[en] Recent metagenomic studies which focused on virus characterization in the entire plant environment have revealed a remarkable viral diversity in plants. The exponential discovery of viruses also requires the concomitant implementation of high-throughput methods to perform their functional characterization. Despite several limitations, the development of viral infectious clones remains a method of choice to understand virus biology, their role in the phytobiome, and plant resilience. Here, we review the latest approaches for efficient characterization of plant viruses and technical advances built on high-throughput sequencing and synthetic biology to streamline assembly of viral infectious clones. We then discuss the applications of plant viral vectors in fundamental and applied plant research as well as their technical and regulatory limitations, and we propose strategies for their safer field applications.
Disciplines :
Genetics & genetic processes
Author, co-author :
Shakir, Sara ; Université de Liège - ULiège > Département GxABT > Plant Sciences
Zaidi, Syed Shan-E-Ali; Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
Hashemi, Farahnaz Sadat Golestan; Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
The authors have been supported by several grants, including FNRS (grants F.4515.17, J.0187.21 and 1.B.456.20), LEAP-Agri (CASSANDRA project, grant 288), ARES (PRD iCARE), WBI (SOR/2018/391751), KULeuven C1 (ZKE0440), H2020 VIRTIGATION (grant agreement No 101000570), and the ULiege COFUND. No interests are declared.The authors have been supported by several grants, including FNRS (grants F.4515.17 , J.0187.21 and 1.B.456.20 ), LEAP-Agri (CASSANDRA project, grant 288 ), ARES (PRD iCARE), WBI ( SOR/2018/391751 ), KULeuven C1 ( ZKE0440 ), H2020 VIRTIGATION (grant agreement No 101000570 ), and the ULiege COFUND .
Zhang, Y.Z., et al. Using metagenomics to characterize an expanding virosphere. Cell 172 (2018), 1168–1172.
Lefeuvre, P., et al. Evolution and ecology of plant viruses. Nat. Rev. Microbiol. 17 (2019), 632–644.
French, R.K., Holmes, E.C., An ecosystems perspective on virus evolution and emergence. Trends Microbiol. 28 (2020), 165–175.
Susi, H., et al. Diverse and variable virus communities in wild plant populations revealed by metagenomic tools. Peer J., 2019, 2019, e6140.
Susi, H., Laine, A.L., Agricultural land use disrupts biodiversity mediation of virus infections in wild plant populations. New Phytol. 230 (2021), 2447–2458.
Bernardo, P., et al. Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale. ISME J. 12 (2017), 173–184.
Bačnik, K., et al. Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment. Water Res., 177, 2020, 115628.
Maclot, F., et al. Illuminating an ecological blackbox: using high throughput sequencing to characterize the plant virome across scales. Front. Microbiol., 11, 2020, 2575.
Wenger, A.M., et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat. Biotechnol. 37 (2019), 1155–1162.
Mehta, D., et al. Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq. Nat. Protoc. 15 (2020), 1673–1689.
Mehta, D., et al. A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field. Nucleic Acids Res., 47, 2019, e9.
Pollard, M.O., et al. Long reads: their purpose and place. Hum. Mol. Genet. 27 (2018), R234–R241.
Lu, H., et al. Oxford nanopore MinION sequencing and genome assembly. Genom. Proteom. Bioinform. 14 (2016), 265–279.
Rhoads, A., Au, K.F., PacBio sequencing and its applications. Genom. Proteom. Bioinform. 13 (2015), 278–289.
Mehetre, G.T., et al. Current developments and challenges in plant viral diagnostics: a systematic review. Viruses, 13, 2021, 412.
Liefting, L.W., et al. Application of Oxford nanopore technology to plant virus detection. Viruses, 13, 2021, 1424.
Roossinck, M.J., García-Arenal, F., Ecosystem simplification, biodiversity loss and plant virus emergence. Curr. Opin. Virol. 10 (2015), 56–62.
Brum, J.R., et al. Illuminating structural proteins in viral ‘dark matter’ with metaproteomics. Proc. Natl. Acad. Sci. U. S. A. 113 (2016), 2436–2441.
Seguritan, V., et al. Artificial neural networks trained to detect viral and phage structural proteins. PLoS Comput. Biol., 8, 2012, e1002657.
Zayed, A.A., et al. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 376 (2022), 156–162.
Ren, J., et al. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome, 5, 2017, 69.
Torti, S., et al. Transient reprogramming of crop plants for agronomic performance. Nat. Plants 7 (2021), 159–171.
Rampersad, S., Tennant, P., Replication and expression strategies of viruses. Viruses 2018 (2018), 55–82.
Stenger, D.C., et al. Replicational release of geminivirus genomes from tandemly repeated copies: evidence for rolling-circle replication of a plant viral DNA. Proc. Natl. Acad. Sci. U. S. A. 88 (1991), 8029–8033.
Duff-Farrier, C.R.A., et al. Strategies for the construction of cassava brown streak disease viral infectious clones. Mol. Biotechnol., 61, 2019, 93.
Nilsson-Payant, B.E., et al. Reduced nucleoprotein availability impairs negative-sense RNA virus replication and promotes host recognition. J. Virol., 95, 2021, e02274–20.
Jacob, D., et al. Plant-specific promoter sequences carry elements that are recognised by the eubacterial transcription machinery. Transgenic Res. 11 (2002), 291–303.
Satyanarayana, T., et al. Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli. Virology 313 (2003), 481–491.
Bedoya, L.C., Daròs, J.A., Stability of tobacco etch virus infectious clones in plasmid vectors. Virus Res. 149 (2010), 234–240.
Fakhfakh, H., et al. Cell-free cloning and biolistic inoculation of an infectious cDNA of potato virus Y. J. Gen. Virol. 77 (1996), 519–523.
Tran, P.T., et al. A plant intron enhances the performance of an infectious clone in planta. J. Virol. Methods 265 (2019), 26–34.
Nagata, T., Inoue-Nagata, A.K., Simplified methods for the construction of RNA and DNA virus infectious clones. Methods Mol. Biol. 1236 (2015), 241–254.
Tuo, D., et al. Generation of stable infectious clones of plant viruses by using Rhizobium radiobacter for both cloning and inoculation. Virology 510 (2017), 99–103.
Yin, J., et al. Discovery of the Agrobacterium growth inhibition sequence in virus and its application to recombinant clone screening. AMB Express 9 (2019), 1–9.
Youssef, F., et al. Strategies to facilitate the development of uncloned or cloned infectious full-length viral cDNAs: apple chlorotic leaf spot virus as a case study. Virol. J. 8 (2011), 1–12.
Fernandez-Delmond, I., et al. A novel strategy for creating recombinant infectious RNA virus genomes. J. Virol. Methods 121 (2004), 247–257.
Liang, D., et al. Site-directed mutagenesis and generation of chimeric viruses by homologous recombination in yeast to facilitate analysis of plant–virus interactions. Mol. Plant-Microbe Interact. 17 (2004), 571–576.
Sun, K., et al. Rapid construction of complex plant RNA virus infectious cDNA clones for agroinfection using a Yeast–E. coli–Agrobacterium shuttle vector. Viruses, 9, 2017, 332.
Schindler, D., et al. Synthetic genomics: a new venture to dissect genome fundamentals and engineer new functions. Curr. Opin. Chem. Biol. 46 (2018), 56–62.
Pasin, F., et al. Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses. Plant Biotechnol. J. 17 (2019), 1010–1026.
Massart, S., et al. A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologies. Front. Microbiol., 8, 2017, 45.
Simmonds, P., et al. Virus taxonomy in the age of metagenomics. Nat. Rev. Microbiol. 15 (2017), 161–168.
Cooper, B., Proof by synthesis of tobacco mosaic virus. Genome Biol., 15, 2014, R67.
Burgess, D.J., Next regeneration sequencing for reference genomes. Nat. Rev. Genet., 19, 2018, 125.
Koch, L., A platform for RNA virus cloning. Nat. Rev. Genet., 21, 2020, 388.
Lovato, A., et al. Construction of a synthetic infectious cDNA clone of Grapevine Algerian latent virus (GALV-Nf) and its biological activity in Nicotiana benthamiana and grapevine plants. Virol. J., 11, 2014, 186.
Bouton, C., et al. Foxtail mosaic virus: a viral vector for protein expression in cereals. Plant Physiol. 177 (2018), 1352–1367.
Brewer, H.C., et al. A guide to the contained use of plant virus infectious clones. Plant Biotechnol. J. 16 (2018), 832–843.
Wang, L., et al. A virus-encoded protein suppresses methylation of the viral genome through its interaction with ago4 in the cajal body. Elife 9 (2020), 1–21.
Dai, Z., et al. The cis-expression of the coat protein of turnip mosaic virus is essential for viral intercellular movement in plants. Mol. Plant Pathol. 21 (2020), 1194–1211.
Tomlinson, K.R., et al. Utilization of infectious clones to visualize Cassava brown streak virus replication in planta and gain insights into symptom development. Virus Gene. 55 (2019), 825–833.
Bak, A., et al. A viral protease relocalizes in the presence of the vector to promote vector performance. Nat. Commun. 8 (2017), 1–10.
Steele, J.F.C., et al. Synthetic plant virology for nanobiotechnology and nanomedicine. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol., 9, 2017, e1447.
Regnard, G.L., et al. High level protein expression in plants through the use of a novel autonomously replicating geminivirus shuttle vector. Plant Biotechnol. J. 8 (2009), 1–9.
Diamos, A.G., Mason, H.S., Modifying the replication of geminiviral vectors reduces cell death and enhances expression of biopharmaceutical proteins in Nicotiana benthamiana leaves. Front. Plant Sci., 9, 2019, 1974.
Mardanova, E.S., et al. Efficient transient expression of recombinant proteins in plants by the novel pEff vector based on the genome of potato virus X. Front. Plant Sci., 8, 2017, 247.
Rössner, C., et al. VIGS goes viral: how VIGS transforms our understanding of plant science. Annu. Rev. Plant Biol. 73 (2022), 703–728.
Dommes, A.B., et al. Virus-induced gene silencing: empowering genetics in non-model organisms. J. Exp. Bot. 70 (2019), 757–770.
Agüero, J., et al. Development of viral vectors based on citrus leaf blotch virus to express foreign proteins or analyze gene function in citrus plants. Mol. Plant-Microbe Interact. 25 (2012), 1326–1337.
Ramegowda, V., et al. Virus-induced gene silencing is a versatile tool for unraveling the functional relevance of multiple abiotic-stress-responsive genes in crop plants. Front. Plant Sci., 5, 2014, 323.
Zhao, J., et al. Potato virus X-based microRNA silencing (VbMS) in potato. J. Vis. Exp., 159, 2020, e61067.
Faivre-Rampant, O., et al. Potato virus X-induced gene silencing in leaves and tubers of potato. Plant Physiol., 134, 2004, 1308.
Lentz, E.M., et al. Cassava geminivirus agroclones for virus-induced gene silencing in cassava leaves and roots. Plant Methods 14 (2018), 1–9.
Zhou, B., Zeng, L., Elucidating the role of highly homologous Nicotiana benthamiana ubiquitin E2 gene family members in plant immunity through an improved virus-induced gene silencing approach. Plant Methods 13 (2017), 1–17.
Shteinberg, M., et al. Tomato yellow leaf curl virus (TYLCV) promotes plant tolerance to drought. Cells, 10, 2021, 2875.
González, R., et al. Plant virus evolution under strong drought conditions results in a transition from parasitism to mutualism. Proc. Natl. Acad. Sci. U. S. A., 118, 2021, e2020990118.
Lozano-Durán, R., et al. Identification of host genes involved in geminivirus infection using a reverse genetics approach. PLoS One, 6, 2011, e22383.
Li, S., et al. Genome-edited powdery mildew resistance in wheat without growth penalties. Nature 602 (2022), 455–460.
Voytas, D.F., Gao, C., Precision genome engineering and agriculture: opportunities and regulatory challenges. PLoS Biol., 12, 2014, e1001877.
Honig, A., et al. Transient expression of virally delivered meganuclease in planta generates inherited genomic deletions. Mol. Plant 8 (2015), 1292–1294.
Gao, Q., et al. Rescue of a plant cytorhabdovirus as versatile expression platforms for planthopper and cereal genomic studies. New Phytol. 223 (2019), 2120–2133.
Ma, X., et al. Highly efficient DNA-free plant genome editing using virally delivered CRISPR–Cas9. Nat. Plants 6 (2020), 773–779.
Baltes, N.J., et al. DNA replicons for plant genome engineering. Plant Cell 1 (2014), 151–163.
Ali, Z., et al. Efficient virus-mediated genome editing in plants using the CRISPR/Cas9 system. Mol. Plant 8 (2015), 1288–1291.
Ellison, E.E., et al. Multiplexed heritable gene editing using RNA viruses and mobile single guide RNAs. Nat. Plants 6 (2020), 620–624.
Pechinger, K., et al. A new era for mild strain cross-protection. Viruses, 11, 2019, 670.
McGarry, R.C., et al. Virus-induced flowering: an application of reproductive biology to benefit plant research and breeding. Plant Physiol. 173 (2017), 47–55.
Majer, E., et al. Rewiring carotenoid biosynthesis in plants using a viral vector. Sci. Rep. 7 (2017), 1–10.
Cao, J., et al. Development of abamectin loaded plant virus nanoparticles for efficacious plant parasitic nematode control. ACS Appl. Mater. Interfaces 7 (2015), 9546–9553.
Cheuk, A., Houde, M., A new barley stripe mosaic virus allows large protein overexpression for rapid function analysis. Plant Physiol. 176 (2018), 1919–1931.
Liou, M.R., et al. Development and application of satellite-based vectors. Hadidi, et al. (eds.) Viroids and Satellites, 2017, Academic Press, 597–604.
Chung, Y.H., et al. Integrating plant molecular farming and materials research for next-generation vaccines. Nat. Rev. Mater. 7 (2021), 372–388.
Rybicki, E.P., Plant molecular farming of virus-like nanoparticles as vaccines and reagents. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol., 12, 2020, e1587.
Shahgolzari, M., et al. Plant viral nanoparticles for packaging and in vivo delivery of bioactive cargos. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol., 12, 2020, 5.
Wi, S., et al. Engineering a plant viral coat protein for in vitro hybrid self-assembly of CO2-capturing catalytic nanofilaments. Biomacromolecules 21 (2020), 3847–3856.
Chung, Y.H., et al. Viral nanoparticles for drug delivery, imaging, immunotherapy, and theranostic applications. Adv. Drug Deliv. Rev. 156 (2020), 214–235.
Chan, S.K., et al. Biomimetic virus-like particles as severe acute respiratory syndrome coronavirus 2 diagnostic tools. ACS Nano 15 (2021), 1259–1272.
Chariou, P.L., Steinmetz, N.F., Delivery of pesticides to plant parasitic nematodes using tobacco mild green mosaic virus as a nanocarrier. ACS Nano 11 (2017), 4719–4730.
Lebel, M.E., et al. Plant viruses as nanoparticle-based vaccines and adjuvants. Vaccines (Basel) 3 (2015), 620–637.
Kerstetter-Fogle, A., et al. Plant virus-like particle in situ vaccine for intracranial glioma immunotherapy. Cancers (Basel), 11, 2019, 515.
Lizotte, P.H., et al. In situ vaccination with cowpea mosaic virus nanoparticles suppresses metastatic cancer. Nat. Nanotechnol. 11 (2016), 295–303.
Shukla, S., et al. Antibody response against cowpea mosaic viral nanoparticles improves in situ vaccine efficacy in ovarian cancer. ACS Appl. Mater. Interfaces 14 (2020), 2994–3003.
Murray, A.A., et al. In situ vaccination with cowpea vs tobacco mosaic virus against melanoma. Mol. Pharm. 15 (2018), 3700–3716.
Cai, H., et al. Cowpea mosaic virus immunotherapy combined with cyclophosphamide reduces breast cancer tumor burden and inhibits lung metastasis. Adv. Sci. (Weinh), 6, 2019, 1802281.
Barone, P.W., et al. Viral contamination in biologic manufacture and implications for emerging therapies. Nat. Biotechnol. 38 (2020), 563–572.
Ortega-Rivera, O.A., et al. Trivalent subunit vaccine candidates for COVID-19 and their delivery devices. J. Am. Chem. Soc. 143 (2021), 14748–14765.
Beso-Ngndika, J., et al. Toward the reconstitution of a two-enzyme cascade for resveratrol synthesis on potyvirus particles. Front. Plant Sci., 7, 2016, 89.
Bonning, B.C., et al. Toxin delivery by the coat protein of an aphid-vectored plant virus provides plant resistance to aphids. Nat. Biotechnol. 32 (2013), 102–105.
Leach, J.E., et al. Communication in the phytobiome. Cell 169 (2017), 587–596.
Roossinck, M.J., Viruses in the phytobiome. Curr. Opin. Virol. 37 (2019), 72–76.
Rigling, D., Prospero, S., Cryphonectria parasitica, the causal agent of chestnut blight: invasion history, population biology and disease control. Mol. Plant Pathol. 19 (2018), 7–20.
Safari, M., et al. Manipulation of aphid behavior by a persistent plant virus. J. Virol., 93, 2019, e01781–18.
Morella, N.M., et al. The impact of bacteriophages on phyllosphere bacterial abundance and composition. Mol. Ecol. 27 (2018), 2025–2038.
Álvarez, B., Biosca, E.G., Bacteriophage-based bacterial wilt biocontrol for an environmentally sustainable agriculture. Front. Plant Sci., 8, 2017, 1218.
Bonanomi, G., et al. Organic amendments modulate soil microbiota and reduce virus disease incidence in the TSWV–tomato pathosystem. Pathogens, 9, 2020, 379.
Eckerstorfer, M.F., et al. An EU perspective on biosafety considerations for plants developed by genome editing and other new genetic modification techniques (nGMs). Front. Bioeng. Biotechnol., 7, 2019, 31.
Tepfer, M., et al. A critical evaluation of whether recombination in virus-resistant transgenic plants will lead to the emergence of novel viral diseases. New Phytol. 207 (2015), 536–541.
Willemsen, A., Zwart, M.P., On the stability of sequences inserted into viral genomes. Virus Evol., 5, 2019, vez045.
Bedoya, L., et al. Simultaneous equimolar expression of multiple proteins in plants from a disarmed potyvirus vector. J. Biotechnol. 150 (2010), 268–275.
Gleba, Y., et al. Engineering viral expression vectors for plants: the ‘full virus’ and the ‘deconstructed virus’ strategies. Curr. Opin. Plant Biol. 7 (2004), 182–188.
Lee, J.W., et al. Next-generation biocontainment systems for engineered organisms. Nat. Chem. Biol. 14 (2018), 530–537.
Zhong, G., et al. Rational design of aptazyme riboswitches for efficient control of gene expression in mammalian cells. Elife, 5, 2016, e18858.
Liu, M., et al. Aptasensors for pesticide detection. Biosens. Bioelectron. 130 (2019), 174–184.
Kang, M., et al. Establishment of a simple and rapid gene delivery system for cucurbits by using engineered of zucchini yellow mosaic virus. Plant Pathol. J. 32 (2016), 70–76.
Altpeter, F., et al. Particle bombardment and the genetic enhancement of crops: myths and realities. Mol. Breed. 15 (2005), 305–327.
Chen, Q., et al. Agroinfiltration as an effective and scalable strategy of gene delivery for production of pharmaceutical proteins. Adv. Tech. Biol. Med., 1, 2013, 103.
Ryu, C.M., et al. Agrodrench: a novel and effective agroinoculation method for virus-induced gene silencing in roots and diverse solanaceous species. Plant J. 40 (2004), 322–331.
Abrahamian, P., et al. Plant virus-derived vectors: applications in agricultural and medical biotechnology. Annu. Rev. Virol. 7 (2020), 513–535.
Madriz-Ordeñana, K., et al. Mechanical transmission of maize rayado fino marafivirus (MRFV) to maize and barley by means of the vascular puncture technique. Plant Pathol. 49 (2000), 302–307.
Bhat, A.I., Rao, G.P., Transmission through grafting and budding. In Characterization of Plant Viruses. Springer Protocols Handbooks, pp. 45–56. Humana 7 (2020), 45–56.
Lv, Z., et al. Nanoparticle-mediated gene transformation strategies for plant genetic engineering. Plant J. 104 (2020), 880–891.
Nagata, T., et al. Delivery of tobacco mosaic virus RNA into plant protoplasts mediated by reverse-phase evaporation vesicles (liposomes). Mol. Gen. Genet. 184 (1981), 161–165.
