Alternative Non-Agrobacterium Based Methods for Plant Transformation
Dheeraj S. Rathore
Dept. Crop Science, Teagasc, Oak Park, Carlow, Ireland
Search for more papers by this authorEwen Mullins
Dept. Crop Science, Teagasc, Oak Park, Carlow, Ireland
Search for more papers by this authorDheeraj S. Rathore
Dept. Crop Science, Teagasc, Oak Park, Carlow, Ireland
Search for more papers by this authorEwen Mullins
Dept. Crop Science, Teagasc, Oak Park, Carlow, Ireland
Search for more papers by this authorAbstract
Plant breeding continues to play a crucial role in generating crops fit for purpose to tackle the increasing number of a biotic stressors that farmers face. While the majority of engineered varieties have been and continue to be generated through the use of Agrobacterium tumefaciens via Agrobacterium-mediated transformation (AMT), more recently, the potential of non-Agrobacterium systems is coming to the fore, specifically in regard to rhizobia such as Ensifer adhaerens, Ochrobactrum haywardense, Rhizobium etli, and the collective of strains termed Transbacter™. This article reviews the landscapes of non-Agrobacterium species from the perspective of crop improvement, highlighting the mechanisms they use to manipulate host genomes as the basis for their possible transinfection strategies. Recruiting enhanced versions of these non-Agrobacterium strains empowered with stealthy mechanisms to deliver DNA/proteins into plant cells provides the potential to make a positive contribution to enhancing existing breeding programmes.
References
- Altpeter, F., Springer, N.M., Bartley, L.E. et al. (2016). Advancing crop transformation in the era of genome editing. The Plant Cell 28: 1510–1520.
- Anand, A., Bazz, S.H., Bertain, S.M. et al. (2017a). Ochrobactrum-mediated transformation of plants. (WO/2017/040343, ed.).
- Anand, A., Bass, S.H., Cho, H.J. et al. (2017b). Methods and compositions of improved plant transformation. Vol. WO/2017/078836 A1 p.
- Bebber, D.P., Ramotowski, M.A.T., and Gurr, S.J. (2013). Crop pests and pathogens move polewards in a warming world. Nature Climate Change 3: 985.
- Bevan, M.W. and Uauy, C. (2013). Genomics reveals new landscapes for crop improvement. Genome Biology 14: 206.
- Bevan, M. and Waugh, R. (2007). Applying plant genomics to crop improvement. Genome Biology 8: 302.
- Bittinger, M., Gross, J., Widom, J. et al. (2000). Rhizobium etli CE3 carries vir gene homologs on a self-transmissible plasmid. Molecular Plant–Microbe Interactions 13: 1019–1021.
- Boeke, J.D., Church, G., Hessel, A. et al. (2016). The genome project-write. Science 353: 126–127.
- Bradford, K.J., Van Deynze, A., Gutterson, N. et al. (2005). Regulating transgenic crops sensibly: lessons from plant breeding, biotechnology and genomics. Nature Biotechnology 23: 439–444.
- Breseghello, F. and Coelho, A.S.G. (2013). Traditional and modern plant breeding methods with examples in rice (Oryza sativa L.). Journal of Agricultural and Food Chemistry 61: 8277–8286.
- Broothaerts, W., Mitchell, H.J., Weir, B. et al. (2005). Gene transfer to plants by diverse species of bacteria. Nature 433: 629–633.
- Casida, J.L.E. (1982). Ensifer adhaerens gen. nov., sp. nov.: a bacterial predator of bacteria in soil. International Journal of Systematic Bacteriology 32: 339–345.
- Chapotin, S.M. and Wolt, J.D. (2007). Genetically modified crops for the bioeconomy: meeting public and regulatory expectations. Transgenic research 16: 675–688.
- Chavarriaga-Aguirre, P., Brand, A., Medina, A. et al. (2016). The potential of using biotechnology to improve cassava: a review. In Vitro Cellular & Developmental Biology 52: 461–478.
- Chi-Ham, C.L., Boettiger, S., Figueroa-Balderas, R. et al. (2012). An intellectual property sharing initiative in agricultural biotechnology: development of broadly accessible technologies for plant transformation. Plant Biotechnology Journal 10: 501–510.
- Chilton, M.-D. (2005). Adding diversity to plant transformation. Nature Biotechnology 23: 309–310.
- Chung, S.-M., Vaidya, M., and Tzfira, T. (2006). Agrobacterium is not alone: gene transfer to plants by viruses and other bacteria. Trends in Plant Science 11: 1–4.
- Delmont, T.O., Robe, P., Cecillon, S. et al. (2011). Accessing the soil metagenome for studies of microbial diversity. Applied and Environmental Microbiology 77: 1315–1324.
- ECOSOC Youth Forum (2017). 6th Economic and Social Council Youth Forum Concept Note. https://wwwunorg/ecosoc/sites/wwwunorgecosoc/files/files/en/2017doc/End-hunger-achieve-food-security-and-improved-nutrition-and-promote-sustainable-agriculturepdf (accessed 12 September 2018).
- Escobar, M.A. and Dandekar, A.M. (2003). Agrobacterium tumefaciens as an agent of disease. Trends in Plant Science 8: 380–386.
- FAO (2017). http://www.fao.org/3/a-i6583e.pdf (accessed 12 September 2018).
- Gelvin, S.B. (2005). Gene exchange by design. Nature 433: 583–584.
- Gelvin, S.B. (2009). Agrobacterium in the genomics age. Plant Physiology 150: 1665–1676.
- Germida, J.J. and Casida, L.E. (1983). Ensifer adhaerens predatory activity against other bacteria in soil, as monitored by indirect phage analysis. Applied and Environmental Microbiology 45: 1380–1388.
- Gilbert, J.A., Jansson, J.K., and Knight, R. (2014). The Earth microbiome project: successes and aspirations. BMC Biology 12: 69.
- González, V., Santamaría, R.I., Bustos, P. et al. (2006). The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proceedings of the National Academy of Sciences of the United States of America 103: 3834–3839.
- Harwood, W.A. (2012). Advances and remaining challenges in the transformation of barley and wheat. Journal of Experimental Botany 63: 1791–1798.
-
Harwood, W.A., Bartlett, J.G., Alves, S.C. et al. (2009). Barley transformation using Agrobacterium-mediated techniques. In: Transgenic Wheat, Barley and Oats: Production and Characterization Protocols (ed. H.D. Jones and P.R. Shewry), pp. 137–147. Totowa, NJ: Humana Press.
10.1007/978-1-59745-379-0_9 Google Scholar
- Heeres, P., Schippers-Rozenboom, M., Jacobsen, E., and Visser, R.F. (2002). Transformation of a large number of potato varieties: genotype-dependent variation in efficiency and somaclonal variability. Euphytica 124: 13–22.
- Hiei, Y., Ishida, Y., and Komari, T. (2014). Progress of cereal transformation technology mediated by Agrobacterium tumefaciens . Frontiers in Plant Science 5: 628.
- Hooykaas, P. and Schilperoort, R. (1984). The molecular genetics of crown gall tumorigenesis. Advances in Genetics 22: 209–283.
- Hooykaas, P., Klapwijk, P., Nuti, M. et al. (1977). Transfer of the Agrobacterium tumefaciens Ti plasmid to avirulent Agrobacteria and to Rhizobium ex planta. Journal of General Microbiology 98: 477–484.
- Jefferson, R.A., Jefferson, O.A., Smith, L. et al. (2006). Freedom to co-operate: transbacter as a biological open source (BIOS) tool for gene transfer. 8th international congress of plant molecular biology abstracts. Plant Molecular Biology Reporter 24: 141–160.
- Key, S., Ma, J.K.C., and Drake, P.M.W. (2008). Genetically modified plants and human health. Journal of the Royal Society of Medicine 101: 290–298.
- Lacroix, B. and Citovsky, V. (2016a). A functional bacterium-to-plant DNA transfer machinery of Rhizobium etli . PLOS Pathogens 12: e1005502.
- Lacroix, B. and Citovsky, V. (2016b). Transfer of DNA from bacteria to eukaryotes. mBio 7: e00863-16.
- Li, J., Ye, X., An, B. et al. (2012). Genetic transformation of wheat: current status and future prospects. Plant Biotechnology Reports 6: 183–193.
- Lopez Vernaza, M.A., Rathore, D.S., Wendt, T. et al. (2015). Ensifer-mediated transformation (EMT): a novel technology platform for engineering plant genomes. Plant & Animal Genome XXIII 293.
- Nesme, J., Achouak, W., Agathos, S.N. et al. (2016). Back to the future of soil metagenomics. Frontiers in Microbiology 7: 73–78.
-
Nottenburg, C. and Rodríguez, C. (2008). Agrobacterium-mediated gene transfer: a lawyer's perspective. In: Agrobacterium: From Biology to Biotechnology (ed. T. Tzfira and V. Citovsky), 699–735. New York: Springer.
10.1007/978-0-387-72290-0_20 Google Scholar
-
Ortiz Ríos, R. (2015). Genetic engineering and transgenic breeding. In: Plant Breeding in the Omics Era, 103–123. Cham: Springer International Publishing.
10.1007/978-3-319-20532-8_7 Google Scholar
- Petti, C., Wendt, T., Meade, C., and Mullins, E. (2009). Evidence of genotype dependency within Agrobacterium tumefaciens in relation to the integration of vector backbone sequence in transgenic Phytophthora infestans-tolerant potato. Journal of Bioscience and Bioengineering 107: 301–306.
- Prado, J.R., Segers, G., Voelker, T. et al. (2014). Genetically engineered crops: from idea to product. Annual Review of Plant Biology 65: 769–790.
- Rahmawati, S., Jefferson, O., Sopandie, D. et al. (2010). Comparative analysis of rice transformation using Agrobacterium tumefaciens and Rhyzobium leguminosarum . Indonesian Journal of Biotechnology 15: 37–45.
- Rathore, D.S., Lopez-Vernaza, M.A., Doohan, F. et al. (2015). Profiling antibiotic resistance and electrotransformation potential of Ensifer adhaerens OV14; a non-Agrobacterium species capable of efficient rates of plant transformation. FEMS Microbiology Letters 362: fnv126.
- Rathore, D.S., Doohan, F., and Mullins, E. (2016). Capability of the plant-associated bacterium, Ensifer adhaerens strain OV14, to genetically transform its original host Brassica napus . Plant Cell, Tissue and Organ Culture 127: 85–94.
- Rathore, D.S., Doohan, F.M., and Mullins, E. (2017). Ensifer-mediated Arabidopsis thaliana root transformation (E-ART): a protocol to analyse the factors that support Ensifer-mediated transformation (EMT) of plant cells. Bio-protocol 7: e2564.
- Rogel, M.A., Hernandez-Lucas, I., Kuykendall, L.D. et al. (2001). Nitrogen-fixing nodules with Ensifer adhaerens harbouring Rhizobium tropici symbiotic plasmids. Applied and Environmental Microbiology 67: 3264–3268.
- Rudder, S., Doohan, F., Creevey, C.J. et al. (2014). Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes. BMC Genomics 15: 268–285.
- Sharma, T.R., Devanna, B.N., Kiran, K. et al. (2018). Status and prospects of next generation sequencing technologies in crop plants. Current Issues in Molecular Biology 27: 1–36.
- Toniutti, L., Breitler, J.-C., Etienne, H. et al. (2017). Influence of environmental conditions and genetic background of arabica coffee (C. arabica L) on leaf rust (Hemileia vastatrix) pathogenesis. Frontiers in Plant Science 8: 2025.
- Treangen, T.J. and Rocha, E.P.C. (2011). Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLOS Genetics 7: e1001284.
- Trevors, J.T. (2010). One gram of soil: a microbial biochemical gene library. Antonie Van Leeuwenhoek 97: 99–106.
- Tzfira, T. and Citovsky, V. (2006). Agrobacterium-mediated genetic transformation of plants: biology and biotechnology. Current Opinion in Biotechnology 17: 147–154.
- Unamba, C.I.N., Nag, A., and Sharma, R.K. (2015). Next generation sequencing technologies: the doorway to the unexplored genomics of non-model plants. Frontiers in Plant Science 6: 1074.
-
Van Veen, R., den Dulk-Ras, H., Bisseling, T. et al. (1988). Crown gall tumor and root nodule formation by the bacterium Phyllobacterium myrsinacearum after the introduction of an Agrobacterium Ti plasmid or a Rhizobium Sym plasmid. Molecular Plant–Microbe Interactions Journal
1: 231–234.
10.1094/MPMI-1-231 Google Scholar
- Van Veen, R., den Dulk-Ras, H., Schilperoort, R., and Hooykaas, P. (1989). Ti plasmid containing Rhizobium meliloti are non-tumorigenic on plants, despite proper virulence gene induction and T-strand formation. Archives of Microbiology 153: 85–89.
- Vu, H.T., Itoh, H., Ishii, S. et al. (2013). Identification and phylogenetic characterization of cobalamin biosynthetic genes of Ensifer adhaerens . Microbes and Environments 28: 153–155.
- Wendt, T. (2010). Developing an alternative delivery system to facilitate gene transfer into major crops. Thesis, University College Dublin, Dublin.
- Wendt, T., Doohan, F., Winckelmann, D., and Mullins, E. (2011). Gene transfer into Solanum tuberosum via Rhizobium spp. Transgenic Research 20: 377–386.
- Wendt, T., Doohan, F., and Mullins, E. (2012). Production of Phytophthora infestans-resistant potato (Solanum tuberosum) utilising Ensifer adhaerens OV14. Transgenic Research 21: 567–578.
- Wright, S. (1986). Recombinant DNA technology and its social transformation, 1972–1982. Osiris 2: 303–360.
- Xu, L., Chen, X., Li, H. et al. (2016). Characterization of the biosorption and biodegradation properties of Ensifer adhaerens: a potential agent to remove polychlorinated biphenyls from contaminated water. Journal of Hazardous Materials 302: 314–322.
- Yutani, M., Taniguchi, H., Borjihan, H. et al. (2011). Alliinase from Ensifer adhaerens and its use for generation of fungicidal activity. AMB Express 1: 2.
- Zhou, G., Wang, Y., Zhai, S. et al. (2013). Biodegradation of the neonicotinoid insecticide thiamethoxam by the nitrogen-fixing and plant-growth-promoting rhizobacterium Ensifer adhaerens strain TMX-23. Applied Microbiology and Biotechnology 97: 4065–4074.
- Zhou, G., Wang, Y., Ma, Y. et al. (2014). The metabolism of neonicotinoid insecticide thiamethoxam by soil enrichment cultures, and the bacterial diversity and plant growth-promoting properties of the cultured isolates. Journal of Environmental Science and Health, Part B 49: 381–390.
- Zuniga-Soto, E., Mullins, E., and Dedicova, B. (2015). Ensifer-mediated transformation: an efficient non-Agrobacterium protocol for the genetic modification of rice. SpringerPlus 4: 1–10.
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