- -

Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

Mostrar el registro completo del ítem

Pasin, F.; Menzel, W.; Daròs, J. (2019). Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses. Plant Biotechnology Journal. 17(6):1010-1026. https://doi.org/10.1111/pbi.13084

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/160001

Ficheros en el ítem

Metadatos del ítem

Título: Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses
Autor: Pasin, Fabio Menzel, Wulf Daròs, José-Antonio
Entidad UPV: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Fecha difusión:
Resumen:
[EN] Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and ...[+]
Palabras clave: Plant virus , Infectious clone , Agrobacterium , Transient expression systems , Synthetic virus population , Crop gene therapy
Derechos de uso: Reconocimiento (by)
Fuente:
Plant Biotechnology Journal. (issn: 1467-7644 )
DOI: 10.1111/pbi.13084
Editorial:
Blackwell Publishing
Versión del editor: https://doi.org/10.1111/pbi.13084
Código del Proyecto:
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2017-83184-R/ES/VIRUS DE PLANTAS: PATOGENOS Y TAMBIEN VECTORES PARA LA PRODUCCION DE PROTEINAS, METABOLITOS, RNAS Y NANOPARTICULAS/
Agradecimientos:
We are grateful to Catherine Mark for editorial assistance. We apologize to all colleagues whose relevant publications have not been cited because of space constraints or involuntary forgetfulness. F.P. is supported by a ...[+]
Tipo: Artículo

References

Ahlquist, P., French, R., Janda, M., & Loesch-Fries, L. S. (1984). Multicomponent RNA plant virus infection derived from cloned viral cDNA. Proceedings of the National Academy of Sciences, 81(22), 7066-7070. doi:10.1073/pnas.81.22.7066

Ali, Z., Abul-faraj, A., Li, L., Ghosh, N., Piatek, M., Mahjoub, A., … Mahfouz, M. M. (2015). Efficient Virus-Mediated Genome Editing in Plants Using the CRISPR/Cas9 System. Molecular Plant, 8(8), 1288-1291. doi:10.1016/j.molp.2015.02.011

Ambrós, S., El-Mohtar, C., Ruiz-Ruiz, S., Peña, L., Guerri, J., Dawson, W. O., & Moreno, P. (2011). Agroinoculation of Citrus tristeza virus Causes Systemic Infection and Symptoms in the Presumed Nonhost Nicotiana benthamiana. Molecular Plant-Microbe Interactions®, 24(10), 1119-1131. doi:10.1094/mpmi-05-11-0110 [+]
Ahlquist, P., French, R., Janda, M., & Loesch-Fries, L. S. (1984). Multicomponent RNA plant virus infection derived from cloned viral cDNA. Proceedings of the National Academy of Sciences, 81(22), 7066-7070. doi:10.1073/pnas.81.22.7066

Ali, Z., Abul-faraj, A., Li, L., Ghosh, N., Piatek, M., Mahjoub, A., … Mahfouz, M. M. (2015). Efficient Virus-Mediated Genome Editing in Plants Using the CRISPR/Cas9 System. Molecular Plant, 8(8), 1288-1291. doi:10.1016/j.molp.2015.02.011

Ambrós, S., El-Mohtar, C., Ruiz-Ruiz, S., Peña, L., Guerri, J., Dawson, W. O., & Moreno, P. (2011). Agroinoculation of Citrus tristeza virus Causes Systemic Infection and Symptoms in the Presumed Nonhost Nicotiana benthamiana. Molecular Plant-Microbe Interactions®, 24(10), 1119-1131. doi:10.1094/mpmi-05-11-0110

Ameur, A., Kloosterman, W. P., & Hestand, M. S. (2019). Single-Molecule Sequencing: Towards Clinical Applications. Trends in Biotechnology, 37(1), 72-85. doi:10.1016/j.tibtech.2018.07.013

Andreou, A. I., & Nakayama, N. (2018). Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly. PLOS ONE, 13(1), e0189892. doi:10.1371/journal.pone.0189892

Annamalai, A. S., Pattnaik, A., Sahoo, B. R., Muthukrishnan, E., Natarajan, S. K., Steffen, D., … Pattnaik, A. K. (2017). Zika Virus Encoding Nonglycosylated Envelope Protein Is Attenuated and Defective in Neuroinvasion. Journal of Virology, 91(23). doi:10.1128/jvi.01348-17

Aumiller, W. M., Uchida, M., & Douglas, T. (2018). Protein cage assembly across multiple length scales. Chemical Society Reviews, 47(10), 3433-3469. doi:10.1039/c7cs00818j

Azhakanandam, K., Weissinger, S. M., Nicholson, J. S., Qu, R., & Weissinger, A. K. (2007). Amplicon-plus targeting technology (APTT) for rapid production of a highly unstable vaccine protein in tobacco plants. Plant Molecular Biology, 63(3), 393-404. doi:10.1007/s11103-006-9096-9

Azzi, L., Deluche, C., Gévaudant, F., Frangne, N., Delmas, F., Hernould, M., & Chevalier, C. (2015). Fruit growth-related genes in tomato. Journal of Experimental Botany, 66(4), 1075-1086. doi:10.1093/jxb/eru527

Badran, A. H., Guzov, V. M., Huai, Q., Kemp, M. M., Vishwanath, P., Kain, W., … Liu, D. R. (2016). Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature, 533(7601), 58-63. doi:10.1038/nature17938

Baltes, N. J., Gil-Humanes, J., Cermak, T., Atkins, P. A., & Voytas, D. F. (2014). DNA Replicons for Plant Genome Engineering  . The Plant Cell, 26(1), 151-163. doi:10.1105/tpc.113.119792

Baulcombe, D. C., Chapman, S., & Cruz, S. (1995). Jellyfish green fluorescent protein as a reporter for virus infections. The Plant Journal, 7(6), 1045-1053. doi:10.1046/j.1365-313x.1995.07061045.x

Becker, M. M., Graham, R. L., Donaldson, E. F., Rockx, B., Sims, A. C., Sheahan, T., … Denison, M. R. (2008). Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice. Proceedings of the National Academy of Sciences, 105(50), 19944-19949. doi:10.1073/pnas.0808116105

Bedoya, L. C., & Daròs, J.-A. (2010). Stability of Tobacco etch virus infectious clones in plasmid vectors. Virus Research, 149(2), 234-240. doi:10.1016/j.virusres.2010.02.004

Bedoya, L. C., Martínez, F., Orzáez, D., & Daròs, J.-A. (2012). Visual Tracking of Plant Virus Infection and Movement Using a Reporter MYB Transcription Factor That Activates Anthocyanin Biosynthesis  . Plant Physiology, 158(3), 1130-1138. doi:10.1104/pp.111.192922

Bhat, A., Hohn, T., & Selvarajan, R. (2016). Badnaviruses: The Current Global Scenario. Viruses, 8(6), 177. doi:10.3390/v8060177

Bijora, T., Blawid, R., Costa, D. K. T., Aragão, F. J. L., Souto, E. R., & Nagata, T. (2017). Construction of an agroinfectious clone of bean rugose mosaic virus using Gibson Assembly. Virus Genes, 53(3), 495-499. doi:10.1007/s11262-017-1446-y

Blawid, R., & Nagata, T. (2015). Construction of an infectious clone of a plant RNA virus in a binary vector using one-step Gibson Assembly. Journal of Virological Methods, 222, 11-15. doi:10.1016/j.jviromet.2015.05.003

Bonning, B. C., Pal, N., Liu, S., Wang, Z., Sivakumar, S., Dixon, P. M., … Miller, W. A. (2013). Toxin delivery by the coat protein of an aphid-vectored plant virus provides plant resistance to aphids. Nature Biotechnology, 32(1), 102-105. doi:10.1038/nbt.2753

Bordat, A., Houvenaghel, M.-C., & German-Retana, S. (2015). Gibson assembly: an easy way to clone potyviral full-length infectious cDNA clones expressing an ectopic VPg. Virology Journal, 12(1). doi:10.1186/s12985-015-0315-3

Bouton, C., King, R. C., Chen, H., Azhakanandam, K., Bieri, S., Hammond-Kosack, K. E., & Kanyuka, K. (2018). Foxtail mosaic virus: A Viral Vector for Protein Expression in Cereals. Plant Physiology, 177(4), 1352-1367. doi:10.1104/pp.17.01679

Brasch, M., Putri, R. M., de Ruiter, M. V., Luque, D., Koay, M. S. T., Castón, J. R., & Cornelissen, J. J. L. M. (2017). Assembling Enzymatic Cascade Pathways inside Virus-Based Nanocages Using Dual-Tasking Nucleic Acid Tags. Journal of the American Chemical Society, 139(4), 1512-1519. doi:10.1021/jacs.6b10948

Brewer, H. C., Hird, D. L., Bailey, A. M., Seal, S. E., & Foster, G. D. (2018). A guide to the contained use of plant virus infectious clones. Plant Biotechnology Journal, 16(4), 832-843. doi:10.1111/pbi.12876

Brisson, N., Paszkowski, J., Penswick, J. R., Gronenborn, B., Potrykus, I., & Hohn, T. (1984). Expression of a bacterial gene in plants by using a viral vector. Nature, 310(5977), 511-514. doi:10.1038/310511a0

Brödel, A. K., Isalan, M., & Jaramillo, A. (2018). Engineering of biomolecules by bacteriophage directed evolution. Current Opinion in Biotechnology, 51, 32-38. doi:10.1016/j.copbio.2017.11.004

Brophy, J. A. N., Triassi, A. J., Adams, B. L., Renberg, R. L., Stratis-Cullum, D. N., Grossman, A. D., & Voigt, C. A. (2018). Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria. Nature Microbiology, 3(9), 1043-1053. doi:10.1038/s41564-018-0216-5

Bukovinszki, Á., Götz, R., Johansen, E., Maiss, E., & Balázs, E. (2007). The role of the coat protein region in symptom formation on Physalis floridana varies between PVY strains. Virus Research, 127(1), 122-125. doi:10.1016/j.virusres.2007.03.023

Butterfield, G. L., Lajoie, M. J., Gustafson, H. H., Sellers, D. L., Nattermann, U., Ellis, D., … Baker, D. (2017). Evolution of a designed protein assembly encapsulating its own RNA genome. Nature, 552(7685), 415-420. doi:10.1038/nature25157

Callaway, E. (2018). CRISPR plants now subject to tough GM laws in European Union. Nature, 560(7716), 16-16. doi:10.1038/d41586-018-05814-6

Calles, B., & Lorenzo, V. de. (2013). Expanding the Boolean Logic of the Prokaryotic Transcription Factor XylR by Functionalization of Permissive Sites with a Protease-Target Sequence. ACS Synthetic Biology, 2(10), 594-603. doi:10.1021/sb400050k

Canuti, M., & van der Hoek, L. (2014). Virus discovery: are we scientists or genome collectors? Trends in Microbiology, 22(5), 229-231. doi:10.1016/j.tim.2014.02.004

Cao, J., Guenther, R. H., Sit, T. L., Lommel, S. A., Opperman, C. H., & Willoughby, J. A. (2015). Development of Abamectin Loaded Plant Virus Nanoparticles for Efficacious Plant Parasitic Nematode Control. ACS Applied Materials & Interfaces, 7(18), 9546-9553. doi:10.1021/acsami.5b00940

Carvalho, S. L., Nagata, T., Junqueira, B. R., Zanardo, L. G., Paiva, A. C. S., & Carvalho, C. M. (2016). Construction of a full-length infectious cDNA clone of Cowpea mild mottle virus. Virus Genes, 53(1), 137-140. doi:10.1007/s11262-016-1395-x

Charudattan, R., & Hiebert, E. (2007). A Plant Virus as a Bioherbicide for Tropical Soda Apple, <I>Solanum Viarum</I>. Outlooks on Pest Management, 18(4), 167-171. doi:10.1564/18aug07

Charudattan R. Pettersen M.S.andHiebert E.(2009)Use of tobacco mild green mosaic virus (TMGMV) mediated lethal hypersensitive response (HR) as a novel method of weed control. U.S. Patent 7 4949 55 B2.

Chen, Y., Wan, Y., Wang, N., Yuan, Z., Niu, W., Li, Q., & Guo, J. (2018). Controlling the Replication of a Genomically Recoded HIV-1 with a Functional Quadruplet Codon in Mammalian Cells. ACS Synthetic Biology, 7(6), 1612-1617. doi:10.1021/acssynbio.8b00096

Cheuk, A., & Houde, M. (2017). A New Barley Stripe Mosaic Virus Allows Large Protein Overexpression for Rapid Function Analysis. Plant Physiology, 176(3), 1919-1931. doi:10.1104/pp.17.01412

Chikh Ali, M., Said Omar, A., & Natsuaki, T. (2011). An infectious full-length cDNA clone of potato virus YNTN-NW, a recently reported strain of PVY that causes potato tuber necrotic ringspot disease. Archives of Virology, 156(11), 2039-2043. doi:10.1007/s00705-011-1062-4

Cho, T.-J., & Dreher, T. W. (2006). Encapsidation of genomic but not subgenomic Turnip yellow mosaic virus RNA by coat protein provided in trans. Virology, 356(1-2), 126-135. doi:10.1016/j.virol.2006.06.038

Chujo, T., Yoshikawa, M., Ariga, H., Endo, M., Toki, S., & Ishibashi, K. (2017). A removable virus vector suitable for plant genome editing. The Plant Journal, 91(3), 558-561. doi:10.1111/tpj.13581

Collens, J. I., Lee, D. R., Seeman, A. M., & Curtis, W. R. (2004). Development of Auxotrophic Agrobacterium tumefaciens for Gene Transfer in Plant Tissue Culture. Biotechnology Progress, 20(3), 890-896. doi:10.1021/bp034306w

Comellas-Aragonès, M., Engelkamp, H., Claessen, V. I., Sommerdijk, N. A. J. M., Rowan, A. E., Christianen, P. C. M., … Nolte, R. J. M. (2007). A virus-based single-enzyme nanoreactor. Nature Nanotechnology, 2(10), 635-639. doi:10.1038/nnano.2007.299

Cooper, B. (2014). Proof by synthesis of Tobacco mosaic virus. Genome Biology, 15(5), R67. doi:10.1186/gb-2014-15-5-r67

Cordero, T., Rosado, A., Majer, E., Jaramillo, A., Rodrigo, G., & Daròs, J.-A. (2018). Boolean Computation in Plants Using Post-translational Genetic Control and a Visual Output Signal. ACS Synthetic Biology, 7(10), 2322-2330. doi:10.1021/acssynbio.8b00214

Cress, D. E., Kiefer, M. C., & Owens, R. A. (1983). Construction of infectious potato spindle tuber viroid cDNA clones. Nucleic Acids Research, 11(19), 6821-6835. doi:10.1093/nar/11.19.6821

Crivelli, G., Ciuffo, M., Genre, A., Masenga, V., & Turina, M. (2011). Reverse Genetic Analysis of Ourmiaviruses Reveals the Nucleolar Localization of the Coat Protein in Nicotiana benthamiana and Unusual Requirements for Virion Formation. Journal of Virology, 85(10), 5091-5104. doi:10.1128/jvi.02565-10

Cui, T., Bin, Y., Yan, J., Mei, P., Li, Z., Zhou, C., & Song, Z. (2018). Development of Infectious cDNA Clones of Citrus Yellow Vein Clearing Virus Using a Novel and Rapid Strategy. Phytopathology®, 108(10), 1212-1218. doi:10.1094/phyto-02-18-0029-r

Daros, J.-A., & Flores, R. (2004). Arabidopsis thaliana has the enzymatic machinery for replicating representative viroid species of the family Pospiviroidae. Proceedings of the National Academy of Sciences, 101(17), 6792-6797. doi:10.1073/pnas.0401090101

Dawson, W. O., & Folimonova, S. Y. (2013). Virus-Based Transient Expression Vectors for Woody Crops: A New Frontier for Vector Design and Use. Annual Review of Phytopathology, 51(1), 321-337. doi:10.1146/annurev-phyto-082712-102329

Delbianco, A., Lanzoni, C., Klein, E., Rubies Autonell, C., Gilmer, D., & Ratti, C. (2013). Agroinoculation ofBeet necrotic yellow vein virus cDNA clones results in plant systemic infection and efficientPolymyxa betaetransmission. Molecular Plant Pathology, 14(4), 422-428. doi:10.1111/mpp.12018

Desselberger, U. (2017). Reverse genetics of rotavirus. Proceedings of the National Academy of Sciences, 114(9), 2106-2108. doi:10.1073/pnas.1700738114

Donson, J. (1993). Broad Resistance to Tobamoviruses Is Mediated by a Modified Tobacco Mosaic Virus Replicase Transgene. Molecular Plant-Microbe Interactions, 6(5), 635. doi:10.1094/mpmi-6-635

Dugdale, B., Mortimer, C. L., Kato, M., James, T. A., Harding, R. M., & Dale, J. L. (2013). In Plant Activation: An Inducible, Hyperexpression Platform for Recombinant Protein Production in Plants. The Plant Cell, 25(7), 2429-2443. doi:10.1105/tpc.113.113944

Elena, S. F., Bernet, G. P., & Carrasco, J. L. (2014). The games plant viruses play. Current Opinion in Virology, 8, 62-67. doi:10.1016/j.coviro.2014.07.003

Engler, C., Kandzia, R., & Marillonnet, S. (2008). A One Pot, One Step, Precision Cloning Method with High Throughput Capability. PLoS ONE, 3(11), e3647. doi:10.1371/journal.pone.0003647

Fakhfakh, H., Vilaine, F., Makni, M., & Robaglia, C. (1996). Cell-free cloning and biolistic inoculation of an infectious cDNA of potato virus Y. Journal of General Virology, 77(3), 519-523. doi:10.1099/0022-1317-77-3-519

Farrand, S. K., O’Morchoe, S. P., & McCutchan, J. (1989). Construction of an Agrobacterium tumefaciens C58 recA mutant. Journal of Bacteriology, 171(10), 5314-5321. doi:10.1128/jb.171.10.5314-5321.1989

Fernandez-Rodriguez, J., & Voigt, C. A. (2016). Post-translational control of genetic circuits usingPotyvirusproteases. Nucleic Acids Research, 44(13), 6493-6502. doi:10.1093/nar/gkw537

Ferro, M. M. M., Ramos-Sobrinho, R., Xavier, C. A. D., Zerbini, F. M., Lima, G. S. A., Nagata, T., & Assunção, I. P. (2019). New approach for the construction of infectious clones of a circular DNA plant virus using Gibson Assembly. Journal of Virological Methods, 263, 20-23. doi:10.1016/j.jviromet.2018.10.017

Firdaus, S., van Heusden, A. W., Hidayati, N., Supena, E. D. J., Visser, R. G. F., & Vosman, B. (2012). Resistance to Bemisia tabaci in tomato wild relatives. Euphytica, 187(1), 31-45. doi:10.1007/s10681-012-0704-2

French, R., Janda, M., & Ahlquist, P. (1986). Bacterial Gene Inserted in an Engineered RNA Virus: Efficient Expression in Monocotyledonous Plant Cells. Science, 231(4743), 1294-1297. doi:10.1126/science.231.4743.1294

Fu, J., Bian, X., Hu, S., Wang, H., Huang, F., Seibert, P. M., … Zhang, Y. (2012). Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nature Biotechnology, 30(5), 440-446. doi:10.1038/nbt.2183

Fukuzawa, N., Ishihara, T., Itchoda, N., Tabayashi, N., Kataoka, C., Masuta, C., & Matsumura, T. (2010). Risk-managed production of bioactive recombinant proteins using a novel plant virus vector with a helper plant to complement viral systemic movement. Plant Biotechnology Journal, 9(1), 38-49. doi:10.1111/j.1467-7652.2010.00529.x

Gao, R., Tian, Y.-P., Wang, J., Yin, X., Li, X.-D., & Valkonen, J. P. T. (2012). Construction of an infectious cDNA clone and gene expression vector of Tobacco vein banding mosaic virus (genus Potyvirus). Virus Research, 169(1), 276-281. doi:10.1016/j.virusres.2012.07.010

Gao, X. J., Chong, L. S., Kim, M. S., & Elowitz, M. B. (2018). Programmable protein circuits in living cells. Science, 361(6408), 1252-1258. doi:10.1126/science.aat5062

Gardner, R. C., Chonoles, K. R., & Owens, R. A. (1986). Potato spindle tuber viroid infections mediated by the Ti plasmid of Agrobacterium tumefaciens. Plant Molecular Biology, 6(4), 221-228. doi:10.1007/bf00015228

Gibson, D. G., Benders, G. A., Axelrod, K. C., Zaveri, J., Algire, M. A., Moodie, M., … Hutchison, C. A. (2008). One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proceedings of the National Academy of Sciences, 105(51), 20404-20409. doi:10.1073/pnas.0811011106

Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009). Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Methods, 6(5), 343-345. doi:10.1038/nmeth.1318

Gil‐Humanes, J., Wang, Y., Liang, Z., Shan, Q., Ozuna, C. V., Sánchez‐León, S., … Voytas, D. F. (2017). High‐efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR /Cas9. The Plant Journal, 89(6), 1251-1262. doi:10.1111/tpj.13446

Giritch, A., Marillonnet, S., Engler, C., van Eldik, G., Botterman, J., Klimyuk, V., & Gleba, Y. (2006). Rapid high-yield expression of full-size IgG antibodies in plants coinfected with noncompeting viral vectors. Proceedings of the National Academy of Sciences, 103(40), 14701-14706. doi:10.1073/pnas.0606631103

Giritch A. Symonenko Y. Hahn S. Tiede D. Shvarts A. Roemer P.andGleba Y.(2013)Process for transfecting plants. U.S. Patent 2013/0212739 A1.

Gleba, Y., Marillonnet, S., & Klimyuk, V. (2004). Engineering viral expression vectors for plants: the ‘full virus’ and the ‘deconstructed virus’ strategies. Current Opinion in Plant Biology, 7(2), 182-188. doi:10.1016/j.pbi.2004.01.003

Globus, R., & Qimron, U. (2017). A technological and regulatory outlook on CRISPR crop editing. Journal of Cellular Biochemistry, 119(2), 1291-1298. doi:10.1002/jcb.26303

Godiska, R., Mead, D., Dhodda, V., Wu, C., Hochstein, R., Karsi, A., … Ravin, N. (2009). Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli. Nucleic Acids Research, 38(6), e88-e88. doi:10.1093/nar/gkp1181

Goh, C.-H., Veliz Vallejos, D. F., Nicotra, A. B., & Mathesius, U. (2013). The Impact of Beneficial Plant-Associated Microbes on Plant Phenotypic Plasticity. Journal of Chemical Ecology, 39(7), 826-839. doi:10.1007/s10886-013-0326-8

González, J. M., Pénzes, Z., Almazán, F., Calvo, E., & Enjuanes, L. (2002). Stabilization of a Full-Length Infectious cDNA Clone of Transmissible Gastroenteritis Coronavirus by Insertion of an Intron. Journal of Virology, 76(9), 4655-4661. doi:10.1128/jvi.76.9.4655-4661.2002

González-Guzmán, M., Rodríguez, L., Lorenzo-Orts, L., Pons, C., Sarrión-Perdigones, A., Fernández, M. A., … Rodríguez, P. L. (2014). Tomato PYR/PYL/RCAR abscisic acid receptors show high expression in root, differential sensitivity to the abscisic acid agonist quinabactin, and the capability to enhance plant drought resistance. Journal of Experimental Botany, 65(15), 4451-4464. doi:10.1093/jxb/eru219

Govind, K., Mäkinen, K., & Savithri, H. S. (2012). Sesbania Mosaic Virus (SeMV) Infectious Clone: Possible Mechanism of 3′ and 5′ End Repair and Role of Polyprotein Processing in Viral Replication. PLoS ONE, 7(2), e31190. doi:10.1371/journal.pone.0031190

Gray, D. C., Mahrus, S., & Wells, J. A. (2010). Activation of Specific Apoptotic Caspases with an Engineered Small-Molecule-Activated Protease. Cell, 142(4), 637-646. doi:10.1016/j.cell.2010.07.014

Grigoras, I., Timchenko, T., Katul, L., Grande-Pérez, A., Vetten, H.-J., & Gronenborn, B. (2009). Reconstitution of Authentic Nanovirus from Multiple Cloned DNAs. Journal of Virology, 83(20), 10778-10787. doi:10.1128/jvi.01212-09

Grimsley, N., Hohn, B., Hohn, T., & Walden, R. (1986). «Agroinfection,» an alternative route for viral infection of plants by using the Ti plasmid. Proceedings of the National Academy of Sciences, 83(10), 3282-3286. doi:10.1073/pnas.83.10.3282

Grimsley, N., Hohn, T., Davies, J. W., & Hohn, B. (1987). Agrobacterium-mediated delivery of infectious maize streak virus into maize plants. Nature, 325(6100), 177-179. doi:10.1038/325177a0

.Groen, S. C., Wamonje, F. O., Murphy, A. M., & Carr, J. P. (2017). Engineering resistance to virus transmission. Current Opinion in Virology, 26, 20-27. doi:10.1016/j.coviro.2017.07.005

Gronenborn, B., Gardner, R. C., Schaefer, S., & Shepherd, R. J. (1981). Propagation of foreign DNA in plants using cauliflower mosaic virus as vector. Nature, 294(5843), 773-776. doi:10.1038/294773a0

Großkinsky, D. K., Syaifullah, S. J., & Roitsch, T. (2017). Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants. Journal of Experimental Botany, 69(4), 825-844. doi:10.1093/jxb/erx333

Hahn, S., Giritch, A., Bartels, D., Bortesi, L., & Gleba, Y. (2014). A novel and fully scalableAgrobacteriumspray-based process for manufacturing cellulases and other cost-sensitive proteins in plants. Plant Biotechnology Journal, 13(5), 708-716. doi:10.1111/pbi.12299

Haible, D., Kober, S., & Jeske, H. (2006). Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. Journal of Virological Methods, 135(1), 9-16. doi:10.1016/j.jviromet.2006.01.017

Hamilton, C. M., Frary, A., Lewis, C., & Tanksley, S. D. (1996). Stable transfer of intact high molecular weight DNA into plant chromosomes. Proceedings of the National Academy of Sciences, 93(18), 9975-9979. doi:10.1073/pnas.93.18.9975

Harding, D. P., & Raizada, M. N. (2015). Controlling weeds with fungi, bacteria and viruses: a review. Frontiers in Plant Science, 6. doi:10.3389/fpls.2015.00659

Hefferon, K. (2017). Plant Virus Expression Vectors: A Powerhouse for Global Health. Biomedicines, 5(4), 44. doi:10.3390/biomedicines5030044

Hellens, R., Mullineaux, P., & Klee, H. (2000). Technical Focus:A guide to Agrobacterium binary Ti vectors. Trends in Plant Science, 5(10), 446-451. doi:10.1016/s1360-1385(00)01740-4

Honig, A., Marton, I., Rosenthal, M., Smith, J. J., Nicholson, M. G., Jantz, D., … Vainstein, A. (2015). Transient Expression of Virally Delivered Meganuclease In Planta Generates Inherited Genomic Deletions. Molecular Plant, 8(8), 1292-1294. doi:10.1016/j.molp.2015.04.001

Houle, D., Govindaraju, D. R., & Omholt, S. (2010). Phenomics: the next challenge. Nature Reviews Genetics, 11(12), 855-866. doi:10.1038/nrg2897

Howell, S. H., Walker, L. L., & Dudley, R. K. (1980). Cloned Cauliflower Mosaic Virus DNA Infects Turnips ( Brassica rapa ). Science, 208(4449), 1265-1267. doi:10.1126/science.208.4449.1265

Idris, A. M., Shahid, M. S., Briddon, R. W., Khan, A. J., Zhu, J.-K., & Brown, J. K. (2010). An unusual alphasatellite associated with monopartite begomoviruses attenuates symptoms and reduces betasatellite accumulation. Journal of General Virology, 92(3), 706-717. doi:10.1099/vir.0.025288-0

Irwin, C. R., Farmer, A., Willer, D. O., & Evans, D. H. (2012). In-Fusion® Cloning with Vaccinia Virus DNA Polymerase. Vaccinia Virus and Poxvirology, 23-35. doi:10.1007/978-1-61779-876-4_2

Ishibashi, K., Matsumoto-Yokoyama, E., & Ishikawa, M. (2017). A Tomato Spotted Wilt Virus S RNA-based Replicon System in Yeast. Scientific Reports, 7(1). doi:10.1038/s41598-017-12687-8

Jailani, A. A. K., Shilpi, S., & Mandal, B. (2017). Rapid demonstration of infectivity of a hybrid strain of potato virus Y occurring in India through overlapping extension PCR. Physiological and Molecular Plant Pathology, 98, 62-68. doi:10.1016/j.pmpp.2017.03.001

Jarugula, S., Gowda, S., Dawson, W. O., & Naidu, R. A. (2018). Development of infectious cDNA clones of Grapevine leafroll-associated virus 3 and analyses of the 5′ non-translated region for replication and virion formation. Virology, 523, 89-99. doi:10.1016/j.virol.2018.07.023

Johansen, I. E. (1996). Intron insertion facilitates amplification of cloned virus cDNA in Escherichia coli while biological activity is reestablished after transcription in vivo. Proceedings of the National Academy of Sciences, 93(22), 12400-12405. doi:10.1073/pnas.93.22.12400

Johansen, I. E., & Lund, O. S. (2008). Insertion of Introns: A Strategy to Facilitate Assembly of Infectious Full Length Clones. Methods in Molecular Biology™, 535-544. doi:10.1007/978-1-59745-102-4_36

Johns, N. I., Blazejewski, T., Gomes, A. L., & Wang, H. H. (2016). Principles for designing synthetic microbial communities. Current Opinion in Microbiology, 31, 146-153. doi:10.1016/j.mib.2016.03.010

Julve Parreño, J. M., Huet, E., Fernández-del-Carmen, A., Segura, A., Venturi, M., Gandía, A., … Orzáez, D. (2017). A synthetic biology approach for consistent production of plant-made recombinant polyclonal antibodies against snake venom toxins. Plant Biotechnology Journal, 16(3), 727-736. doi:10.1111/pbi.12823

Karimi, M., Depicker, A., & Hilson, P. (2007). Recombinational Cloning with Plant Gateway Vectors. Plant Physiology, 145(4), 1144-1154. doi:10.1104/pp.107.106989

Kassaw, T. K., Donayre-Torres, A. J., Antunes, M. S., Morey, K. J., & Medford, J. I. (2018). Engineering synthetic regulatory circuits in plants. Plant Science, 273, 13-22. doi:10.1016/j.plantsci.2018.04.005

Kaufman, H. L., Kohlhapp, F. J., & Zloza, A. (2015). Oncolytic viruses: a new class of immunotherapy drugs. Nature Reviews Drug Discovery, 14(9), 642-662. doi:10.1038/nrd4663

Kelemen, R. E., Erickson, S. B., & Chatterjee, A. (2018). Synthesis at the interface of virology and genetic code expansion. Current Opinion in Chemical Biology, 46, 164-171. doi:10.1016/j.cbpa.2018.07.015

Kerfeld, C. A., Aussignargues, C., Zarzycki, J., Cai, F., & Sutter, M. (2018). Bacterial microcompartments. Nature Reviews Microbiology, 16(5), 277-290. doi:10.1038/nrmicro.2018.10

Knott, G. J., & Doudna, J. A. (2018). CRISPR-Cas guides the future of genetic engineering. Science, 361(6405), 866-869. doi:10.1126/science.aat5011

Koonin, E. V., & Krupovic, M. (2018). The depths of virus exaptation. Current Opinion in Virology, 31, 1-8. doi:10.1016/j.coviro.2018.07.011

Koonin, E. V., Dolja, V. V., & Krupovic, M. (2015). Origins and evolution of viruses of eukaryotes: The ultimate modularity. Virology, 479-480, 2-25. doi:10.1016/j.virol.2015.02.039

Kotterman, M. A., Chalberg, T. W., & Schaffer, D. V. (2015). Viral Vectors for Gene Therapy: Translational and Clinical Outlook. Annual Review of Biomedical Engineering, 17(1), 63-89. doi:10.1146/annurev-bioeng-071813-104938

Krenek, P., Samajova, O., Luptovciak, I., Doskocilova, A., Komis, G., & Samaj, J. (2015). Transient plant transformation mediated by Agrobacterium tumefaciens: Principles, methods and applications. Biotechnology Advances, 33(6), 1024-1042. doi:10.1016/j.biotechadv.2015.03.012

Kumagai, M. H., Donson, J., della-Cioppa, G., Harvey, D., Hanley, K., & Grill, L. K. (1995). Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proceedings of the National Academy of Sciences, 92(5), 1679-1683. doi:10.1073/pnas.92.5.1679

Kurth, E. G., Peremyslov, V. V., Prokhnevsky, A. I., Kasschau, K. D., Miller, M., Carrington, J. C., & Dolja, V. V. (2012). Virus-Derived Gene Expression and RNA Interference Vector for Grapevine. Journal of Virology, 86(11), 6002-6009. doi:10.1128/jvi.00436-12

Lacroix, B., Tzfira, T., Vainstein, A., & Citovsky, V. (2006). A case of promiscuity: Agrobacterium’s endless hunt for new partners. Trends in Genetics, 22(1), 29-37. doi:10.1016/j.tig.2005.10.004

Laufer, M., Mohammad, H., Maiss, E., Richert-Pöggeler, K., Dall’Ara, M., Ratti, C., … Varrelmann, M. (2018). Biological properties of Beet soil-borne mosaic virus and Beet necrotic yellow vein virus cDNA clones produced by isothermal in vitro recombination: Insights for reassortant appearance. Virology, 518, 25-33. doi:10.1016/j.virol.2018.01.029

Lazo, G. R., Stein, P. A., & Ludwig, R. A. (1991). A DNA Transformation–Competent Arabidopsis Genomic Library in Agrobacterium. Bio/Technology, 9(10), 963-967. doi:10.1038/nbt1091-963

Lee, J. W., Chan, C. T. Y., Slomovic, S., & Collins, J. J. (2018). Next-generation biocontainment systems for engineered organisms. Nature Chemical Biology, 14(6), 530-537. doi:10.1038/s41589-018-0056-x

Lefkowitz, E. J., Dempsey, D. M., Hendrickson, R. C., Orton, R. J., Siddell, S. G., & Smith, D. B. (2017). Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Research, 46(D1), D708-D717. doi:10.1093/nar/gkx932

Leiser, R. M., Ziegler-Graff, V., Reutenauer, A., Herrbach, E., Lemaire, O., Guilley, H., … Jonard, G. (1992). Agroinfection as an alternative to insects for infecting plants with beet western yellows luteovirus. Proceedings of the National Academy of Sciences, 89(19), 9136-9140. doi:10.1073/pnas.89.19.9136

Lellis, A. D., Kasschau, K. D., Whitham, S. A., & Carrington, J. C. (2002). Loss-of-Susceptibility Mutants of Arabidopsis thaliana Reveal an Essential Role for eIF(iso)4E during Potyvirus Infection. Current Biology, 12(12), 1046-1051. doi:10.1016/s0960-9822(02)00898-9

Lemire, S., Yehl, K. M., & Lu, T. K. (2018). Phage-Based Applications in Synthetic Biology. Annual Review of Virology, 5(1), 453-476. doi:10.1146/annurev-virology-092917-043544

Liang, D., Gray, S. M., Kaplan, I., & Palukaitis, P. (2004). Site-Directed Mutagenesis and Generation of Chimeric Viruses by Homologous Recombination in Yeast to Facilitate Analysis of Plant-Virus Interactions. Molecular Plant-Microbe Interactions®, 17(6), 571-576. doi:10.1094/mpmi.2004.17.6.571

Lifschitz, E., Eviatar, T., Rozman, A., Shalit, A., Goldshmidt, A., Amsellem, Z., … Eshed, Y. (2006). The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse environmental stimuli. Proceedings of the National Academy of Sciences, 103(16), 6398-6403. doi:10.1073/pnas.0601620103

Lin, M.-K., Belanger, H., Lee, Y.-J., Varkonyi-Gasic, E., Taoka, K.-I., Miura, E., … Lucas, W. J. (2007). FLOWERING LOCUS T Protein May Act as the Long-Distance Florigenic Signal in the Cucurbits. The Plant Cell, 19(5), 1488-1506. doi:10.1105/tpc.107.051920

Lin, M. T., Occhialini, A., Andralojc, P. J., Devonshire, J., Hines, K. M., Parry, M. A. J., & Hanson, M. R. (2014). β-Carboxysomal proteins assemble into highly organized structures inNicotianachloroplasts. The Plant Journal, 79(1), 1-12. doi:10.1111/tpj.12536

Liou, M., Huang, Y., Hu, C., Lin, N., & Hsu, Y. (2013). A dual gene‐silencing vector system for monocot and dicot plants. Plant Biotechnology Journal, 12(3), 330-343. doi:10.1111/pbi.12140

Liou, M.-R., Hu, C.-C., Lin, N.-S., & Hsu, Y.-H. (2017). Development and Application of Satellite-Based Vectors. Viroids and Satellites, 597-604. doi:10.1016/b978-0-12-801498-1.00055-3

Liu, L., & Lomonossoff, G. P. (2002). Agroinfection as a rapid method for propagating Cowpea mosaic virus-based constructs. Journal of Virological Methods, 105(2), 343-348. doi:10.1016/s0166-0934(02)00121-0

Liu, W., & Stewart, C. N. (2015). Plant synthetic biology. Trends in Plant Science, 20(5), 309-317. doi:10.1016/j.tplants.2015.02.004

Liu, W., Yuan, J. S., & Stewart Jr, C. N. (2013). Advanced genetic tools for plant biotechnology. Nature Reviews Genetics, 14(11), 781-793. doi:10.1038/nrg3583

López-Moya, J. J., & Garcı́a, J. A. (2000). Construction of a stable and highly infectious intron-containing cDNA clone of plum pox potyvirus and its use to infect plants by particle bombardment. Virus Research, 68(2), 99-107. doi:10.1016/s0168-1702(00)00161-1

Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011). ViennaRNA Package 2.0. Algorithms for Molecular Biology, 6(1). doi:10.1186/1748-7188-6-26

Lou, C., Stanton, B., Chen, Y.-J., Munsky, B., & Voigt, C. A. (2012). Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nature Biotechnology, 30(11), 1137-1142. doi:10.1038/nbt.2401

Lovato, A., Faoro, F., Gambino, G., Maffi, D., Bracale, M., Polverari, A., & Santi, L. (2014). Construction of a synthetic infectious cDNA clone of Grapevine Algerian latent virus (GALV-Nf) and its biological activity in Nicotiana benthamianaand grapevine plants. Virology Journal, 11(1). doi:10.1186/1743-422x-11-186

Lu, H.-C., Hsieh, M.-H., Chen, C.-E., Chen, H.-H., Wang, H.-I., & Yeh, H.-H. (2012). A High-Throughput Virus-Induced Gene-Silencing Vector for Screening Transcription Factors in Virus-Induced Plant Defense Response in Orchid. Molecular Plant-Microbe Interactions®, 25(6), 738-746. doi:10.1094/mpmi-10-11-0266

Lucas, H., Feuerbach, F., Kunert, K., Grandbastien, M. A., & Caboche, M. (1995). RNA-mediated transposition of the tobacco retrotransposon Tnt1 in Arabidopsis thaliana. The EMBO Journal, 14(10), 2364-2373. doi:10.1002/j.1460-2075.1995.tb07231.x

Mahas, A., Neal Stewart, C., & Mahfouz, M. M. (2018). Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation. Biotechnology Advances, 36(1), 295-310. doi:10.1016/j.biotechadv.2017.11.008

Majer, E., Navarro, J., & Daròs, J. (2015). A potyvirus vector efficiently targets recombinant proteins to chloroplasts, mitochondria and nuclei in plant cells when expressed at the amino terminus of the polyprotein. Biotechnology Journal, 10(11), 1792-1802. doi:10.1002/biot.201500042

Majer, E., Llorente, B., Rodríguez-Concepción, M., & Daròs, J.-A. (2017). Rewiring carotenoid biosynthesis in plants using a viral vector. Scientific Reports, 7(1). doi:10.1038/srep41645

Maliogka, V., Minafra, A., Saldarelli, P., Ruiz-García, A., Glasa, M., Katis, N., & Olmos, A. (2018). Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies. Viruses, 10(8), 436. doi:10.3390/v10080436

Marillonnet, S., Giritch, A., Gils, M., Kandzia, R., Klimyuk, V., & Gleba, Y. (2004). In planta engineering of viral RNA replicons: Efficient assembly by recombination of DNA modules delivered by Agrobacterium. Proceedings of the National Academy of Sciences, 101(18), 6852-6857. doi:10.1073/pnas.0400149101

Marillonnet, S., Thoeringer, C., Kandzia, R., Klimyuk, V., & Gleba, Y. (2005). Systemic Agrobacterium tumefaciens–mediated transfection of viral replicons for efficient transient expression in plants. Nature Biotechnology, 23(6), 718-723. doi:10.1038/nbt1094

Marillonnet S. Engler C. Mühlbauer S. Herz S. Werner S. Klimyuk V.andGleba Y.(2012)Biologically safe transient protein expression in plants. U.S. Patent 8 093 458 B2.

Martín-Trillo, M., Grandío, E. G., Serra, F., Marcel, F., Rodríguez-Buey, M. L., Schmitz, G., … Cubas, P. (2011). Role of tomato BRANCHED1-like genes in the control of shoot branching. The Plant Journal, 67(4), 701-714. doi:10.1111/j.1365-313x.2011.04629.x

Marton, I., Zuker, A., Shklarman, E., Zeevi, V., Tovkach, A., Roffe, S., … Vainstein, A. (2010). Nontransgenic Genome Modification in Plant Cells. Plant Physiology, 154(3), 1079-1087. doi:10.1104/pp.110.164806

Massart, S., Candresse, T., Gil, J., Lacomme, C., Predajna, L., Ravnikar, M., … Wetzel, T. (2017). A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies. Frontiers in Microbiology, 8. doi:10.3389/fmicb.2017.00045

McGarry, R. C., Klocko, A. L., Pang, M., Strauss, S. H., & Ayre, B. G. (2016). Virus-Induced Flowering: An Application of Reproductive Biology to Benefit Plant Research and Breeding. Plant Physiology, 173(1), 47-55. doi:10.1104/pp.16.01336

Mitter, N., Worrall, E. A., Robinson, K. E., Li, P., Jain, R. G., Taochy, C., … Xu, Z. P. (2017). Clay nanosheets for topical delivery of RNAi for sustained protection against plant viruses. Nature Plants, 3(2). doi:10.1038/nplants.2016.207

Mogler, M. A., & Kamrud, K. I. (2014). RNA-based viral vectors. Expert Review of Vaccines, 14(2), 283-312. doi:10.1586/14760584.2015.979798

Mrl, M., Lizano, E., Willkomm, D. K., & Hartmann, R. K. (s. f.). Production of RNAs with Homogeneous 5′ and 3′ Ends. Handbook of RNA Biochemistry, 22-35. doi:10.1002/9783527619504.ch2

Mozes-Koch, R., Gover, O., Tanne, E., Peretz, Y., Maori, E., Chernin, L., & Sela, I. (2012). Expression of an Entire Bacterial Operon in Plants    . Plant Physiology, 158(4), 1883-1892. doi:10.1104/pp.111.186197

Mueller, U. G., & Sachs, J. L. (2015). Engineering Microbiomes to Improve Plant and Animal Health. Trends in Microbiology, 23(10), 606-617. doi:10.1016/j.tim.2015.07.009

Murovec, J., Pirc, Ž., & Yang, B. (2017). New variants of CRISPR RNA-guided genome editing enzymes. Plant Biotechnology Journal, 15(8), 917-926. doi:10.1111/pbi.12736

Murphy, K. C. (1998). Use of Bacteriophage λ Recombination Functions To Promote Gene Replacement in Escherichia coli. Journal of Bacteriology, 180(8), 2063-2071. doi:10.1128/jb.180.8.2063-2071.1998

Nagata, T., & Inoue-Nagata, A. K. (2014). Simplified Methods for the Construction of RNA and DNA Virus Infectious Clones. Plant Virology Protocols, 241-254. doi:10.1007/978-1-4939-1743-3_18

Nakahara, K. S., Nishino, K., & Uyeda, I. (2014). Construction of Infectious cDNA Clones Derived from the Potyviruses Clover Yellow Vein Virus and Bean Yellow Mosaic Virus. Plant Virology Protocols, 219-227. doi:10.1007/978-1-4939-1743-3_16

Naylor, M., Reeves, J., Cooper, J. I., Edwards, M.-L., & Wang, H. (2005). Construction and properties of a gene-silencing vector based on Poplar mosaic virus (genus Carlavirus). Journal of Virological Methods, 124(1-2), 27-36. doi:10.1016/j.jviromet.2004.10.007

Ng, T. F. F., Chen, L.-F., Zhou, Y., Shapiro, B., Stiller, M., Heintzman, P. D., … Delwart, E. (2014). Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Proceedings of the National Academy of Sciences, 111(47), 16842-16847. doi:10.1073/pnas.1410429111

Nissim, L., Wu, M.-R., Pery, E., Binder-Nissim, A., Suzuki, H. I., Stupp, D., … Lu, T. K. (2017). Synthetic RNA-Based Immunomodulatory Gene Circuits for Cancer Immunotherapy. Cell, 171(5), 1138-1150.e15. doi:10.1016/j.cell.2017.09.049

Noyce, R. S., Lederman, S., & Evans, D. H. (2018). Construction of an infectious horsepox virus vaccine from chemically synthesized DNA fragments. PLOS ONE, 13(1), e0188453. doi:10.1371/journal.pone.0188453

Paez-Espino, D., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Thomas, A. D., Huntemann, M., Mikhailova, N., … Kyrpides, N. C. (2016). Uncovering Earth’s virome. Nature, 536(7617), 425-430. doi:10.1038/nature19094

Pagán, I., & García-Arenal, F. (2018). Population Genomics of Plant Viruses. Population Genomics, 233-265. doi:10.1007/13836_2018_15

Pasin, F., Simón-Mateo, C., & García, J. A. (2014). The Hypervariable Amino-Terminus of P1 Protease Modulates Potyviral Replication and Host Defense Responses. PLoS Pathogens, 10(3), e1003985. doi:10.1371/journal.ppat.1003985

Pasin, F., Bedoya, L. C., Bernabé-Orts, J. M., Gallo, A., Simón-Mateo, C., Orzaez, D., & García, J. A. (2017). Multiple T-DNA Delivery to Plants Using Novel Mini Binary Vectors with Compatible Replication Origins. ACS Synthetic Biology, 6(10), 1962-1968. doi:10.1021/acssynbio.6b00354

Pasin, F., Tseng, X.-A., Bedoya, L. C., Heydarnejad, J., Deng, T.-C., García, J. A., & Chen, Y.-R. (2018). Streamlined generation of plant virus infectious clones using the pLX mini binary vectors. Journal of Virological Methods, 262, 48-55. doi:10.1016/j.jviromet.2018.09.007

Current Protocols in Microbiology 2007 John Wiley & Sons Inc Hoboken NJ USA V.V. Peremyslov V.V. Dolja Cloning of large positive‐strand RNA viruses 16F.1.1 16F.1.26

Perrone, I., Chitarra, W., Boccacci, P., & Gambino, G. (2016). Grapevine–virus–environment interactions: an intriguing puzzle to solve. New Phytologist, 213(3), 983-987. doi:10.1111/nph.14271

Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera?A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605-1612. doi:10.1002/jcc.20084

Peyret, H., & Lomonossoff, G. P. (2015). When plant virology metAgrobacterium: the rise of the deconstructed clones. Plant Biotechnology Journal, 13(8), 1121-1135. doi:10.1111/pbi.12412

Pickett, J. A., & Khan, Z. R. (2016). Plant volatile‐mediated signalling and its application in agriculture: successes and challenges. New Phytologist, 212(4), 856-870. doi:10.1111/nph.14274

Pieters, B. J. G. E., van Eldijk, M. B., Nolte, R. J. M., & Mecinović, J. (2016). Natural supramolecular protein assemblies. Chemical Society Reviews, 45(1), 24-39. doi:10.1039/c5cs00157a

Potapov, V., & Ong, J. L. (2017). Examining Sources of Error in PCR by Single-Molecule Sequencing. PLOS ONE, 12(1), e0169774. doi:10.1371/journal.pone.0169774

Prokhnevsky, A. I., Peremyslov, V. V., Napuli, A. J., & Dolja, V. V. (2002). Interaction between Long-Distance Transport Factor and Hsp70-Related Movement Protein of Beet Yellows Virus. Journal of Virology, 76(21), 11003-11011. doi:10.1128/jvi.76.21.11003-11011.2002

Pu, S.-Y., Wu, R.-H., Yang, C.-C., Jao, T.-M., Tsai, M.-H., Wang, J.-C., … Yueh, A. (2011). Successful Propagation of Flavivirus Infectious cDNAs by a Novel Method To Reduce the Cryptic Bacterial Promoter Activity of Virus Genomes. Journal of Virology, 85(6), 2927-2941. doi:10.1128/jvi.01986-10

Ramegowda, V., & Senthil-Kumar, M. (2015). The interactive effects of simultaneous biotic and abiotic stresses on plants: Mechanistic understanding from drought and pathogen combination. Journal of Plant Physiology, 176, 47-54. doi:10.1016/j.jplph.2014.11.008

Ranch J.P. Liebergesell M. Garnaat C.W.andHuffman G.A.(2012)Auxotrophic Agrobacterium for plant transformation and methods thereof. U.S. Patent 8 334 429 B2.

Roemer P. Bortesi L. Tiede D. Giritch A.andGleba Y.(2015)Agrobacterium for transient transfection of whole plants. U.S. Patent 2015/0052638 A1.

Rojas‐Gracia, P., Roque, E., Medina, M., Rochina, M., Hamza, R., Angarita‐Díaz, M. P., … Gómez‐Mena, C. (2017). The parthenocarpic hydra mutant reveals a new function for a SPOROCYTELESS ‐like gene in the control of fruit set in tomato. New Phytologist, 214(3), 1198-1212. doi:10.1111/nph.14433

Rome, L. H., & Kickhoefer, V. A. (2012). Development of the Vault Particle as a Platform Technology. ACS Nano, 7(2), 889-902. doi:10.1021/nn3052082

Roossinck, M. J. (2010). Lifestyles of plant viruses. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1548), 1899-1905. doi:10.1098/rstb.2010.0057

Roossinck, M. J., Martin, D. P., & Roumagnac, P. (2015). Plant Virus Metagenomics: Advances in Virus Discovery. Phytopathology®, 105(6), 716-727. doi:10.1094/phyto-12-14-0356-rvw

Rose, H., & Maiss, E. (2018). Complete genome sequence and construction of an infectious full-length cDNA clone of a German isolate of celery mosaic virus. Archives of Virology, 163(4), 1107-1111. doi:10.1007/s00705-018-3705-1

Sanjuán, R., & Daròs, J.-A. (2007). One-step site-directed mutagenesis of viroid dimeric cDNA. Journal of Virological Methods, 145(1), 71-75. doi:10.1016/j.jviromet.2007.05.027

Satyanarayana, T., Gowda, S., Ayllón, M. A., & Dawson, W. O. (2003). Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli. Virology, 313(2), 481-491. doi:10.1016/s0042-6822(03)00387-8

Saunders, K., Bedford, I. D., Briddon, R. W., Markham, P. G., Wong, S. M., & Stanley, J. (2000). A unique virus complex causes Ageratum yellow vein disease. Proceedings of the National Academy of Sciences, 97(12), 6890-6895. doi:10.1073/pnas.97.12.6890

Schindler, D., Dai, J., & Cai, Y. (2018). Synthetic genomics: a new venture to dissect genome fundamentals and engineer new functions. Current Opinion in Chemical Biology, 46, 56-62. doi:10.1016/j.cbpa.2018.04.002

Schoelz, J. E., & Stewart, L. R. (2018). The Role of Viruses in the Phytobiome. Annual Review of Virology, 5(1), 93-111. doi:10.1146/annurev-virology-092917-043421

Schoenfeld, T., Liles, M., Wommack, K. E., Polson, S. W., Godiska, R., & Mead, D. (2010). Functional viral metagenomics and the next generation of molecular tools. Trends in Microbiology, 18(1), 20-29. doi:10.1016/j.tim.2009.10.001

Schoonen, L., Pille, J., Borrmann, A., Nolte, R. J. M., & van Hest, J. C. M. (2015). Sortase A-Mediated N-Terminal Modification of Cowpea Chlorotic Mottle Virus for Highly Efficient Cargo Loading. Bioconjugate Chemistry, 26(12), 2429-2434. doi:10.1021/acs.bioconjchem.5b00485

Scofield, S. R., & Nelson, R. S. (2009). Resources for Virus-Induced Gene Silencing in the Grasses. Plant Physiology, 149(1), 152-157. doi:10.1104/pp.108.128702

Shao, S., Zhang, X., van Heusden, G. P. H., & Hooykaas, P. J. J. (2018). Complete sequence of the tumor-inducing plasmid pTiChry5 from the hypervirulent Agrobacterium tumefaciens strain Chry5. Plasmid, 96-97, 1-6. doi:10.1016/j.plasmid.2018.02.001

Shi, Y., Shi, Y., Gu, Q., Yan, F., Sun, X., Li, H., … Wang, Z. (2016). Infectious clones of the crinivirus cucurbit chlorotic yellows virus are competent for plant systemic infection and vector transmission. Journal of General Virology, 97(6), 1458-1461. doi:10.1099/jgv.0.000453

Shukla, S., Ablack, A. L., Wen, A. M., Lee, K. L., Lewis, J. D., & Steinmetz, N. F. (2012). Increased Tumor Homing and Tissue Penetration of the Filamentous Plant Viral Nanoparticle Potato virus X. Molecular Pharmaceutics, 10(1), 33-42. doi:10.1021/mp300240m

Si, L., Xu, H., Zhou, X., Zhang, Z., Tian, Z., Wang, Y., … Zhou, D. (2016). Generation of influenza A viruses as live but replication-incompetent virus vaccines. Science, 354(6316), 1170-1173. doi:10.1126/science.aah5869

Sigmund, F., Massner, C., Erdmann, P., Stelzl, A., Rolbieski, H., Desai, M., … Westmeyer, G. G. (2018). Bacterial encapsulins as orthogonal compartments for mammalian cell engineering. Nature Communications, 9(1). doi:10.1038/s41467-018-04227-3

Steele, J. F. C., Peyret, H., Saunders, K., Castells-Graells, R., Marsian, J., Meshcheriakova, Y., & Lomonossoff, G. P. (2017). Synthetic plant virology for nanobiotechnology and nanomedicine. Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, 9(4), e1447. doi:10.1002/wnan.1447

Stein, V., Nabi, M., & Alexandrov, K. (2017). Ultrasensitive Scaffold-Dependent Protease Sensors with Large Dynamic Range. ACS Synthetic Biology, 6(7), 1337-1342. doi:10.1021/acssynbio.6b00370

Sun, K., Zhao, D., Liu, Y., Huang, C., Zhang, W., & Li, Z. (2017). Rapid Construction of Complex Plant RNA Virus Infectious cDNA Clones for Agroinfection Using a Yeast-E. coli-Agrobacterium Shuttle Vector. Viruses, 9(11), 332. doi:10.3390/v9110332

Takamatsu, N., Ishikawa, M., Meshi, T., & Okada, Y. (1987). Expression of bacterial chloramphenicol acetyltransferase gene in tobacco plants mediated by TMV-RNA. The EMBO Journal, 6(2), 307-311. doi:10.1002/j.1460-2075.1987.tb04755.x

Tang, Y., Wang, F., Zhao, J., Xie, K., Hong, Y., & Liu, Y. (2010). Virus-Based MicroRNA Expression for Gene Functional Analysis in Plants    . Plant Physiology, 153(2), 632-641. doi:10.1104/pp.110.155796

Thomas, C. L., Leh, V., Lederer, C., & Maule, A. J. (2003). Turnip crinkle virus coat protein mediates suppression of RNA silencing in nicotiana benthamiana. Virology, 306(1), 33-41. doi:10.1016/s0042-6822(02)00018-1

Tieman, D., Zhu, G., Resende, M. F. R., Lin, T., Nguyen, C., Bies, D., … Klee, H. (2017). A chemical genetic roadmap to improved tomato flavor. Science, 355(6323), 391-394. doi:10.1126/science.aal1556

Touriño, A., Sánchez, F., Fereres, A., & Ponz, F. (2008). High expression of foreign proteins from a biosafe viral vector derived from Turnip mosaic virus. Spanish Journal of Agricultural Research, 6(S1), 48. doi:10.5424/sjar/200806s1-373

Tran, P.-T., Fang, M., Widyasari, K., & Kim, K.-H. (2019). A plant intron enhances the performance of an infectious clone in planta. Journal of Virological Methods, 265, 26-34. doi:10.1016/j.jviromet.2018.12.012

Tuo, D., Shen, W., Yan, P., Li, X., & Zhou, P. (2015). Rapid Construction of Stable Infectious Full-Length cDNA Clone of Papaya Leaf Distortion Mosaic Virus Using In-Fusion Cloning. Viruses, 7(12), 6241-6250. doi:10.3390/v7122935

Tuo, D., Fu, L., Shen, W., Li, X., Zhou, P., & Yan, P. (2017). Generation of stable infectious clones of plant viruses by using Rhizobium radiobacter for both cloning and inoculation. Virology, 510, 99-103. doi:10.1016/j.virol.2017.07.012

Turpen, T. H., Turpen, A. M., Weinzettl, N., Kumagai, M. H., & Dawson, W. O. (1993). Transfection of whole plants from wounds inoculated with Agrobacterium tumefaciens containing cDNA of tobacco mosaic virus. Journal of Virological Methods, 42(2-3), 227-239. doi:10.1016/0166-0934(93)90035-p

Valverde, R. A., Sabanadzovic, S., & Hammond, J. (2012). Viruses that Enhance the Aesthetics of Some Ornamental Plants: Beauty or Beast? Plant Disease, 96(5), 600-611. doi:10.1094/pdis-11-11-0928-fe

Vasques, R. M., Lacorte, C., da Luz, L. L., Aranda, M. A., & Nagata, T. (2018). Development of a new tobamovirus-based viral vector for protein expression in plants. Molecular Biology Reports, 46(1), 97-103. doi:10.1007/s11033-018-4449-4

Velázquez, K., Agüero, J., Vives, M. C., Aleza, P., Pina, J. A., Moreno, P., … Guerri, J. (2016). Precocious flowering of juvenile citrus induced by a viral vector based onCitrus leaf blotch virus: a new tool for genetics and breeding. Plant Biotechnology Journal, 14(10), 1976-1985. doi:10.1111/pbi.12555

Vidalakis, G., Pagliaccia, D., Bash, J. A., Afunian, M., & Semancik, J. S. (2010). Citrus dwarfing viroid: effects on tree size and scion performance specific to Poncirus trifoliata rootstock for high-density planting. Annals of Applied Biology, 158(2), 204-217. doi:10.1111/j.1744-7348.2010.00454.x

Vlot, A. C., Neeleman, L., Linthorst, H. J. M., & Bol, J. F. (2001). Role of the 3′-Untranslated Regions of Alfalfa Mosaic Virus RNAs in the Formation of a Transiently Expressed Replicase in Plants and in the Assembly of Virions. Journal of Virology, 75(14), 6440-6449. doi:10.1128/jvi.75.14.6440-6449.2001

Waltz, E. (2017). A new crop of microbe startups raises big bucks, takes on the establishment. Nature Biotechnology, 35(12), 1120-1122. doi:10.1038/nbt1217-1120

Wang, Q., Ma, X., Qian, S., Zhou, X., Sun, K., Chen, X., … Li, Z. (2015). Rescue of a Plant Negative-Strand RNA Virus from Cloned cDNA: Insights into Enveloped Plant Virus Movement and Morphogenesis. PLOS Pathogens, 11(10), e1005223. doi:10.1371/journal.ppat.1005223

Wang, M., Lu, Y., Botella, J. R., Mao, Y., Hua, K., & Zhu, J. (2017). Gene Targeting by Homology-Directed Repair in Rice Using a Geminivirus-Based CRISPR/Cas9 System. Molecular Plant, 10(7), 1007-1010. doi:10.1016/j.molp.2017.03.002

Wehr, M. C., Laage, R., Bolz, U., Fischer, T. M., Grünewald, S., Scheek, S., … Rossner, M. J. (2006). Monitoring regulated protein-protein interactions using split TEV. Nature Methods, 3(12), 985-993. doi:10.1038/nmeth967

Wen, A. M., & Steinmetz, N. F. (2016). Design of virus-based nanomaterials for medicine, biotechnology, and energy. Chemical Society Reviews, 45(15), 4074-4126. doi:10.1039/c5cs00287g

Wetzel, V., Brault, V., & Varrelmann, M. (2018). Production of a Beet chlorosis virus full-length cDNA clone by means of Gibson assembly and analysis of biological properties. Journal of General Virology, 99(11), 1522-1527. doi:10.1099/jgv.0.001146

Whitham, S. A., Yamamoto, M. L., & Carrington, J. C. (1999). Selectable viruses and altered susceptibility mutants in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, 96(2), 772-777. doi:10.1073/pnas.96.2.772

Wieczorek, P., Budziszewska, M., & Obrępalska-Stęplowska, A. (2014). Construction of infectious clones of tomato torrado virus and their delivery by agroinfiltration. Archives of Virology, 160(2), 517-521. doi:10.1007/s00705-014-2266-1

Wrzesińska, B., Wieczorek, P., & Obrępalska-Stęplowska, A. (2016). Recombination-based generation of the agroinfectious clones of Peanut stunt virus. Journal of Virological Methods, 237, 179-186. doi:10.1016/j.jviromet.2016.09.011

Wu, Q., Wang, Y., Cao, M., Pantaleo, V., Burgyan, J., Li, W.-X., & Ding, S.-W. (2012). Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proceedings of the National Academy of Sciences, 109(10), 3938-3943. doi:10.1073/pnas.1117815109

Wurtzel, E. T., & Kutchan, T. M. (2016). Plant metabolism, the diverse chemistry set of the future. Science, 353(6305), 1232-1236. doi:10.1126/science.aad2062

Xiang, C., Han, P., Lutziger, I., Wang, K., & Oliver, D. J. (1999). Plant Molecular Biology, 40(4), 711-717. doi:10.1023/a:1006201910593

Yount, B., Curtis, K. M., & Baric, R. S. (2000). Strategy for Systematic Assembly of Large RNA and DNA Genomes: Transmissible Gastroenteritis Virus Model. Journal of Virology, 74(22), 10600-10611. doi:10.1128/jvi.74.22.10600-10611.2000

Youssef, F., Marais, A., Faure, C., Gentit, P., & Candresse, T. (2011). Strategies to facilitate the development of uncloned or cloned infectious full-length viral cDNAs: Apple chlorotic leaf spot virus as a case study. Virology Journal, 8(1). doi:10.1186/1743-422x-8-488

Zaidi, S. S.-A., & Mansoor, S. (2017). Viral Vectors for Plant Genome Engineering. Frontiers in Plant Science, 8. doi:10.3389/fpls.2017.00539

Zhang, L., & Jelkmann, W. (2017). Construction of Full-length Infectious cDNA Clones of Apple chlorotic leaf spot virus and Their Agroinoculation to Woody Plants by a Novel Method of Vacuum Infiltration. Plant Disease, 101(12), 2110-2115. doi:10.1094/pdis-04-17-0573-re

Zhang, Y., Buchholz, F., Muyrers, J. P. P., & Stewart, A. F. (1998). A new logic for DNA engineering using recombination in Escherichia coli. Nature Genetics, 20(2), 123-128. doi:10.1038/2417

Zhang, H., Wang, L., Hunter, D., Voogd, C., Joyce, N., & Davies, K. (2013). A Narcissus mosaic viral vector system for protein expression and flavonoid production. Plant Methods, 9(1), 28. doi:10.1186/1746-4811-9-28

Zhi, L., TeRonde, S., Meyer, S., Arling, M. L., Register III, J. C., Zhao, Z.-Y., … Anand, A. (2015). Effect of Agrobacterium strain and plasmid copy number on transformation frequency, event quality and usable event quality in an elite maize cultivar. Plant Cell Reports, 34(5), 745-754. doi:10.1007/s00299-014-1734-0

Zhou, M., Liang, L., & Hänninen, H. (2017). A transposition-active Phyllostachys edulis long terminal repeat (LTR) retrotransposon. Journal of Plant Research, 131(2), 203-210. doi:10.1007/s10265-017-0983-8

Zhu, G., Wang, S., Huang, Z., Zhang, S., Liao, Q., Zhang, C., … Huang, S. (2018). Rewiring of the Fruit Metabolome in Tomato Breeding. Cell, 172(1-2), 249-261.e12. doi:10.1016/j.cell.2017.12.019

Ziebell, H., & Carr, J. P. (2010). Cross-Protection. Advances in Virus Research, 211-264. doi:10.1016/s0065-3527(10)76006-1

[-]

recommendations

 

Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro completo del ítem