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標題: 利用轉錄體學研究農桿菌媒介阿拉伯芥轉殖效率之基因 及次級代謝物
Employment of transcriptome analysis for studies of Arabidopsis genes and secondary metabolites involved in Agrobacterium-mediated transformation
作者: 施博原
Po-Yuan Shih
關鍵字: 農桿菌;農桿菌媒介轉殖法;glucosinolate;camalexin;EFR;植物免疫;癌腫病;轉錄體學;Agrobacterium tumefaciens;Agrobacterium-mediated plant transformation;glucosinolate;camalexin;crown gall;EFR;plant immune;transcriptome
引用: Agrios, G. N. (2005) Plant pathology. Amsterdam ; Boston: Elsevier Academic Press. Ahuja, I., Kissen, R. and Bones, A. M. (2012) Phytoalexins in defense against pathogens. Trends Plant Sci, 17, 73-90. Aires, A., Mota, V. R., Saavedra, M. J., Monteiro, A. A., Simões, M., Rosa, E. A., et al. (2009) Initial in vitro evaluations of the antibacterial activities of glucosinolate enzymatic hydrolysis products against plant pathogenic bacteria. J Appl Microbiol, 106, 2096-2105. Alazem, M. and Lin, N. S. (2015) Roles of plant hormones in the regulation of host-virus interactions. Mol Plant Pathol, 16, 529-540. Alexa, A., Rahnenführer, J. and Lengauer, T. (2006) Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics, 22, 1600-1607. Anand, A., Krichevsky, A., Schomack, S., Lahaye, T., Tzfira, T., Tang, Y. H., et al. (2007) Arabidopsis VIRE2 INTERACTING PROTEIN2 is required for Agrobacterium T-DNA integration in plants. Plant Cell, 19, 1695-1708. Anand, A., Rojas, C. M., Tang, Y. H. and Mysore, K. S. (2012) Several components of SKP1/Cullin/F-box E3 ubiquitin ligase complex and associated factors play a role in Agrobacterium-mediated plant transformation. New Phytologist, 195, 203-216. Arnaud, D., Lee, S., Takebayashi, Y., Choi, D., Choi, J., Sakakibara, H., et al. (2017) Cytokinin-Mediated Regulation of Reactive Oxygen Species Homeostasis Modulates Stomatal Immunity in Arabidopsis. Plant Cell, 29, 543-559. Asai, T., Tena, G., Plotnikova, J., Willmann, M. R., Chiu, W. L., Gomez-Gomez, L., et al. (2002) MAP kinase signalling cascade in Arabidopsis innate immunity. Nature, 415, 977-983. Auguy, F., Fahr, M., Moulin, P., Brugel, A., Laplaze, L., El Mzibri, M., et al. (2013) Lead Tolerance and Accumulation in Hirschfeldia incana, a Mediterranean Brassicaceae from Metalliferous Mine Spoils. Plos One, 8. Backert, S., Fronzes, R. and Waksman, G. (2008) VirB2 and VirB5 proteins: specialized adhesins in bacterial type-IV secretion systems? Trends Microbiol, 16, 409-413. Banerjee, J., Magnani, R., Nair, M., Dirk, L. M., DeBolt, S., Maiti, I. B., et al. (2013) Calmodulin-mediated signal transduction pathways in Arabidopsis are fine-tuned by methylation. Plant Cell, 25, 4493-4511. Bao, Y., Song, W. M., Pan, J., Jiang, C. M., Srivastava, R., Li, B., et al. (2016) Overexpression of the NDR1/HIN1-Like Gene NHL6 Modifies Seed Germination in Response to Abscisic Acid and Abiotic Stresses in Arabidopsis. PLoS One, 11, e0148572. Bednarek, P. (2012) Sulfur-containing secondary metabolites from Arabidopsis thaliana and other Brassicaceae with function in plant immunity. Chembiochem, 13, 1846-1859. Bednarek, P., Pislewska-Bednarek, M., Svatos, A., Schneider, B., Doubsky, J., Mansurova, M., et al. (2009) A glucosinolate metabolism pathway in living plant cells mediates broad-spectrum antifungal defense. Science, 323, 101-106. Beekwilder, J., van Leeuwen, W., van Dam, N. M., Bertossi, M., Grandi, V., Mizzi, L., et al. (2008) The impact of the absence of aliphatic glucosinolates on insect herbivory in Arabidopsis. PLoS One, 3, e2068. Bezrutczyk, M., Yang, J. I., Eom, J. S., Prior, M., Sosso, D., Hartwig, T., et al. (2018) Sugar flux and signaling in plant-microbe interactions. Plant Journal, 93, 675-685. Bhattacharjee, S., Lee, L. Y., Oltmanns, H., Cao, H. B., Veena, Cuperus, J., et al. (2008) IMPa-4, an Arabidopsis Importin alpha Isoform, Is Preferentially Involved in Agrobacterium-Mediated Plant Transformation. Plant Cell, 20, 2661-2680. Boerjan, W., Cervera, M. T., Delarue, M., Beeckman, T., Dewitte, W., Bellini, C., et al. (1995) Superroot, a Recessive Mutation in Arabidopsis, Confers Auxin Overproduction. Plant Cell, 7, 1405-1419. Boudsocq, M., Willmann, M. R., McCormack, M., Lee, H., Shan, L., He, P., et al. (2010) Differential innate immune signalling via Ca(2+) sensor protein kinases. Nature, 464, 418-422. Brader, G., Mikkelsen, M. D., Halkier, B. A. and Palva, E. T. (2006) Altering glucosinolate profiles modulates disease resistance in plants. Plant Journal, 46, 758-767. Britton, M. T., Escobar, M. A. and Dandekar, A. M. (2008) The Oncogenes of Agrobacterium Tumefaciens and Agrobacterium Rhizogenes. In: Agrobacterium: From Biology to Biotechnology. (Tzfira, T. and Citovsky, V., eds.). New York, NY: Springer New York, pp. 523-563. Cascales, E. and Christie, P. J. (2004) Definition of a bacterial type IV secretion pathway for a DNA substrate. Science, 304, 1170-1173. Chen, L. Q., Hou, B. H., Lalonde, S., Takanaga, H., Hartung, M. L., Qu, X. Q., et al. (2010) Sugar transporters for intercellular exchange and nutrition of pathogens. Nature, 468, 527-U199. Chen, S., Petersen, B. L., Olsen, C. E., Schulz, A. and Halkier, B. A. (2001) Long-distance phloem transport of glucosinolates in Arabidopsis. Plant Physiol, 127, 194-201. Chinchilla, D., Bauer, Z., Regenass, M., Boller, T. and Felix, G. (2006) The Arabidopsis receptor kinase FLS2 binds flg22 and determines the specificity of flagellin perception. Plant Cell, 18, 465-476. Chinchilla, D., Zipfel, C., Robatzek, S., Kemmerling, B., Nurnberger, T., Jones, J. D., et al. (2007) A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature, 448, 497-500. Christie, P. J., Atmakuri, K., Krishnamoorthy, V., Jakubowski, S. and Cascales, E. (2005) Biogenesis, architecture, and function of bacterial type IV secretion systems. Annu Rev Microbiol, 59, 451-485. Christie, P. J., Whitaker, N. and Gonzalez-Rivera, C. (2014) Mechanism and structure of the bacterial type IV secretion systems. Bba-Mol Cell Res, 1843, 1578-1591. Ciolkowski, I., Wanke, D., Birkenbihl, R. P. and Somssich, I. E. (2008) Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function. Plant Mol Biol, 68, 81-92. Citovsky, V., Kapelnikov, A., Oliel, S., Zakai, N., Rojas, M. R., Gilbertson, R. L., et al. (2004) Protein interactions involved in nuclear import of the Agrobacterium VirE2 protein in vivo and in vitro. J Biol Chem, 279, 29528-29533. Clay, N. K., Adio, A. M., Denoux, C., Jander, G. and Ausubel, F. M. (2009) Glucosinolate metabolites required for an Arabidopsis innate immune response. Science, 323, 95-101. Consales, F., Schweizer, F., Erb, M., Gouhier-Darimont, C., Bodenhausen, N., Bruessow, F., et al. (2012) Insect oral secretions suppress wound-induced responses in Arabidopsis. J Exp Bot, 63, 727-737. Crane, Y. M. and Gelvin, S. B. (2007) RNAi-mediated gene silencing reveals involvement of Arabidopsis chromatin-related genes in Agrobacterium-mediated root transformation. Proc Natl Acad Sci U S A, 104, 15156-15161. Daudi, A., Cheng, Z. Y., O'Brien, J. A., Mammarella, N., Khan, S., Ausubel, F. M., et al. (2012) The Apoplastic Oxidative Burst Peroxidase in Arabidopsis Is a Major Component of Pattern-Triggered Immunity. Plant Cell, 24, 275-287. de Hoon, M. J., Imoto, S., Nolan, J. and Miyano, S. (2004) Open source clustering software. Bioinformatics, 20, 1453-1454. Deblaere, R., Bytebier, B., De Greve, H., Deboeck, F., Schell, J., Van Montagu, M., et al. (1985) Efficient octopine Ti plasmid-derived vectors for Agrobacterium-mediated gene transfer to plants. Nucleic Acids Res, 13, 4777-4788. Deeken, R., Engelmann, J. C., Efetova, M., Czirjak, T., Muller, T., Kaiser, W. M., et al. (2006) An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach. Plant Cell, 18, 3617-3634. Desaki, Y., Kouzai, Y., Ninomiya, Y., Iwase, R., Shimizu, Y., Seko, K., et al. (2018) OsCERK1 plays a crucial role in the lipopolysaccharide-induced immune response of rice. New Phytol, 217, 1042-1049. Ditt, R. F., Kerr, K. F., de Figueiredo, P., Delrow, J., Comai, L. and Nester, E. W. (2006) The Arabidopsis thaliana transcriptome in response to Agrobacterium tumefaciens. Mol Plant Microbe Interact, 19, 665-681. Ditt, R. F., Nester, E. W. and Comai, L. (2001) Plant gene expression response to Agrobacterium tumefaciens. Proc Natl Acad Sci U S A, 98, 10954-10959. Djamei, A., Pitzschke, A., Nakagami, H., Rajh, I. and Hirt, H. (2007) Trojan horse strategy in Agrobacterium transformation: abusing MAPK defense signaling. Science, 318, 453-456. Duan, K., Willig, C. J., De Tar, J. R., Spollen, W. G. and Zhang, Z. J. (2018) Transcriptomic Analysis of Arabidopsis Seedlings in Response to an Agrobacterium-Mediated Transformation Process. Mol Plant Microbe Interact, 31, 445-459. Efetova, M., Zeier, J., Riederer, M., Lee, C. W., Stingl, N., Mueller, M., et al. (2007) A central role of abscisic acid in drought stress protection of Agrobacterium-induced tumors on Arabidopsis. Plant Physiol, 145, 853-862. Endo, M., Ishikawa, Y., Osakabe, K., Nakayama, S., Kaya, H., Araki, T., et al. (2006) Increased frequency of homologous recombination and T-DNA integration in Arabidopsis CAF-1 mutants. Embo J, 25, 5579-5590. Erbs, G. and Newman, M. A. (2012) The role of lipopolysaccharide and peptidoglycan, two glycosylated bacterial microbe-associated molecular patterns (MAMPs), in plant innate immunity. Mol Plant Pathol, 13, 95-104. Erbs, G., Silipo, A., Aslam, S., De Castro, C., Liparoti, V., Flagiello, A., et al. (2008) Peptidoglycan and muropeptides from pathogens Agrobacterium and Xanthomonas elicit plant innate immunity: structure and activity. Chem Biol, 15, 438-448. Fan, J., Crooks, C., Creissen, G., Hill, L., Fairhurst, S., Doerner, P., et al. (2011) Pseudomonas sax Genes Overcome Aliphatic Isothiocyanate-Mediated Non-Host Resistance in Arabidopsis. Science, 331, 1185-1188. Felix, G. and Boller, T. (2003) Molecular sensing of bacteria in plants - The highly conserved RNA-binding motif RNP-1 of bacterial cold shock proteins is recognized as an elicitor signal in tobacco. J Biol Chem, 278, 6201-6208. Felix, G., Duran, J. D., Volko, S. and Boller, T. (1999) Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. Plant J, 18, 265-276. Feng, F. and Zhou, J. M. (2012) Plant-bacterial pathogen interactions mediated by type III effectors. Curr Opin Plant Biol, 15, 469-476. Gallego, M. E., Bleuyard, J. Y., Daoudal-Cotterell, S., Jallut, N. and White, C. I. (2003) Ku80 plays a role in non-homologous recombination but is not required for T-DNA integration in Arabidopsis. Plant J, 35, 557-565. Garcia-Rodriguez, F. M., Schrammeijer, B. and Hooykaas, P. J. J. (2006) The Agrobacterium VirE3 effector protein: a potential plant transcriptional activator. Nucleic Acids Res, 34, 6496-6504. Gaspar, Y. M., Nam, J., Schultz, C. J., Lee, L. Y., Gilson, P. R., Gelvin, S. B., et al. (2004a) Characterization of the Arabidopsis lysine-rich arabinogalactan-protein AtAGP17 mutant (rat1) that results in a decreased efficiency of agrobacterium transformation. Plant Physiology, 135, 2162-2171. Gaspar, Y. M., Nam, J., Schultz, C. J., Lee, L. Y., Gilson, P. R., Gelvin, S. B., et al. (2004b) Characterization of the Arabidopsis lysine-rich arabinogalactan-protein AtAGP17 mutant (rat1) that results in a decreased efficiency of agrobacterium transformation. Plant Physiol, 135, 2162-2171. Gebauer, P., Korn, M., Engelsdorf, T., Sonnewald, U., Koch, C. and Voll, L. M. (2017) Sugar Accumulation in Leaves of Arabidopsis sweet11/sweet12 Double Mutants Enhances Priming of the Salicylic Acid-Mediated Defense Response. Frontiers in Plant Science, 8. Gechev, T. S. and Hille, J. (2005) Hydrogen peroxide as a signal controlling plant programmed cell death. J Cell Biol, 168, 17-20. Gechev, T. S., Minkov, I. N. and Hille, J. (2005) Hydrogen peroxide-induced cell death in Arabidopsis: transcriptional and mutant analysis reveals a role of an oxoglutarate-dependent dioxygenase gene in the cell death process. IUBMB Life, 57, 181-188. Gelvin, S. B. (1998) Agrobacterium VirE2 proteins can form a complex with T strands in the plant cytoplasm. Journal of Bacteriology, 180, 4300-4302. Gelvin, S. B. (2010) Plant proteins involved in Agrobacterium-mediated genetic transformation. Annu Rev Phytopathol, 48, 45-68. Gelvin, S. B. (2017) Integration of Agrobacterium T-DNA into the Plant Genome. Annu Rev Genet, 51, 195-217. Gigolashvili, T., Geier, M., Ashykhmina, N., Frerigmann, H., Wulfert, S., Krueger, S., et al. (2012) The Arabidopsis Thylakoid ADP/ATP Carrier TAAC Has an Additional Role in Supplying Plastidic Phosphoadenosine 5 '-Phosphosulfate to the Cytosol. Plant Cell, 24, 4187-4204. Glauser, G., Schweizer, F., Turlings, T. C. and Reymond, P. (2012) Rapid profiling of intact glucosinolates in Arabidopsis leaves by UHPLC-QTOFMS using a charged surface hybrid column. Phytochem Anal, 23, 520-528. Glazebrook, J. and Ausubel, F. M. (1994) Isolation of Phytoalexin-Deficient Mutants of Arabidopsis-Thaliana and Characterization of Their Interactions with Bacterial Pathogens. P Natl Acad Sci USA, 91, 8955-8959. Gohlke, J. and Deeken, R. (2014) Plant responses to Agrobacterium tumefaciens and crown gall development. Front Plant Sci, 5, 155. Gomez-Gomez, L. and Boller, T. (2000) FLS2: An LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis. Mol Cell, 5, 1003-1011. Graf, A., Schlereth, A., Stitt, M. and Smith, A. M. (2010) Circadian control of carbohydrate availability for growth in Arabidopsis plants at night. P Natl Acad Sci USA, 107, 9458-9463. Gudlavalleti, S. K. and Forsberg, L. S. (2003) Structural characterization of the lipid A component of Sinorhizobium sp. NGR234 rough and smooth form lipopolysaccharide. Demonstration that the distal amide-linked acyloxyacyl residue containing the long chain fatty acid is conserved in rhizobium and Sinorhizobium sp. J Biol Chem, 278, 3957-3968. Gust, A. A., Biswas, R., Lenz, H. D., Rauhut, T., Ranf, S., Kemmerling, B., et al. (2007) Bacteria-derived peptidoglycans constitute pathogen-associated molecular patterns triggering innate immunity in Arabidopsis. J Biol Chem, 282, 32338-32348. Halkier, B. A. and Gershenzon, J. (2006) Biology and biochemistry of glucosinolates. Annu Rev Plant Biol, 57, 303-333. Hamilton, R. H. and Fall, M. Z. (1971) The loss of tumor-initiating ability in Agrobacterium tumefaciens by incubation at high temperature. Experientia, 27, 229-230. Hammond, J. P., Bennett, M. J., Bowen, H. C., Broadley, M. R., Eastwood, D. C., May, S. T., et al. (2003) Changes in gene expression in Arabidopsis shoots during phosphate starvation and the potential for developing smart plants. Plant Physiol, 132, 578-596. Heese, A., Hann, D. R., Gimenez-Ibanez, S., Jones, A. M. E., He, K., Li, J., et al. (2007) The receptor-like kinase SERK3/BAK1 is a central regulator of innate immunity in plants. P Natl Acad Sci USA, 104, 12217-12222. 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. Hind, S. R., Strickler, S. R., Boyle, P. C., Dunham, D. M., Bao, Z., O'Doherty, I. M., et al. (2016) Tomato receptor FLAGELLIN-SENSING 3 binds flgII-28 and activates the plant immune system. Nat Plants, 2, 16128. Hruz, T., Laule, O., Szabo, G., Wessendorp, F., Bleuler, S., Oertle, L., et al. (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics, 2008, 420747. Hsu, F. C., Chou, M. Y., Peng, H. P., Chou, S. J. and Shih, M. C. (2011) Insights into Hypoxic Systemic Responses Based on Analyses of Transcriptional Regulation in Arabidopsis. Plos One, 6. Hu, Y. X., Xie, O. and Chua, N. H. (2003) The Arabidopsis auxin-inducible gene ARGOS controls lateral organ size. Plant Cell, 15, 1951-1961. Huffaker, A., Pearce, G. and Ryan, C. A. (2006) An endogenous peptide signal in Arabidopsis activates components of the innate immune response. Proc Natl Acad Sci U S A, 103, 10098-10103. Huffaker, A. and Ryan, C. A. (2007) Endogenous peptide defense signals in Arabidopsis differentially amplify signaling for the innate immune response. Proc Natl Acad Sci U S A, 104, 10732-10736. Hwang, H. H. and Gelvin, S. B. (2004) Plant proteins that interact with VirB2, the Agrobacterium tumefaciens pilin protein, mediate plant transformation. Plant Cell, 16, 3148-3167. Hwang, H. H., Wang, M. H., Lee, Y. L., Tsai, Y. L., Li, Y. H., Yang, F. J., et al. (2010) Agrobacterium-produced and exogenous cytokinin-modulated Agrobacterium-mediated plant transformation. Mol Plant Pathol, 11, 677-690. Hwang, H. H., Yang, F. J., Cheng, T. F., Chen, Y. C., Lee, Y. L., Tsai, Y. L., et al. (2013) The Tzs protein and exogenous cytokinin affect virulence gene expression and bacterial growth of Agrobacterium tumefaciens. Phytopathology, 103, 888-899. Hwang, H. H., Yu, M. and Lai, E. M. (2017) Agrobacterium-Mediated Plant Transformation: Biology and Applications. The Arabidopsis Book, 15, e0186. Iizasa, S., Iizasa, E., Matsuzaki, S., Tanaka, H., Kodama, Y., Watanabe, K., et al. (2016) Arabidopsis LBP/BPI related-1 and -2 bind to LPS directly and regulate PR1 expression. Sci Rep, 6, 27527. Inze, A., Vanderauwera, S., Hoeberichts, F. A., Vandorpe, M., Van Gaever, T. and Van Breusegem, F. (2012) A subcellular localization compendium of hydrogen peroxide-induced proteins. Plant Cell Environ, 35, 308-320. Jelenska, J., Davern, S. M., Standaert, R. F., Mirzadeh, S. and Greenberg, J. T. (2017) Flagellin peptide flg22 gains access to long-distance trafficking in Arabidopsis via its receptor, FLS2. J Exp Bot, 68, 1769-1783. Jeworutzki, E., Roelfsema, M. R. G., Anschutz, U., Krol, E., Elzenga, J. T. M., Felix, G., et al. (2010) Early signaling through the Arabidopsis pattern recognition receptors FLS2 and EFR involves Ca2+-associated opening of plasma membrane anion channels. Plant Journal, 62, 367-378. Jin, S., Roitsch, T., Ankenbauer, R. G., Gordon, M. P. and Nester, E. W. (1990a) The VirA protein of Agrobacterium tumefaciens is autophosphorylated and is essential for vir gene regulation. J Bacteriol, 172, 525-530. Jin, S. G., Prusti, R. K., Roitsch, T., Ankenbauer, R. G. and Nester, E. W. (1990b) Phosphorylation of the VirG protein of Agrobacterium tumefaciens by the autophosphorylated VirA protein: essential role in biological activity of VirG. J Bacteriol, 172, 4945-4950. Jin, S. G., Roitsch, T., Christie, P. J. and Nester, E. W. (1990c) The regulatory VirG protein specifically binds to a cis-acting regulatory sequence involved in transcriptional activation of Agrobacterium tumefaciens virulence genes. J Bacteriol, 172, 531-537. Kado, C. I. and Heskett, M. G. (1970) Selective media for isolation of Agrobacterium, Corynebacterium, Erwinia, Pseudomonas, and Xanthomonas. Phytopathology, 60, 969-976. Kimbrough, J. M., Salinas-Mondragon, R., Boss, W. E., Brown, C. S. and Sederoff, H. W. (2004) The fast and transient transcriptional network of gravity and mechanical stimulation in the Arabidopsis root Apex. Plant Physiology, 136, 2790-2805. Krishnaswamy, S., Verma, S., Rahman, M. H. and Kav, N. N. V. (2011) Functional characterization of four APETALA2-family genes (RAP2.6, RAP2.6L, DREB19 and DREB26) in Arabidopsis. Plant Mol Biol, 75, 107-127. Krol, E., Mentzel, T., Chinchilla, D., Boller, T., Felix, G., Kemmerling, B., et al. (2010) Perception of the Arabidopsis danger signal peptide 1 involves the pattern recognition receptor AtPEPR1 and its close homologue AtPEPR2. J Biol Chem, 285, 13471-13479. Kunze, G., Zipfel, C., Robatzek, S., Niehaus, K., Boller, T. and Felix, G. (2004) The N terminus of bacterial elongation factor Tu elicits innate immunity in Arabidopsis plants. Plant Cell, 16, 3496-3507. Kutacek, M. and Rovenska, J. (1991) Auxin Synthesis in Agrobacterium-Tumefaciens and a-Tumefaciens-Transformed Plant-Tissue. Plant Growth Regul, 10, 313-327. Lacroix, B., Vaidya, M., Tzfira, T. and Citovsky, V. (2005) The VirE3 protein of Agrobacterium mimics a host cell function required for plant genetic transformation. Embo J, 24, 428-437. Lal, N. K., Nagalakshmi, U., Hurlburt, N. K., Flores, R., Bak, A., Sone, P., et al. (2018) The Receptor-like Cytoplasmic Kinase BIK1 Localizes to the Nucleus and Regulates Defense Hormone Expression during Plant Innate Immunity. Cell Host Microbe, 23, 485-497 e485. Lapham, R., Lee, L. Y., Tsugama, D., Lee, S., Mengiste, T. and Gelvin, S. B. (2018) VIP1 and Its Homologs Are Not Required for Agrobacterium-Mediated Transformation, but Play a Role in Botrytis and Salt Stress Responses. Front Plant Sci, 9, 749. Larroque, M., Belmas, E., Martinez, T., Vergnes, S., Ladouce, N., Lafitte, C., et al. (2013) Pathogen-associated molecular pattern-triggered immunity and resistance to the root pathogen Phytophthora parasitica in Arabidopsis. J Exp Bot, 64, 3615-3625. Lee, C. W., Efetova, M., Engelmann, J. C., Kramell, R., Wasternack, C., Ludwig-Müller, J., et al. (2009) Agrobacterium tumefaciens promotes tumor induction by modulating pathogen defense in Arabidopsis thaliana. Plant Cell, 21, 2948-2962. Lee, L. Y., Fang, M. J., Kuang, L. Y. and Gelvin, S. B. (2008) Vectors for multi-color bimolecular fluorescence complementation to investigate protein-protein interactions in living plant cells. Plant Methods, 4. Lee, Y. J., Kim, D. H., Kim, Y. W. and Hwang, I. (2001) Identification of a signal that distinguishes between the chloroplast outer envelope membrane and the endomembrane system in vivo. Plant Cell, 13, 2175-2190. Li, J., Krichevsky, A., Vaidya, M., Tzfira, T. and Citovsky, V. (2005a) Uncoupling of the functions of the Arabidopsis VIP1 protein in transient and stable plant genetic transformation by Agrobacterium. Proc Natl Acad Sci U S A, 102, 5733-5738. Li, J., Vaidya, M., White, C., Vainstein, A., Citovsky, V. and Tzfira, T. (2005b) Involvement of KU80 in T-DNA integration in plant cells. Proc Natl Acad Sci U S A, 102, 19231-19236. Li, X. Y. and Pan, S. Q. (2017) Agrobacterium delivers VirE2 protein into host cells via clathrin-mediated endocytosis. Sci Adv, 3. Lin, W. D., Chen, Y. C., Ho, J. M. and Hsiao, C. D. (2006) GOBU: Toward an integration interface for biological objects. Journal of Information Science and Engineering, 22, 19-29. Lipka, V., Dittgen, J., Bednarek, P., Bhat, R., Wiermer, M., Stein, M., et al. (2005) Pre- and postinvasion defenses both contribute to nonhost resistance in Arabidopsis. Science, 310, 1180-1183. Liu, G., Ji, Y., Bhuiyan, N. H., Pilot, G., Selvaraj, G., Zou, J., et al. (2010a) Amino acid homeostasis modulates salicylic acid-associated redox status and defense responses in Arabidopsis. Plant Cell, 22, 3845-3863. Liu, G. S., Ji, Y. Y., Bhuiyan, N. H., Pilot, G., Selvaraj, G., Zou, J. T., et al. (2010b) Amino Acid Homeostasis Modulates Salicylic Acid-Associated Redox Status and Defense Responses in Arabidopsis. Plant Cell, 22, 3845-3863. Liu, X. M., An, J., Han, H. J., Kim, S. H., Lim, C. O., Yun, D. J., et al. (2014) ZAT11, a zinc finger transcription factor, is a negative regulator of nickel ion tolerance in Arabidopsis. Plant Cell Rep, 33, 2015-2021. Logemann, E., Birkenbihl, R. P., Rawat, V., Schneeberger, K., Schmelzer, E. and Somssich, I. E. (2013) Functional dissection of the PROPEP2 and PROPEP3 promoters reveals the importance of WRKY factors in mediating microbe-associated molecular pattern-induced expression. New Phytol, 198, 1165-1177. Lopez-Martin, M. C., Becana, M., Romero, L. C. and Gotor, C. (2008) Knocking out cytosolic cysteine synthesis compromises the antioxidant capacity of the cytosol to maintain discrete concentrations of hydrogen peroxide in Arabidopsis. Plant Physiol, 147, 562-572. Lu, F., Wang, H. Q., Wang, S. Z., Jiang, W. D., Shan, C. L., Li, B., et al. (2015) Enhancement of innate immune system in monocot rice by transferring the dicotyledonous elongation factor Tu receptor EFR. J Integr Plant Biol, 57, 641-652. Ma, Y., Walker, R. K., Zhao, Y. and Berkowitz, G. A. (2012) Linking ligand perception by PEPR pattern recognition receptors to cytosolic Ca2+ elevation and downstream immune signaling in plants. Proc Natl Acad Sci U S A, 109, 19852-19857. Macho, A. P., Schwessinger, B., Ntoukakis, V., Brutus, A., Segonzac, C., Roy, S., et al. (2014) A bacterial tyrosine phosphatase inhibits plant pattern recognition receptor activation. Science, 343, 1509-1512. Magori, S. and Citovsky, V. (2011) Agrobacterium counteracts host-induced degradation of its effector F-box protein. Sci Signal, 4, ra69. Malka, S. K. and Cheng, Y. F. (2017) Possible Interactions between the Biosynthetic Pathways of Indole Glucosinolate and Auxin. Frontiers in Plant Science, 8. Melotto, M., Underwood, W., Koczan, J., Nomura, K. and He, S. Y. (2006) Plant stomata function in innate immunity against bacterial invasion. Cell, 126, 969-980. Millet, Y. A., Danna, C. H., Clay, N. K., Songnuan, W., Simon, M. D., Werck-Reichhart, D., et al. (2010) Innate Immune Responses Activated in Arabidopsis Roots by Microbe-Associated Molecular Patterns. Plant Cell, 22, 973-990. Mohr, P. G. and Cahill, D. M. (2007) Suppression by ABA of salicylic acid and lignin accumulation and the expression of multiple genes, in Arabidopsis infected with Pseudomonas syringae pv. tomato. Funct Integr Genomics, 7, 181-191. Mueller, K., Bittel, P., Chinchilla, D., Jehle, A. K., Albert, M., Boller, T., et al. (2012) Chimeric FLS2 Receptors Reveal the Basis for Differential Flagellin Perception in Arabidopsis and Tomato. Plant Cell, 24, 2213-2224. Naito, T., Yamashino, T., Kiba, T., Koizumi, N., Kojima, M., Sakakibara, H., et al. (2007) A link between cytokinin and ASL9 (ASYMMETRIC LEAVES 2 LIKE 9) that belongs to the AS2/LOB (LATERAL ORGAN BOUNDARIES) family genes in Arabidopsis thaliana. Biosci Biotech Bioch, 71, 1269-1278. Narasimhulu, S. B., Deng, X. B., Sarria, R. and Gelvin, S. B. (1996) Early transcription of Agrobacterium T-DNA genes in tobacco and maize. Plant Cell, 8, 873-886. Newman, M. A., Daniels, M. J. and Dow, J. M. (1995) Lipopolysaccharide from Xanthomonas campestris induces defense-related gene expression in Brassica campestris. Mol Plant Microbe Interact, 8, 778-780. Newman, M. A., Dow, J. M., Molinaro, A. and Parrilli, M. (2007) Priming, induction and modulation of plant defence responses by bacterial lipopolysaccharides. J Endotoxin Res, 13, 69-84. Niu, C., Smith, N., Garteiser, P., Towner, R. and Verchot, J. (2011) Comparative analysis of protein transport in the N. benthamiana vasculature reveals different destinations. Plant Signal Behav, 6, 1793-1808. Niu, X. L., Zhou, M. L., Henkel, C. V., van Heusden, G. P. H. and Hooykaas, P. J. J. (2015) The Agrobacterium tumefaciens virulence protein VirE3 is a transcriptional activator of the F-box gene VBF. Plant Journal, 84, 914-924. Nonaka, S., Yuhashi, K., Takada, K., Sugaware, M., Minamisawa, K. and Ezura, H. (2008) Ethylene production in plants during transformation suppresses vir gene expression in Agrobacterium tumefaciens. New Phytol, 178, 647-656. Pansegrau, W., Schoumacher, F., Hohn, B. and Lanka, E. (1993) Site-specific cleavage and joining of single-stranded DNA by VirD2 protein of Agrobacterium tumefaciens Ti plasmids: analogy to bacterial conjugation. Proc Natl Acad Sci U S A, 90, 11538-11542. Pfund, C., Tans-Kersten, J., Dunning, F. M., Alonso, J. M., Ecker, J. R., Allen, C., et al. (2004) Flagellin is not a major defense elicitor in Ralstonia solanacearum cells or extracts applied to Arabidopsis thaliana. Mol Plant Microbe In, 17, 696-706. Pieterse, C. M., Leon-Reyes, A., Van der Ent, S. and Van Wees, S. C. (2009) Networking by small-molecule hormones in plant immunity. Nat Chem Biol, 5, 308-316. Pitzschke, A. (2013) Agrobacterium infection and plant defense-transformation success hangs by a thread. Front Plant Sci, 4, 519. Pitzschke, A., Djamei, A., Teige, M. and Hirt, H. (2009) VIP1 response elements mediate mitogen-activated protein kinase 3-induced stress gene expression. Proc Natl Acad Sci U S A, 106, 18414-18419. Preger, V., Tango, N., Marchand, C., Lemaire, S. D., Carbonera, D., Di Valentin, M., et al. (2009) Auxin-Responsive Genes AIR12 Code for a New Family of Plasma Membrane b-Type Cytochromes Specific to Flowering Plants. Plant Physiology, 150, 606-620. Rajniak, J., Barco, B., Clay, N. K. and Sattely, E. S. (2015) A new cyanogenic metabolite in Arabidopsis required for inducible pathogen defence. Nature, 525, 376-+. Ranf, S., Eschen-Lippold, L., Pecher, P., Lee, J. and Scheel, D. (2011) Interplay between calcium signalling and early signalling elements during defence responses to microbe- or damage-associated molecular patterns. Plant Journal, 68, 100-113. Ranf, S., Gisch, N., Schaffer, M., Illig, T., Westphal, L., Knirel, Y. A., et al. (2015) A lectin S-domain receptor kinase mediates lipopolysaccharide sensing in Arabidopsis thaliana. Nat Immunol, 16, 426-433. Rasul, S., Dubreuil-Maurizi, C., Lamotte, O., Koen, E., Poinssot, B., Alcaraz, G., et al. (2012) Nitric oxide production mediates oligogalacturonide-triggered immunity and resistance to Botrytis cinerea in Arabidopsis thaliana. Plant Cell Environ, 35, 1483-1499. Regier, D. A. and Morris, R. O. (1982) Secretion of Trans-Zeatin by Agrobacterium-Tumefaciens - a Function Determined by the Nopaline Ti Plasmid. Biochem Bioph Res Co, 104, 1560-1566. Rogers, E. E., Glazebrook, J. and Ausubel, F. N. (1996) Mode of action of the Arabidopsis thaliana phytoalexin camalexin and its role in Arabidopsis-pathogen interactions. Mol Plant Microbe In, 9, 748-757. Rouet, M. A., Mathieu, Y. and Lauriere, C. (2006) Characterization of active oxygen-producing proteins in response to hypo-osmolarity in tobacco and Arabidopsis cell suspensions: identification of a cell wall peroxidase. J Exp Bot, 57, 1323-1332. Salinas, J. and Sánchez-Serrano, J. J. (2006) Arabidopsis protocols. Totowa, N.J.: Humana Press. Sardesai, N., Lee, L. Y., Chen, H., Yi, H., Olbricht, G. R., Stirnberg, A., et al. (2013a) Cytokinins secreted by Agrobacterium promote transformation by repressing a plant myb transcription factor. Sci Signal, 6, ra100. Sardesai, N., Lee, L. Y., Chen, H. B., Yi, H. C., Olbricht, G. R., Stirnberg, A., et al. (2013b) Cytokinins Secreted by Agrobacterium Promote Transformation by Repressing a Plant Myb Transcription Factor. Sci Signal, 6. Saur, I. M., Kadota, Y., Sklenar, J., Holton, N. J., Smakowska, E., Belkhadir, Y., et al. (2016) NbCSPR underlies age-dependent immune responses to bacterial cold shock protein in Nicotiana benthamiana. Proc Natl Acad Sci U S A, 113, 3389-3394. Scarpeci, T. E., Zanor, M. I., Mueller-Roeber, B. and Valle, E. M. (2013) Overexpression of AtWRKY30 enhances abiotic stress tolerance during early growth stages in Arabidopsis thaliana. Plant Mol Biol, 83, 265-277. Scheidle, H., Gross, A. and Niehaus, K. (2005) The Lipid A substructure of the Sinorhizobium meliloti lipopolysaccharides is sufficient to suppress the oxidative burst in host plants. New Phytologist, 165, 559-565. Schoonbeek, H. J., Wang, H. H., Stefanato, F. L., Craze, M., Bowden, S., Wallington, E., et al. (2015) Arabidopsis EF-Tu receptor enhances bacterial disease resistance in transgenic wheat. New Phytol, 206, 606-613. Schrammeijer, B., Risseeuw, E., Pansegrau, W., Regensburg-Tuink, T. J., Crosby, W. L. and Hooykaas, P. J. (2001) Interaction of the virulence protein VirF of Agrobacterium tumefaciens with plant homologs of the yeast Skp1 protein. Curr Biol, 11, 258-262. Schwessinger, B., Bahar, O., Thomas, N., Holton, N., Nekrasov, V., Ruan, D., et al. (2015) Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses. Plos Pathog, 11, e1004809. Shaw, C. H., Loake, G. J., Brown, A. P., Garrett, C. S., Deakin, W., Alton, G., et al. (1991) Isolation and Characterization of Behavioral Mutants and Genes of Agrobacterium-Tumefaciens. J Gen Microbiol, 137, 1939-1953. Shi, Y., Lee, L. Y. and Gelvin, S. B. (2014) Is VIP1 important for Agrobacterium-mediated transformation? Plant Journal, 79, 848-860. Shibuya, K., Yamada, T., Suzuki, T., Shimizu, K. and Ichimura, K. (2009) InPSR26, a Putative Membrane Protein, Regulates Programmed Cell Death during Petal Senescence in Japanese Morning Glory. Plant Physiology, 149, 816-824. Shih, P. Y., Chou, S. J., Muller, C., Halkier, B. A., Deeken, R. and Lai, E. M. (2018) Differential Roles of Glucosinolates and Camalexin at Different Stages of Agrobacterium-Mediated Transformation. Mol Plant Pathol. Shlezinger, N., Minz, A., Gur, Y., Hatam, I., Dagdas, Y. F., Talbot, N. J., et al. (2011) Anti-Apoptotic Machinery Protects the Necrotrophic Fungus Botrytis cinerea from Host-Induced Apoptotic-Like Cell Death during Plant Infection. Plos Pathog, 7. Silipo, A., De Castro, C., Lanzetta, R., Molinaro, A. and Parrilli, M. (2004) Full structural characterization of the lipid A components from the Agrobacterium tumefaciens strain C58 lipopolysaccharide fraction. Glycobiology, 14, 805-815. Stachel, S. E., Messens, E., Vanmontagu, M. and Zambryski, P. (1985) Identification of the Signal Molecules Produced by Wounded Plant-Cells That Activate T-DNA Transfer in Agrobacterium-Tumefaciens. Nature, 318, 624-629. Stepanova, A. N., Yun, J., Robles, L. M., Novak, O., He, W., Guo, H., et al. (2011) The Arabidopsis YUCCA1 flavin monooxygenase functions in the indole-3-pyruvic acid branch of auxin biosynthesis. Plant Cell, 23, 3961-3973. Stotz, H. U., Sawada, Y., Shimada, Y., Hirai, M. Y., Sasaki, E., Krischke, M., et al. (2011) Role of camalexin, indole glucosinolates, and side chain modification of glucosinolate-derived isothiocyanates in defense of Arabidopsis against Sclerotinia sclerotiorum. Plant J, 67, 81-93. Sugawara, S., Hishiyama, S., Jikumaru, Y., Hanada, A., Nishimura, T., Koshiba, T., et al. (2009) Biochemical analyses of indole-3-acetaldoxime-dependent auxin biosynthesis in Arabidopsis. Proc Natl Acad Sci U S A, 106, 5430-5435. Sun, C. W. and Callis, J. (1997) Independent modulation of Arabidopsis thaliana polyubiquitin mRNAs in different organs and in response to environmental changes. Plant J, 11, 1017-1027. Sun, F., Liu, P. Q., Xu, J. and Dong, H. S. (2010) Mutation in RAP2.6L, a transactivator of the ERF transcription factor family, enhances Arabidopsis resistance to Pseudomonas syringae. Physiol Mol Plant P, 74, 295-302. Tao, Y., Rao, P. K., Bhattacharjee, S. and Gelvin, S. B. (2004) Expression of plant protein phosphatase 2C interferes with nuclear import of the Agrobacterium T-complex protein VirD2. P Natl Acad Sci USA, 101, 5164-5169. Tenea, G. N., Spantzel, J., Lee, L. Y., Zhu, Y., Lin, K., Johnson, S. J., et al. (2009) Overexpression of several Arabidopsis histone genes increases agrobacterium-mediated transformation and transgene expression in plants. Plant Cell, 21, 3350-3367. Tremousaygue, D., Garnier, L., Bardet, C., Dabos, P., Herve, C. and Lescure, B. (2003) Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells. Plant J, 33, 957-966. Tzfira, T., Vaidya, M. and Citovsky, V. (2001) VIP1, an Arabidopsis protein that interacts with Agrobacterium VirE2, is involved in VirE2 nuclear import and Agrobacterium infectivity. Embo J, 20, 3596-3607. Tzfira, T., Vaidya, M. and Citovsky, V. (2002) Increasing plant susceptibility to Agrobacterium infection by overexpression of the Arabidopsis nuclear protein VIP1. P Natl Acad Sci USA, 99, 10435-10440. Tzfira, T., Vaidya, M. and Citovsky, V. (2004) Involvement of targeted proteolysis in plant genetic transformation by Agrobacterium. Nature, 431, 87-92. Tzfira, T. C., V. (2008) Agrobacterium: From Biology to Biotechnology. Springer New York. Urao, T., Yakubov, B., Yamaguchi-Shinozaki, K. and Shinozaki, K. (1998) Stress-responsive expression of genes for two-component response regulator-like proteins in Arabidopsis thaliana. Febs Lett, 427, 175-178. Van Larebeke, N., Engler, G., Holsters, M., Van den Elsacker, S., Zaenen, I., Schilperoort, R. A., et al. (1974) Large plasmid in Agrobacterium tumefaciens essential for crown gall-inducing ability. Nature, 252, 169-170. Veena, Jiang, H., Doerge, R. W. and Gelvin, S. B. (2003) Transfer of T-DNA and Vir proteins to plant cells by Agrobacterium tumefaciens induces expression of host genes involved in mediating transformation and suppresses host defense gene expression. Plant J, 35, 219-236. Vergunst, A. C., Schrammeijer, B., den Dulk-Ras, A., de Vlaam, C. M. T., Regensburg-Tuink, T. J. G. and Hooykaas, P. J. J. (2000) VirB/D4-dependent protein translocation from Agrobacterium into plant cells. Science, 290, 979-982. Vetter, M. M., Kronholm, I., He, F., Haweker, H., Reymond, M., Bergelson, J., et al. (2012) Flagellin Perception Varies Quantitatively in Arabidopsis thaliana and Its Relatives. Mol Biol Evol, 29, 1655-1667. Wang, L., Lacroix, B., Guo, J. and Citovsky, V. (2018) The Agrobacterium VirE2 effector interacts with multiple members of the Arabidopsis VIP1 protein family. Mol Plant Pathol, 19, 1172-1183. Wang, Y., Peng, W., Zhou, X., Huang, F., Shao, L. and Luo, M. (2014) The putative Agrobacterium transcriptional activator-like virulence protein VirD5 may target T-complex to prevent the degradation of coat proteins in the plant cell nucleus. New Phytol, 203, 1266-1281. Willmann, R., Lajunen, H. M., Erbs, G., Newman, M. A., Kolb, D., Tsuda, K., et al. (2011) Arabidopsis lysin-motif proteins LYM1 LYM3 CERK1 mediate bacterial peptidoglycan sensing and immunity to bacterial infection. Proc Natl Acad Sci U S A, 108, 19824-19829. Wittstock, U. and Burow, M. (2010) Glucosinolate breakdown in Arabidopsis: mechanism, regulation and biological significance. Arabidopsis Book, 8, e0134. Wu, H. Y., Chen, C. Y. and Lai, E. M. (2014a) Expression and functional characterization of the Agrobacterium VirB2 amino acid substitution variants in T-pilus biogenesis, virulence, and transient transformation efficiency. PLoS One, 9, e101142. Wu, H. Y., Liu, K. H., Wang, Y. C., Wu, J. F., Chiu, W. L., Chen, C. Y., et al. (2014b) AGROBEST: an efficient Agrobacterium-mediated transient expression method for versatile gene function analyses in Arabidopsis seedlings. Plant Methods, 10, 19. Yan, X. F. and Chen, S. X. (2007) Regulation of plant glucosinolate metabolism. Planta, 226, 1343-1352. Yanofsky, M. F., Porter, S. G., Young, C., Albright, L. M., Gordon, M. P. and Nester, E. W. (1986) The virD operon of Agrobacterium tumefaciens encodes a site-specific endonuclease. Cell, 47, 471-477. Yasuda, M., Ishikawa, A., Jikumaru, Y., Seki, M., Umezawa, T., Asami, T., et al. (2008) Antagonistic interaction between systemic acquired resistance and the abscisic acid-mediated abiotic stress response in Arabidopsis. Plant Cell, 20, 1678-1692. Yoo, S. D., Cho, Y. H. and Sheen, J. (2007) Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat Protoc, 2, 1565-1572. Yu, X., Feng, B. M., He, P. and Shan, L. B. (2017) From Chaos to Harmony: Responses and Signaling upon Microbial Pattern Recognition. Annual Review of Phytopathology, Vol 55, 55, 109-137. Yu, Y. B. and Yang, S. F. (1979) Auxin-Induced Ethylene Production and Its Inhibition by Aminoethoxyvinylglycine and Cobalt Ion. Plant Physiology, 64, 1074-1077. Yuan, Z. C., Edlind, M. P., Liu, P., Saenkham, P., Banta, L. M., Wise, A. A., et al. (2007) The plant signal salicylic acid shuts down expression of the vir regulon and activates quormone-quenching genes in Agrobacterium. Proc Natl Acad Sci U S A, 104, 11790-11795. Zandalinas, S. I., Vives-Peris, V., Gómez-Cadenas, A. and Arbona, V. (2012) A fast and precise method to identify indolic glucosinolates and camalexin in plants by combining mass spectrometric and biological information. J Agric Food Chem, 60, 8648-8658. Zeidler, D., Dubery, I. A., Schmitt-Kopplin, P., Von Rad, U. and Durner, J. (2010) Lipopolysaccharide mobility in leaf tissue of Arabidopsis thaliana. Mol Plant Pathol, 11, 747-755. Zeng, W. and He, S. Y. (2010) A prominent role of the flagellin receptor FLAGELLIN-SENSING2 in mediating stomatal response to Pseudomonas syringae pv tomato DC3000 in Arabidopsis. Plant Physiol, 153, 1188-1198. Zhang, X., van Heusden, G. P. H. and Hooykaas, P. J. J. (2017) Virulence protein VirD5 of Agrobacterium tumefaciens binds to kinetochores in host cells via an interaction with Spt4. Proc Natl Acad Sci U S A, 114, 10238-10243. Zhang, Y., Lee, C. W., Wehner, N., Imdahl, F., Svetlana, V., Weiste, C., et al. (2015) Regulation of oncogene expression in T-DNA-transformed host plant cells. Plos Pathog, 11, e1004620. Zhao, Y., Hull, A. K., Gupta, N. R., Goss, K. A., Alonso, J., Ecker, J. R., et al. (2002) Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes Dev, 16, 3100-3112. Zhu, W., Zhao, D. X., Miao, Q., Xue, T. T., Li, X. Z. and Zheng, C. C. (2009) Arabidopsis thaliana Metallothionein, AtMT2a, Mediates ROS Balance during Oxidative Stress. J Plant Biol, 52, 585-592. Zhu, Y. M., Nam, J., Carpita, N. C., Matthysse, A. G. and Gelvin, S. B. (2003) Agrobacterium-mediated root transformation is inhibited by mutation of an Arabidopsis cellulose synthase-like gene. Plant Physiology, 133, 1000-1010. Zipfel, C., Kunze, G., Chinchilla, D., Caniard, A., Jones, J. D., Boller, T., et al. (2006) Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation. Cell, 125, 749-760. Zupan, J., Hackworth, C. A., Aguilar, J., Ward, D. and Zambryski, P. (2007) VirB1* promotes T-pilus formation in the vir-Type IV secretion system of Agrobacterium tumefaciens. J Bacteriol, 189, 6551-6563.
農桿菌是一種會讓植物生成癌腫病的土壤病原菌,藉由第四型分泌系統把特定DNA片段轉殖到植物染色體上,進而促使植物細胞增生形成腫瘤,因此科學家利用此機制來進行基因轉殖。過去的研究發現,農桿菌感染的成效並不單取決於細菌本身,許多植物內部系統,例如免疫系統和賀爾蒙反應都會影響到轉殖的效率,然而關於植物因子如何調控農桿菌的轉殖效率仍有很多需要被研究的地方。因此本研究利用轉錄體學來找出會影響轉殖效率的植物因子,從野生型阿拉伯芥Col-0小苗被農桿菌短暫型轉殖後的基因表現中,我發現根部和莖部的反應基因主要參與在免疫反應、生長調控、次級代謝物代謝、接受外界環境刺激和基礎細胞內反應之上。進一步的研究發現,次級代謝物glucosinolates和camalexin可能在防禦機制上扮演著重要的角色,利用突變株和代謝體學分析,我發現indole glucosinolate的水解對於初期防禦農桿菌感染很重要,而camalexin的累積則會抑制後期的感染和腫瘤發育;另外aliphatic glucosinolate的水解產物則對短暫型的轉殖效率有多樣的影響。這些研究成果提供了一個新的思考方向,將來或許可以利用植物次級代謝物來控制癌腫病或是操控轉殖效率。除此之外,由於EFR已被證實是個上游的免疫受器,能辨識農桿菌的轉錄延伸因子(EF-Tu)來啟動免疫反應並抑制農桿菌轉殖,因此本研究也比較Col-0和efr-1突變株中的基因表現差異,期望找出能調控農桿菌轉殖效率的EFR下游基因。我初步發現許多根部和莖部基因的表現量在Col-0和efr-1中有顯著的差異,暗示著這些基因可能是受到EFR的調控。由於已知的資料顯示EFR主要表現在莖部而非根部,且多數篩選出的莖部基因也同時受到EF-Tu辨識序列elf26的調控,這些結果都支持EFR主要負責莖部對農桿菌的反應而非根部。因此我利用不同的策略,從莖部的資料中篩選潛在的EFR調控基因,利用小苗短暫型轉殖系統在突變株的實驗結果顯示,部分突變株確實會影響到農桿菌的轉殖效率,這些證據支持了上述的篩選結果能提供合適的研究名單,將來則可利用阿拉伯芥的原生質體轉殖系統來做更進一步的功能性分析,以探討EFR是如何抑制農桿菌感染的機制;另一方面,由於植物根部的反應主要並非受EFR調控,所以我們目前先挑選出在Col-0和efr-1皆高度表現的基因,來做未來的功能性探討。

Agrobacterium tumefaciens is a plant pathogenic bacterium which can cause crown gall disease by transferring a piece of DNA from bacterial cells into plant genome via a Type IV secretion system (T4SS). Due to this unique inter-kingdom DNA transfer capability, A. tumefaciens has been widely used as a gene transfer tool to generate transgenic plants. Previous studies have shown that many plant factors such as immune system and hormone responses are important to determine transformation efficiency. However, the plant genes and mechanisms involved in the transformation process are not well understood. In this study, I employed Agrobacterium-mediated transient transformation system on Arabidopsis seedling and used transcriptome analysis of seedling shoots and roots to dissect plant genes responding to Agrobacterium infection. From the gene expression profiles in wild type Col-0 Arabidopsis thaliana seedlings, common and distinct differentially expressed genes involved in growth regulation, response to stimuli, secondary metabolism and cellular reactions were enriched in both shoots and roots. Further analysis on secondary metabolism ontology revealed that the plant secondary metabolites, glucosinolates (GS) and camalexin, may play important roles to modulate Agrobacterium infection and impact transformation efficiency. By combining metabolism and transformation assays using relevant Arabidopsis mutants, the results suggest their differential roles at different infection stages. Indole GSs can be rapidly hydrolyzed to inhibit Agrobacterium infection at the early stage, and then accumulation of camalexin can further inhibit later infection to reduce tumor formation. Moreover, the hydrolysis products of aliphatic GSs have various effects on the transient transformation efficiency. These findings provide a new insight into using plant secondary metabolites to protect plants from Agrobacterium infection or to manipulate transformation efficiency. In addition, I also compared the gene expression profiles between Col-0 and an immune receptor mutant, efr-1, which is defective in perceiving conserved N-terminal epitope (elf26) of the elongation factor Tu, a potent microbe-associated molecular pattern (MAMP) of Agrobacterium. EFR has been shown as the first layer of immune receptor to suppress Agrobacterium transient transformation. I found several differentially expressed shoot and root genes displaying dramatic difference of their expression levels between Col-0 and efr-1, suggesting their gene expression regulated by EFR. The EFR expression patterns in the available microarray data suggested EFR mainly expresses in shoots but not roots, and the comparison between the identified genes and the elf26-responsive genes indicated a half of identified shoot genes can be regulated by elf26. This data supported that EFR mainly contributes to shoot but not root responses to Agrobacterium infection. The seedling transient transformation assay, assessed by T-DNA-encoded beta-glucuronidase (GUS) activity, on the selected mutants suggested that some of EFR-dependent shoot genes may regulate transformation efficiency. To this end, Arabidopsis protoplast system has been used to dissect the roles of EFR-dependent genes in EFR-dependent immune signaling pathways which may regulate Agrobacterium-mediated transformation efficiency. In addition, the genes that are highly expressed in roots of both Col-0 and efr-1 could be used as candidate genes to study underlying mechanisms how roots respond to Agrobacterium infection.
Rights: 同意授權瀏覽/列印電子全文服務,2021-01-16起公開。
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