Editorial: “Agrobacterium biology and its application to transgenic plant production”

The extraordinary Agrobacterium research story started from the search for the causative agent of crown gall disease more than 100 years ago. Agrobacterium tumefaciens was first isolated from grapevine galls in 1897 and later isolated from Paris daisy in 1907 (Cavara, 1897a,b; Smith and Townsend, 1907). The Agrobacterium infection mechanism involves processing and transfer of a specific DNA fragment (the transferred-DNA, T-DNA) from a bacterial tumor-inducing (Ti) plasmid. Transfer to the plant occurs via a type IV secretion system (T4SS), after which T-DNA is integrated into the plant host genome (Gelvin, 2010; Lacroix and Citovsky, 2013). This interkingdom DNA transfer leads to overproduction of the plant hormones auxin and cytokinin, resulting in tumors. The interkingdom DNA transfer ability of Agrobacterium and the possibility to replace the oncogenes in the T-DNA with genes of interest has made Agrobacterium-mediated transformation the most popular technique to generate transgenic plants.

This Research Topic provides a collection of reviews and original research articles on Agrobacterium genes involved in bacterial physiology/virulence and plant genes involved in transformation and defense against Agrobacterium. A review by Kado (2014) provides a historical overview of how A. tumefaciens was first established as the cause of crown gall disease. In this review, Kado highlights key early plant pathology and milestone molecular biology studies leading to the conclusion that the expression of oncogenes in native T-DNA is the cause of tumor growth in plants. With the solid foundation of these pioneering discoveries, A. tumefaciens evolved from a phytopathogen to a powerful genetic transformation tool for plant biology and biotechnology research.

The first complete genome sequence of an Agrobacterium species (A. tumefaciens C58) was completed in 2001 (Goodner et al., 2001; Wood et al., 2001). The 5.67-megabase genome of this strain carries one circular chromosome, one linear chromosome, and two megaplasmids: the Ti plasmid pTiC58 and a second plasmid, pAtC58. In the review by Platt et al. (2014), the properties, ecology, evolution, and complex interactions of these two A. tumefaciens megaplasmids are discussed. The costs and benefits to A. tumefaciens strains carrying the Ti plasmid and/or the pAtC58 plasmid are discussed and presented from an ecological and evolutionary perspective. Modeling predictions are presented for the relative cost and benefits to A. tumefaciens strains harboring the Ti and/or the pAtC58 plasmids determined by environmental resources. Conjugation and amplification of the Ti plasmid are regulated by the TraI/TraR quorum-sensing (QS) system and conjugal opines. Lang and Faure (2014) review current knowledge of the genetic networks and molecular basis of the A. tumefaciens quorum sensing system. These authors also discuss the biological and ecological impact of the QS system on Ti plasmid conjugation, copy number, and interactions between Agrobacterium and host plants.

During the initial interaction between Agrobacterium and plant cells, bacteria sense various plant-derived signals in the rhizosphere with the help of Ti plasmid-encoded virulence gene (vir gene) and chromosomal virulence gene (chv gene) products. The current knowledge of how A. tumefaciens senses and reacts to different plant-derived signals are summarized in the review article by Subramoni et al. (2014), which also discusses the mechanisms of how the plant hormones auxin, salicylic acid, and ethylene, affect bacterial virulence. Finally, this review discusses the complexity and intricacy of Agrobacterium signaling pathways and the underlying regulatory mechanisms during the initial host cell recognition to maximize subsequent successful infection. In the original research article by Lin et al. (2014), the mechanistic regulation of the membrane sensor VirA protein is further dissected. VirA histidine kinase and the cytoplasmic response regulator VirG protein together play a central role in regulating vir gene expression in response to phenolics. Based on a homology model of the VirA linker region, various mutant and chimeric VirA proteins were generated and examined for their ability to induce VirB promoter activity. The ability of VirA to sense and respond to three separate input signals, phenolics, sugars, and environmental pH, plays a significant role in securing successful infection.

Agrobacterium attachment to plant cells is an important early step in crown gall disease progression. Motile bacteria swim toward host cells and then physically interact with host cells to form aggregates and establish a multicellular bacterial community known as a biofilm. Various genetic and environmental factors that affect Agrobacterium attachment and biofilm formation are reviewed in the article by Heindl et al. (2014). The functions of different types of exopolysaccharides that constitute the biofilm and underlying mechanisms involving how the second messenger cyclic-di-GMP, the ChvG/ChvI system, phosphorus levels, and oxygen tension influence bacterial attachment and virulence are also summarized. In the review article by Matthysse (2014), early studies and current knowledge of the mechanisms of polar and lateral bacterial attachment are summarized. These two mechanisms both contribute to bacterial attachment. When the environmental calcium and phosphate levels and pH values are low, polar attachment predominates. In addition, the phospholipids (PLs), phosphatidylcholine (PC), and phosphate-free lipid ornithine lipids (OLs) contribute to Agrobacterium virulence. In the review by Aktas et al. (2014), the biosynthetic pathways and the physiological roles of these membrane lipids are summarized. The typical eukaryotic membrane lipid PC is not frequently found in bacteria, but it constitutes almost 22% of the Agrobacterium membrane lipid. Interestingly, PCs and OLs may play opposite roles in Agrobacterium virulence. The reduction of tumor formation in a PC-deficient Agrobacterium mutant may result from impaired vir gene expressions controlled by VirA/VirG. The absence of OLs in A. tumefaciens may decrease host defense responses and therefore cause earlier and larger tumor formation.

Plant cells have a variety of receptors that recognize so-called microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs), and subsequently activate plant defense responses, a process known as Pattern-recognition receptor-Triggered Immunity (PTI) (Boller and Felix, 2009; Boller and He, 2009). Agrobacteriium may utilize effectors to hijack plant systems and evade plant defense responses. Pitzschke (2013) reviews strategies used by Agrobacterium to turn plant defense responses to its own advantage. Infected plant cells initiate a mitogen-activated protein kinase signaling cascade that causes VIP1 (Agrobacterium VirE2-interacting protein 1) phosphorylation and translocation into the plant nucleus to induce defense gene expression. On the other hand, Agrobacterium may hijack VIP1 to help T-DNA enter the plant nucleus. Based on the current knowledge of plant defense responses against Agrobacterium infection, Pitzschke (2013) discusses several biotechnological approaches to increase transformation efficiency. In another review by Gohlke and Deeken (2014), early plant responses to Agrobacterium, including various defense responses, hypersensitive responses, and phytohormone level alterations are discussed. The alterations in plant morphology, nutrient translocation, and metabolism caused by crown gall tumor formation are also reviewed. The authors summarize important genomic, epigenomic, transcriptomic, and metabolomic studies that reveal epigenetic changes associated with T-DNA integration and gall development. Subsequently, Hwang et al. (2015) review important pathogenic elicitors, host cell receptor molecules, and their downstream signal transduction pathways in host plants during the PAMP-triggered immune response. They highlight recent discoveries linking plant immunity to endomembrane trafficking and actin dynamic changes. Effects of both the host physiology, including hormone levels, circadian clock, developmental stages, and environmental factors, including light exposure lengths and temperature, on plant defense responses and bacterial virulence are reviewed and discussed.

In nature, evidence of ancient horizontal gene transfers (HGT) from Agrobacterium to plants has been observed in the genera Nicotiana and Linaria. Sequences homologous to mikimopine-type Agrobacterium rhizogenes pRiA4 T-DNA were first discovered in the genome of untransformed tree tobacco, Nicotiana glauca, and named “cellular T-DNA” (cT-DNA; White et al., 1983). Matveeva and Lutova (2014) review cT-DNA organization, distribution, expression regulation, and a possible correlation with genetic tumor formation in Nicotiana species. They also review recent findings of cT-DNA in the genomes of Linaria species and in other dicotyledonous families. The authors suggest that plants maintaining cT-DNA in their genomes may potentially benefit microorganisms in the rhizosphere by secreting opines in the root zone. They also propose that footprints of ancient pRi T-DNA insertions in the plant genome may provide selective advantage to these plants.

With this Research Topic we provide a platform for scientists to share their understanding of Agrobacterium biology and how Agrobacterium transforms plants. These contributions demonstrate how a highly active research community in plant and microbial sciences can elucidate important pathogenesis questions. Future research on Agrobacteium will continue to advance our understanding of plant-pathogen interactions, and provide new insights useful for plant genetic engineering.

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Acknowledgments

The authors thank the Ministry of Science and Technology (NSC 100-2311-B-005-002 and MOST 103-2311-B-005-003; H-HH and E-ML), the National Chung Hsing University (H-HH), and the US National Science Foundation (SG) for financial support.

References

Aktas, M., Danne, L., Möller, P., and Narberhaus, F. (2014). Membrane lipids in Agrobacterium tumefaciens: biosynthetic pathways and importance for pathogenesis. Front. Plant Sci. 5:109. doi: 10.3389/fpls.2014.00109

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Boller, T., and Felix, G. (2009). A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu. Rev. Plant Biol. 60, 379–406. doi: 10.1146/annurev.arplant.57.032905.105346

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Boller, T., and He, S. Y. (2009). Innate immunity in plants: an arms race between pattern recognition receptors in plants and effectors in microbial pathogens. Science 324, 742–744. doi: 10.1126/science.1171647

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Cavara, F. (1897a). Eziologia di alcune malattie di piante cultivate. Le Stazioni Sper. Agraric Itliana 30, 482–509.

Cavara, F. (1897b). Tuberculosi della vite.Intorno alla eziologia di alcune malattie di piante cultivate. Le Stazioni Sper. Agraric Itliana 30, 483–487.

Gelvin, S. B. (2010). Plant proteins involved in Agrobacterium-mediated genetic transformation. Annu. Rev. Phytopathol. 48, 45–68. doi: 10.1146/annurev-phyto-080508-081852

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Gohlke, J., and Deeken, R. (2014). Plant responses to Agrobacterium tumefaciens and crown gall development. Front. Plant Sci. 5:155. doi: 10.3389/fpls.2014.00155

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Goodner, B., Hinkle, G., Gattung, S., Miller, N., Blanchard, M., Qurollo, B., et al. (2001). Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294, 2323–2328. doi: 10.1126/science.1066803

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Heindl, J. E., Wang, Y., Heckel, B. C., Mohari, B., Feirer, N., and Fuqua, C. (2014). Mechanisms and regulation of surface interactions and biofilm formation in Agrobacterium. Front. Plant Sci. 5:176. doi: 10.3389/fpls.2014.00176

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Hwang, E. E., Wang, M. B., Bravo, J. E., and Banta, L. M. (2015). Unmasking host and microbial strategies in the Agrobacterium-plant defense tango. Front. Plant Sci. 6:200. doi: 10.3389/fpls.2015.00200

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Kado, C. I. (2014). Historical account on gaining insights on the mechanism of crown gall tumorigenesis induced by Agrobacterium tumefaciens. Front. Microbiol. 5:340. doi: 10.3389/fmicb.2014.00340

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Lacroix, B., and Citovsky, V. (2013). The roles of bacterial and host plant factors in Agrobacterium-mediated genetic transformation. Int. J. Dev. Biol. 57, 467–481. doi: 10.1387/ijdb.130199bl

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Lang, J., and Faure, D. (2014). Functions and regulation of quorum-sensing in Agrobacterium tumefaciens. Front. Plant Sci. 5:14. doi: 10.3389/fpls.2014.00014

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Lin, Y.-H., Pierce, B. D., Fang, F., Wise, A., Binns, A. N., and Lynn, D. G. (2014). Role of the VirA histidine autokinase of Agrobacterium tumefaciens in the initial steps of pathogenesis. Front. Plant Sci. 5:195. doi: 10.3389/fpls.2014.00195

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Matthysse, A. G. (2014). Attachment of Agrobacterium to plant surfaces. Front. Plant Sci. 5:252. doi: 10.3389/fpls.2014.00252

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Matveeva, T. V., and Lutova, L. A. (2014). Horizontal gene transfer from Agrobacterium to plants. Front. Plant Sci. 5:326. doi: 10.3389/fpls.2014.00326

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Pitzschke, A. (2013). Agrobacterium infection and plant defense—transformation success hangs by a thread. Front. Plant Sci. 4:519. doi: 10.3389/fpls.2013.00519

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Platt, T. G., Morton, E. R., Barton, I. S., Bever, J. D., and Fuqua, C. (2014). Ecological dynamics and complex interactions of Agrobacterium megaplasmids. Front. Plant Sci. 5:635. doi: 10.3389/fpls.2014.00635

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Smith, E. F., and Townsend, C. O. (1907). A plant-tumor of bacterial origin. Science 25, 671–673. doi: 10.1126/science.25.643.671

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

Subramoni, S., Nathoo, N., Klimov, E., and Yuan, Z.-C. (2014). Agrobacterium tumefaciens responses to plant-derived signaling molecules. Front. Plant Sci. 5:322. doi: 10.3389/fpls.2014.00322

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar

White, F. F., Garfinkel, D. J., Huffman, G. A., Gordon, M. P., and Nester, E. W. (1983). Sequence homologous to Agrobacterium rhizogenes T-DNA in the genomes of uninfected plants. Nature 301, 348–350. doi: 10.1038/301348a0

CrossRef Full Text | Google Scholar

Wood, D. W., Setubal, J. C., Kaul, R., Monks, D. E., Kitajima, J. P., Okura, V. K., et al. (2001). The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294, 2317–2323. doi: 10.1126/science.1066804

PubMed Abstract | Full Text | CrossRef Full Text | Google Scholar