor Binding Protein (TaCEBiP). Transcriptional level evidence indicates that Fg-sRNA1 can target TaCEBiP mRNA and trigger silencing of TaCEBiP in vivo, and in Nicotiana benthamiana (N. benthamiana) plants, Western blotting experiments and YFP Fluorescence observation proofs show that Fg-sRNA1 can suppress the accumulation of protein coding by TaCEBiP gene in vitro. F. graminearum PH-1 strain displays a weakening ability to invasion when Barley stripe mosaic virus (BSMV) vector induces effective silencing Fg-sRNA1 in PH-1 infected wheat plants. Taken together, our results suggest that a small RNA from F. graminearum can target and silence the wheat TaCEBiP gene to enhance invasion of F. graminearum.

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Sang, Hyunkyu, and Jeong-Il Kim. "Advanced strategies to control plant pathogenic fungi by host-induced gene silencing (HIGS) and spray-induced gene silencing (SIGS)." Plant Biotechnology Reports 14, no. 1 (November 25, 2019): 1–8. http://dx.doi.org/10.1007/s11816-019-00588-3.

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Kusumanegara, Kusumawaty, Masanori Kaido, and Kazuyuki Mise. "Validating Plant Genes Involved in Pepper Yellow Leaf Curl Indonesia Virus Infection Using VIGS in Model Plant Nicotiana benthamiana." Jurnal AgroBiogen 16, no. 1 (July 17, 2020): 7. http://dx.doi.org/10.21082/jbio.v16n1.2020.p7-16.

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<p>Pepper yellow leaf curl disease caused by Pepper yellow leaf curl Indonesia virus (PepYLCIV) has become a challenge to chili pepper cultivation. Development of resistant variety by utilizing recessive resistance gene is expected to control the disease in the field. This study aimed to validate three plant genes, namely deltaCOP, hsc70, and BAM1, in PepYLCIV infection by applying Virus-induced Gene Silencing (VIGS) in a model plant, wild type Nicotiana benthamiana. PepYLCIV and construct of Tobacco rattle virus (TRV) which induced silencing of each gene were co-inoculated into N. benthamiana plants through agroinfiltration. Gene expression and the relative amount of viral DNA were determined by quantitative reverse transcription PCR (qRT-PCR) and quantitative PCR (qPCR), respectively, at 15 days post inoculation. The results showed a decreased level of deltaCOP, hsc70, and BAM1 expressions to 66.4%, 53.0%, and 47.0%, respectively, compared to that in the control (100%). Silencing of the three genes decreased the accumulation of PepYLCIV to 0.1%, 18.4%, and 63.0%, respectively, compared to that in the control. deltaCOP and hsc70 genes were indicated to be involved in the viral infection and could be good candidate genes for obtaining chili pepper varieties resistant to PepYLCIV. This result affirmed that the reverse genetics technique could be an alternative approach for identifying plant genes involved in viral infection, including PepYLCIV. The use of an infectious clone in this study allows the virus inoculations could be carried out without rearing and maintaining its natural vector, hence reduces the risk of virus transmission to healthy plants.</p>

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Eckardt, Nancy A. "Gene Silencing and Resistance to Bacterial Pathogens." Plant Cell 19, no. 11 (November 2007): 3317.2–3317. http://dx.doi.org/10.1105/tpc.107.191111.

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Wu, Zetang, Yali Zhu, David M. Bisaro, and Deborah S. Parris. "Herpes Simplex Virus Type 1 Suppresses RNA-Induced Gene Silencing in Mammalian Cells." Journal of Virology 83, no. 13 (April 15, 2009): 6652–63. http://dx.doi.org/10.1128/jvi.00260-09.

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ABSTRACT RNA-induced silencing is a potent innate antiviral defense strategy in plants, and suppression of silencing is a hallmark of pathogenic plant viruses. However, the impact of silencing as a mammalian antiviral defense mechanism and the ability of mammalian viruses to suppress silencing in natural host cells have remained controversial. The ability of herpes simplex virus type 1 (HSV-1) to suppress silencing was examined in a transient expression system that employed an imperfect hairpin to target degradation of transcripts encoding enhanced green fluorescent protein (EGFP). HSV-1 infection suppressed EGFP-specific silencing as demonstrated by increased EGFP mRNA levels and an increase in the EGFP mRNA half-life. The increase in EGFP mRNA stability occurred despite the well-characterized host macromolecular shutoff functions of HSV-1 that globally destabilize mRNAs. Moreover, mutant viruses defective in these functions increased the stability of EGFP mRNA even more than did the wild-type virus in silenced cells compared to results in control cells. The importance of RNA silencing to HSV-1 replication was confirmed by a significantly enhanced virus burst size in cells in which silencing was knocked down with small inhibitory RNAs directed to Argonaute 2, an integral component of the silencing complex. Given that HSV-1 encodes several microRNAs, it is possible that a dynamic equilibrium exists between silencing and silencing suppression that is capable of modulating viral gene expression to promote replication, to evade host defenses, and/or to promote latency.

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Journal articles on the topic 'Plant gene silencing'

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