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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 賴爾珉(Erh-Min Lai),沈偉強(Wei-Chiang Shen) | |
| dc.contributor.author | Xuan Lai | en |
| dc.contributor.author | 賴軒 | zh_TW |
| dc.date.accessioned | 2022-11-25T03:04:52Z | - |
| dc.date.available | 2026-07-01 | |
| dc.date.copyright | 2021-08-18 | |
| dc.date.issued | 2021 | |
| dc.date.submitted | 2021-07-13 | |
| dc.identifier.citation | Agrios, G. 2005. Plant pathology 5th Edition: Elsevier Academic Press. Burlington, Ma. USA:79-103. Aguilar, J., Zupan, J., Cameron, T. A., and Zambryski, P. C. 2010. Agrobacterium type IV secretion system and its substrates form helical arrays around the circumference of virulence-induced cells. Proceedings of the National Academy of Sciences 107:3758-3763. Albers, R. W. W. 2012. Cell membrane structures and functions. Pages 26-39 in: Basic Neurochemistry. Elsevier, USA. Albright, L., Yanofsky, M., Leroux, B., Ma, D., and Nester, E. W. 1987. Processing of the T-DNA of Agrobacterium tumefaciens generates border nicks and linear, single-stranded T-DNA. Journal of Bacteriology 169:1046-1055. Allardet-Servent, A., Michaux-Charachon, S., Jumas-Bilak, E., Karayan, L., and Ramuz, M. 1993. Presence of one linear and one circular chromosome in the Agrobacterium tumefaciens C58 genome. Journal of Bacteriology 175:7869-7874. Almblad, H., Harrison, J. J., Rybtke, M., Groizeleau, J., Givskov, M., Parsek, M. R., and Tolker-Nielsen, T. 2015. The cyclic AMP-Vfr signaling pathway in Pseudomonas aeruginosa is inhibited by cyclic di-GMP. Journal of Bacteriology 197:2190-2200. Aloni, Y., Delmer, D. P., and Benziman, M. 1982. Achievement of high rates of in vitro synthesis of 1, 4-beta-D-glucan: activation by cooperative interaction of the Acetobacter xylinum enzyme system with GTP, polyethylene glycol, and a protein factor. Proceedings of the National Academy of Sciences 79:6448-6452. Amikam, D., and Benziman, M. 1989. Cyclic diguanylic acid and cellulose synthesis in Agrobacterium tumefaciens. Journal of Bacteriology 171:6649-6655. Anand, A., Krichevsky, A., Schornack, S., Lahaye, T., Tzfira, T., Tang, Y., Citovsky, V., and Mysore, K. S. 2007. Arabidopsis VIRE2 INTERACTING PROTEIN2 is required for Agrobacterium T-DNA integration in plants. The Plant Cell 19:1695-1708. Anand, A., Uppalapati, S. R., Ryu, C.-M., Allen, S. N., Kang, L., Tang, Y., and Mysore, K. S. 2008. Salicylic acid and systemic acquired resistance play a role in attenuating crown gall disease caused by Agrobacterium tumefaciens. Plant Physiology 146:703-715. Backert, S., Fronzes, R., and Waksman, G. 2008. VirB2 and VirB5 proteins: specialized adhesins in bacterial type-IV secretion systems? Trends in Microbiology 16:409-413. Ballas, N., and Citovsky, V. 1997. Nuclear localization signal binding protein from Arabidopsis mediates nuclear import of Agrobacterium VirD2 protein. Proceedings of the National Academy of Sciences 94:10723-10728. Baraquet, C., and Harwood, C. S. 2013. Cyclic diguanosine monophosphate represses bacterial flagella synthesis by interacting with the Walker A motif of the enhancer-binding protein FleQ. Proceedings of the National Academy of Sciences 110:18478-18483. Barnhart, D. M., Su, S., Baccaro, B. E., Banta, L. M., and Farrand, S. K. 2013. CelR, an ortholog of the diguanylate cyclase PleD of Caulobacter, regulates cellulose synthesis in Agrobacterium tumefaciens. Applied and Environmental Microbiology 79:7188-7202. Bertani, G. 1951. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. Journal of Bacteriology 62:293-300. Bevan, M. W., and Chilton, M.-D. 1982. T-DNA of the Agrobacterium Ti and Ri plasmids. Annual Review of Genetics 16:357-384. Bhattacharjee, S., Lee, L.-Y., Oltmanns, H., Cao, H., Cuperus, J., and Gelvin, S. B. 2008. IMPa-4, an Arabidopsis importin α isoform, is preferentially involved in Agrobacterium-mediated plant transformation. The Plant Cell 20:2661-2680. Bolton, G. W., Nester, E. W., and Gordon, M. P. 1986. Plant phenolic compounds induce expression of the Agrobacterium tumefaciens loci needed for virulence. Science 232:983-985. Cabezón, E., Ripoll-Rozada, J., Peña, A., De La Cruz, F., and Arechaga, I. 2015. Towards an integrated model of bacterial conjugation. FEMS Microbiology Reviews 39:81-95. Cangelosi, G. A., Ankenbauer, R. G., and Nester, E. W. 1990. Sugars induce the Agrobacterium virulence genes through a periplasmic binding protein and a transmembrane signal protein. Proceedings of the National Academy of Sciences 87:6708-6712. Cangelosi, G. A., Hung, L., Puvanesarajah, V., Stacey, G., Ozga, D., Leigh, J., and Nester, E. W. 1987. Common loci for Agrobacterium tumefaciens and Rhizobium meliloti exopolysaccharide synthesis and their roles in plant interactions. Journal of Bacteriology 169:2086-2091. Cangelosi, G. A., Martinetti, G., Leigh, J. A., Lee, C. C., Thienes, C., and Nester, E. W. 2007. Role of Agrobacterium tumefaciens ChvA protein in export of β-1,2-Glucan. Journal of Bacteriology 189:6742. Cascales, E., and Christie, P. J. 2004. Definition of a bacterial type IV secretion pathway for a DNA substrate. Science 304:1170-1173. Chan, C., Paul, R., Samoray, D., Amiot, N. C., Giese, B., Jenal, U., and Schirmer, T. 2004. Structural basis of activity and allosteric control of diguanylate cyclase. Proceedings of the National Academy of Sciences 101:17084-17089. Charles, T., and Nester, E. W. 1993. A chromosomally encoded two-component sensory transduction system is required for virulence of Agrobacterium tumefaciens. Journal of Bacteriology 175:6614-6625. Chen, Y.-C. 2008. Expression and regulation analyses of virB genes in Agrobacterium tumefaciens. Master thesis. National Taiwan University, Taipei, Taiwan. Chen, Z.-H., and Schaap, P. 2012. Dictyostelium uses the prokaryote messenger c-di-GMP to trigger stalk cell differentiation. Nature 488:680. Chesnokova, O., Coutinho, J. B., Khan, I. H., Mikhail, M. S., and Kado, C. I. 1997. Characterization of flagella genes of Agrobacterium tumefaciens, and the effect of a bald strain on virulence. Molecular Microbiology 23:579-590. Chou, L., Lin, Y.-C., Haryono, M., Santos, M. N. M., Cho, S.-T., Weisberg, A. J., Wu, C.-F., Chang, J. H., Lai, E.-M., and Kuo, C.-H. 2021. Species boundaries in the Agrobacterium tumefaciens complex and multi-level modular evolution of their antibacterial type VI secretion system and tumor-inducing plasmids. bioRxiv. Chou, S.-H., and Galperin, M. Y. 2016. Diversity of cyclic di-GMP-binding proteins and mechanisms. American Society for Microbiology, USA. Christen, M., Christen, B., Folcher, M., Schauerte, A., and Jenal, U. 2005. Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP. Journal of Biological Chemistry 280:30829-30837. Christie, P. J., Ward, J. E., Winans, S. C., and Nester, E. W. 1988. The Agrobacterium tumefaciens virE2 gene product is a single-stranded-DNA-binding protein that associates with T-DNA. Journal of Bacteriology 170:2659-2667. Christie, P. J., Whitaker, N., and González-Rivera, C. 2014. Mechanism and structure of the bacterial type IV secretion systems. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research 1843:1578-1591. Citovsky, V., Wong, M. L., and Zambryski, P. 1989. Cooperative interaction of Agrobacterium VirE2 protein with single-stranded DNA: implications for the T-DNA transfer process. Proceedings of the National Academy of Sciences 86:1193-1197. Conn, H. 1942. Validity of the genus Alcaligenes. Journal of Bacteriology 44:353. Cooley, R. B., Smith, T. J., Leung, W., Tierney, V., Borlee, B. R., O'Toole, G. A., and Sondermann, H. 2016. Cyclic di-GMP-regulated periplasmic proteolysis of a Pseudomonas aeruginosa type Vb secretion system substrate. Journal of Bacteriology 198:66-76. Crane, Y. M., and Gelvin, S. B. 2007. RNAi-mediated gene silencing reveals involvement of Arabidopsis chromatin-related genes in Agrobacterium-mediated root transformation. Proceedings of the National Academy of Sciences 104:15156-15161. da Costa Vasconcelos, F. N., Maciel, N. K., Favaro, D. C., de Oliveira, L. C., Barbosa, A. S., Salinas, R. K., de Souza, R. F., Farah, C. S., and Guzzo, C. R. 2017. Structural and enzymatic characterization of a cAMP-dependent diguanylate cyclase from pathogenic Leptospira species. Journal of Molecular Biology 429:2337-2352. Dahlstrom, K. M., Giglio, K. M., Sondermann, H., and O'Toole, G. A. 2016. The inhibitory site of a diguanylate cyclase is a necessary element for interaction and signaling with an effector protein. Journal of Bacteriology 198:1595-1603. Dahlstrom, K. M., and O'Toole, G. A. 2017. A symphony of cyclases: specificity in diguanylate cyclase signaling. Annual Review of Microbiology 71:179-195. Dalla Costa, L., Piazza, S., Pompili, V., Salvagnin, U., Cestaro, A., Moffa, L., Vittani, L., Moser, C., and Malnoy, M. 2020. Strategies to produce T-DNA free CRISPRed fruit trees via Agrobacterium tumefaciens stable gene transfer. Scientific Reports 10:1-14. Danilchanka, O., and Mekalanos, J. J. 2013. Cyclic dinucleotides and the innate immune response. Cell 154:962-970. Das, A., Stachel, S., Ebert, P., Allenza, P., Montoya, A., and Nester, E. W. 1986. Promoters of Agrobacterium tumefaciens Ti-plasmid virulence genes. Nucleic Acids Research 14:1355-1364. De Cleene, M., and De Ley, J. 1976. The host range of crown gall. The Botanical Review 42:389-466. De, N., Navarro, M. V., Raghavan, R. V., and Sondermann, H. 2009. Determinants for the activation and autoinhibition of the diguanylate cyclase response regulator WspR. Journal of Molecular Biology 393:619-633. Deng, W., Chen, L., Peng, W. T., Liang, X., Sekiguchi, S., Gordon, M. P., Comai, L., and Nester, E. W. 1999. VirE1 is a specific molecular chaperone for the exported single‐stranded‐DNA‐binding protein VirE2 in Agrobacterium. Molecular Microbiology 31:1795-1807. Dessaux, Y., and Faure, D. 2018. Niche construction and exploitation by Agrobacterium: how to survive and face competition in soil and plant habitats. Agrobacterium Biology:55-86. Douglas, C. J., Staneloni, R. J., Rubin, R., and Nester, E. W. 1985. Identification and genetic analysis of an Agrobacterium tumefaciens chromosomal virulence region. Journal of Bacteriology 161:850-860. Dumas, F., Duckely, M., Pelczar, P., Van Gelder, P., and Hohn, B. 2001. An Agrobacterium VirE2 channel for transferred-DNA transport into plant cells. Proceedings of the National Academy of Sciences 98:485-490. Faure, D. 2021. Is there a unique integration mechanism of Agrobacterium T‐DNA into a plant genome? New Phytologist 229:2386-2388. Feirer, N., Xu, J., Allen, K. D., Koestler, B. J., Bruger, E. L., Waters, C. M., White, R. H., and Fuqua, C. 2015. A pterin-dependent signaling pathway regulates a dual-function diguanylate cyclase-phosphodiesterase controlling surface attachment in Agrobacterium tumefaciens. MBio 6. Flemming, H.-C., and Wingender, J. 2010. The biofilm matrix. Nature Reviews Microbiology 8:623-633. Gelvin, S. B. 1998. Agrobacterium VirE2 proteins can form a complex with T strands in the plant cytoplasm. Journal of Bacteriology 180:4300-4302. Gentner, M., Allan, M. G., Zaehringer, F., Schirmer, T., and Grzesiek, S. 2012. Oligomer formation of the bacterial second messenger c-di-GMP: reaction rates and equilibrium constants indicate a monomeric state at physiological concentrations. Journal of the American Chemical Society 134:1019-1029. Ghai, J., and Das, A. 1989. The virD operon of Agrobacterium tumefaciens Ti plasmid encodes a DNA-relaxing enzyme. Proceedings of the National Academy of Sciences 86:3109-3113. Goodner, B., Hinkle, G., Gattung, S., Miller, N., Blanchard, M., Qurollo, B., Goldman, B. S., Cao, Y., Askenazi, M., and Halling, C. 2001. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:2323-2328. Guo, M., Hou, Q., Hew, C. L., and Pan, S. Q. 2007a. Agrobacterium VirD2-binding protein is involved in tumorigenesis and redundantly encoded in conjugative transfer gene clusters. Molecular Plant-Microbe Interactions 20:1201-1212. Guo, M., Jin, S., Sun, D., Hew, C. L., and Pan, S. Q. 2007b. Recruitment of conjugative DNA transfer substrate to Agrobacterium type IV secretion apparatus. Proceedings of the National Academy of Sciences 104:20019-20024. Hamilton, R., and Fall, M. 1971. The loss of tumor-initiating ability in Agrobacterium tumefaciens by incubation at high temperature. Experientia 27:229-230. Heckel, B. C., Tomlinson, A. D., Morton, E. R., Choi, J.-H., and Fuqua, C. 2014. Agrobacterium tumefaciens exoR controls acid response genes and impacts exopolysaccharide synthesis, horizontal gene transfer, and virulence gene expression. Journal of Bacteriology 196:3221-3233. Heikaus, C. C., Pandit, J., and Klevit, R. E. 2009. Cyclic nucleotide binding GAF domains from phosphodiesterases: structural and mechanistic insights. Structure 17:1551-1557. Heindl, J. E., Crosby, D., Brar, S., Pinto, J. F., Singletary, T., Merenich, D., Eagan, J. L., Buechlein, A. M., Bruger, E. L., and Waters, C. M. 2019. Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens. Microbiology 165:146. 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. Frontiers in Plant Science 5:176. Hengge, R. 2009. Principles of c-di-GMP signalling in bacteria. Nature Reviews Microbiology 7:263-273. Hengge, R. 2021. High-specificity local and global c-di-GMP Signaling. Trends in Microbiology (In Press). Herrera-Estrella, A., Van Montagu, M., and Wang, K. 1990. A bacterial peptide acting as a plant nuclear targeting signal: the amino-terminal portion of Agrobacterium VirD2 protein directs a beta-galactosidase fusion protein into tobacco nuclei. Proceedings of the National Academy of Sciences 87:9534-9537. Hooykaas, P., Hofker, M., den Dulk-Ras, H., and Schilperoort, R. 1984. A comparison of virulence determinants in an octopine Ti plasmid, a nopaline Ti plasmid, and an Ri plasmid by complementation analysis of Agrobacterium tumefaciens mutants. Plasmid 11:195-205. Howard, E. A., Zupan, J. R., Citovsky, V., and Zambryski, P. C. 1992. The VirD2 protein of A. tumefaciens contains a C-terminal bipartite nuclear localization signal: implications for nuclear uptake of DNA in plant cells. Cell 68:109-118. Hwang, H. H., Wu, E., Liu, S. Y., Chang, S. C., Tzeng, K. C., and Kado, C. 2013b. Characterization and host range of five tumorigenic Agrobacterium tumefaciens strains and possible application in plant transient transformation assays. Plant Pathology 62:1384-1397. Hwang, H.-H., Yang, F.-J., Cheng, T.-F., Chen, Y.-C., Lee, Y.-L., Tsai, Y.-L., and Lai, E.-M. 2013a. 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. Jarchow, E., Grimsley, N., and Hohn, B. 1991. virF, the host-range-determining virulence gene of Agrobacterium tumefaciens, affects T-DNA transfer to Zea mays. Proceedings of the National Academy of Sciences 88:10426-10430. Jenal, U., Reinders, A., and Lori, C. 2017. Cyclic di-GMP: second messenger extraordinaire. Nature Reviews Microbiology 15:271-284. Jin, S., 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. Journal of Bacteriology 172:4945-4950. Jin, S., Roitsch, T., Ankenbauer, R., Gordon, M., and Nester, E. W. 1990a. The VirA protein of Agrobacterium tumefaciens is autophosphorylated and is essential for vir gene regulation. Journal of Bacteriology 172:525-530. Jin, S., Song, Y. n., Pan, S. Q., and Nester, E. W. 1993. Characterization of a virG mutation that confers constitutive virulence gene expression in Agrobacterium. Molecular Microbiology 7:555-562. Kado, C. 2002. Crown gall. Crown gall. Kado, C., and Heskett, M. 1970. Selective media for isolation of Agrobacterium, Corynebacterium, Erwinia, Pseudomonas and Xanthomonas. Phytopathology 60:969-976. Karunakaran, R., Mauchline, T., Hosie, A. H., and Poole, P. S. 2005. A family of promoter probe vectors incorporating autofluorescent and chromogenic reporter proteins for studying gene expression in Gram-negative bacteria. Microbiology 151:3249-3256. Keane, P., Kerr, A., and New, P. 1970. Crown gall of stone fruit II. Identification and nomenclature of Agrobacterium isolates. Australian Journal of Biological Sciences 23:585-596. Kerr, A. 1969. Transfer of virulence between isolates of Agrobacterium. Nature 223:1175-1176. Khokhani, D. 2014. Small RNA, Cyclic-di-GMP and Phenolic Compounds Regulate the Type III Secretion System in Bacterial Phytopathogens. Kim, J., Heindl, J. E., and Fuqua, C. 2013. Coordination of division and development influences complex multicellular behavior in Agrobacterium tumefaciens. PloS One 8:e56682. Kim, K.-W., Franceschi, V. R., Davin, L. B., and Lewis, N. G. 2006. β-Glucuronidase as reporter gene. Pages 263-273 in: Arabidopsis protocols. Springer. Kim, S. I., Veena, and Gelvin, S. B. 2007. Genome‐wide analysis of Agrobacterium T‐DNA integration sites in the Arabidopsis genome generated under non‐selective conditions. The Plant Journal 51:779-791. Lacroix, B., and Citovsky, V. 2019. Pathways of DNA transfer to plants from Agrobacterium tumefaciens and related bacterial species. Annual Review of Phytopathology 57:231-251. Lacroix, B., Tzfira, T., Vainstein, A., and Citovsky, V. 2006. A case of promiscuity: Agrobacterium's endless hunt for new partners. TRENDS in Genetics 22:29-37. Lai, E.-M., Chesnokova, O., Banta, L. M., and Kado, C. I. 2000. Genetic and environmental factors affecting T-pilin export and T-pilus biogenesis in relation to flagellation of Agrobacterium tumefaciens. Journal of Bacteriology 182:3705-3716. Lai, E.-M., and Kado, C. I. 1998. Processed VirB2 is the major subunit of the promiscuous pilus of Agrobacterium tumefaciens. Journal of Bacteriology 180:2711-2717. Lassalle, F., Campillo, T., Vial, L., Baude, J., Costechareyre, D., Chapulliot, D., Shams, M., Abrouk, D., Lavire, C., and Oger-Desfeux, C. 2011. Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biology and Evolution 3:762-781. Li, G., Brown, P. J., Tang, J. X., Xu, J., Quardokus, E. M., Fuqua, C., and Brun, Y. V. 2012. Surface contact stimulates the just‐in‐time deployment of bacterial adhesins. Molecular Microbiology 83:41-51. Li, L., Jia, Y., Hou, Q., Charles, T. C., Nester, E. W., and Pan, S. Q. 2002. A global pH sensor: Agrobacterium sensor protein ChvG regulates acid-inducible genes on its two chromosomes and Ti plasmid. Proceedings of the National Academy of Sciences 99:12369-12374. Li, X., Tu, H., and Pan, S. Q. 2018. Agrobacterium delivers anchorage protein VirE3 for companion VirE2 to aggregate at host entry sites for T-DNA protection. Cell Reports 25:302-311. e306. Li, X., and Pan, S. Q. 2017. Agrobacterium delivers VirE2 protein into host cells via clathrin-mediated endocytosis. Science Advances 3:e1601528. Li, X., Yang, Q., Peng, L., Tu, H., Lee, L.-Y., Gelvin, S. B., and Pan, S. Q. 2020b. Agrobacterium-delivered VirE2 interacts with host nucleoporin CG1 to facilitate the nuclear import of VirE2-coated T complex. Proceedings of the National Academy of Sciences 117:26389-26397. Li, X., Zhu, T., Tu, H., and Pan, S. Q. 2020a. Agrobacterium VirE3 Uses its two tandem domains at the C-terminus to retain its companion VirE2 on the cytoplasmic side of the host plasma membrane. Frontiers in Plant Science 11:464. Li, Y. G., Hu, B., and Christie, P. J. 2019. Biological and structural diversity of type IV secretion systems. Protein Secretion in Bacteria:277-289. Liaw, Y.-C., Gao, Y.-G., Robinson, H., Sheldrick, G. M., Sliedregt, L., van der Marel, G. A., van Boom, J. H., and Wang, A. H.-J. 1990. Cyclic diguanylic acid behaves as a host molecule for planar intercalators. FEBS letters 264:223-227. Liu, P., and Nester, E. W. 2006. Indoleacetic acid, a product of transferred DNA, inhibits vir gene expression and growth of Agrobacterium tumefaciens C58. Proceedings of the National Academy of Sciences 103:4658-4662. Möglich, A., Ayers, R. A., and Moffat, K. 2009. Structure and signaling mechanism of Per-ARNT-Sim domains. Structure 17:1282-1294. Ma, L.-S., Lin, J.-S., and Lai, E.-M. 2009. An IcmF family protein, ImpLM, is an integral inner membrane protein interacting with ImpKL, and its walker a motif is required for type VI secretion system-mediated Hcp secretion in Agrobacterium tumefaciens. Journal of Bacteriology 191:4316-4329. Mansfield, J., Genin, S., Magori, S., Citovsky, V., Sriariyanum, M., Ronald, P., Dow, M., Verdier, V., Beer, S. V., and Machado, M. A. 2012. Top 10 plant pathogenic bacteria in molecular plant pathology. Molecular Plant Pathology 13:614-629. Mantis, N. J., and Winans, S. C. 1992. The Agrobacterium tumefaciens vir gene transcriptional activator virG is transcriptionally induced by acid pH and other stress stimuli. Journal of Bacteriology 174:1189-1196. Martínez-Gil, M., Ramos-González, M. I., and Espinosa-Urgel, M. 2014. Roles of cyclic di-GMP and the Gac system in transcriptional control of the genes coding for the Pseudomonas putida adhesins LapA and LapF. Journal of Bacteriology 196:1484-1495. Matthysse, A. 1983. Role of bacterial cellulose fibrils in Agrobacterium tumefaciens infection. Journal of Bacteriology 154:906-915. McCarthy, R. R., Yu, M., Eilers, K., Wang, Y. C., Lai, E. M., and Filloux, A. 2019. Cyclic di‐GMP inactivates T6SS and T4SS activity in Agrobacterium tumefaciens. Molecular Microbiology 112:632-648. McIntosh, M., Stone, B., and Stanisich, V. 2005. Curdlan and other bacterial (1→ 3)-β-D-glucans. Applied Microbiology and Biotechnology 68:163-173. Medina, C., López-Baena, F. J., and Vinardell, J. M. 2019. Regulation of protein secretion systems mediated by cyclic-di-GMP in plant-interacting bacteria. Frontiers in Microbiology 10:1289. Merritt, P. M., Danhorn, T., and Fuqua, C. 2007. Motility and chemotaxis in Agrobacterium tumefaciens surface attachment and biofilm formation. Journal of Bacteriology 189:8005-8014. Mohari, B., Thompson, M. A., Trinidad, J. C., Setayeshgar, S., and Fuqua, C. 2018. Multiple flagellin proteins have distinct and synergistic roles in Agrobacterium tumefaciens motility. Journal of Bacteriology 200. Moscoso, J. A., Mikkelsen, H., Heeb, S., Williams, P., and Filloux, A. 2011. The Pseudomonas aeruginosa sensor RetS switches type III and type VI secretion via c‐di‐GMP signalling. Environmental Microbiology 13:3128-3138. Mougel, C., Thioulouse, J., Perrière, G., and Nesme, X. 2002. A mathematical method for determining genome divergence and species delineation using AFLP. International Journal of Systematic and Evolutionary Microbiology 52:573-586. Nadakuduti, S. S., and Enciso-Rodríguez, F. 2020. Advances in genome editing with CRISPR systems and transformation technologies for plant DNA manipulation. Frontiers in Plant Science 11. Nagel, R., Elliott, A., Masel, A., Birch, R., and Manners, J. 1990. Electroporation of binary Ti plasmid vector into Agrobacterium tumefaciens and Agrobacterium rhizogenes. FEMS Microbiology Letters 67:325-328. Narasimhulu, S. B., Deng, X., Sarria, R., and Gelvin, S. B. 1996. Early transcription of Agrobacterium T-DNA genes in tobacco and maize. The Plant Cell 8:873-886. Nester, E. W. 2015. Agrobacterium: nature’s genetic engineer. Frontiers in Plant Science 5:730. Nishizawa‐Yokoi, A., Saika, H., Hara, N., Lee, L. Y., Toki, S., and Gelvin, S. B. 2021. Agrobacterium T‐DNA integration in somatic cells does not require the activity of DNA polymerase θ. New Phytologist 229:2859-2872. Nonaka, S., Yuhashi, K. I., Takada, K., Sugaware, M., Minamisawa, K., and Ezura, H. 2008. Ethylene production in plants during transformation suppresses vir gene expression in Agrobacterium tumefaciens. New Phytologist 178:647-656. Oliveira, M. C., Teixeira, R. D., Andrade, M. O., Pinheiro, G. M., Ramos, C. H., and Farah, C. S. 2015. Cooperative substrate binding by a diguanylate cyclase. Journal of Molecular Biology 427:415-432. Paul, K., Nieto, V., Carlquist, W. C., Blair, D. F., and Harshey, R. M. 2010. The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a “backstop brake” mechanism. Molecular Cell 38:128-139. Peralta, E. G., and Ream, L. W. 1985. T-DNA border sequences required for crown gall tumorigenesis. Proceedings of the National Academy of Sciences 82:5112-5116. Platt, T. G., Bever, J. D., and Fuqua, C. 2012. A cooperative virulence plasmid imposes a high fitness cost under conditions that induce pathogenesis. Proceedings of the Royal Society B: Biological Sciences 279:1691-1699. Portier, P., Fischer-Le Saux, M., Mougel, C., Lerondelle, C., Chapulliot, D., Thioulouse, J., and Nesme, X. 2006. Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers. Applied and Environmental Microbiology 72:7123-7131. Puławska, J., and Kałużna, M. 2012. Phylogenetic relationship and genetic diversity of Agrobacterium spp. isolated in Poland based on gyrB gene sequence analysis and RAPD. European Journal of Plant Pathology 133:379-390. Quandt, J., and Hynes, M. F. 1993. Versatile suicide vectors which allow direct selection for gene replacement in gram-negative bacteria. Gene 127:15-21. Römling, U., and Galperin, M. Y. 2015. Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. Trends in Microbiology 23:545-557. Ramey, B. E., Matthysse, A. G., and Fuqua, C. 2004. The FNR‐type transcriptional regulator SinR controls maturation of Agrobacterium tumefaciens biofilms. Molecular Microbiology 52:1495-1511. Rao, F., Pasunooti, S., Ng, Y., Zhuo, W., Lim, L., Liu, A. W., and Liang, Z.-X. 2009. Enzymatic synthesis of c-di-GMP using a thermophilic diguanylate cyclase. Analytical Biochemistry 389:138-142. Ross, P., Aloni, Y., Weinhouse, H., Michaeli, D., Weinberger-Ohana, P., Mayer, R., and Benziman, M. 1986. Control of cellulose synthesis Acetobacter xylinum. A unique guanyl oligonucleotide is the immediate activator of the cellulose synthase. Carbohydrate Research 149:101-117. Ross, P., Weinhouse, H., Aloni, Y., Michaeli, D., Weinberger-Ohana, P., Mayer, R., Braun, S., De Vroom, E., Van der Marel, G., and Van Boom, J. 1987. Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid. Nature 325:279-281. Rossi, L., Hohn, B., and Tinland, B. 1996. Integration of complete transferred DNA units is dependent on the activity of virulence E2 protein of Agrobacterium tumefaciens. Proceedings of the National Academy of Sciences 93:126-130. Russell, D. W., and Sambrook, J. 2001. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Cold Spring Harbor, NY. Sarenko, O., Klauck, G., Wilke, F. M., Pfiffer, V., Richter, A. M., Herbst, S., Kaever, V., and Hengge, R. 2017. More than enzymes that make or break cyclic di-GMP—local signaling in the interactome of GGDEF/EAL domain proteins of Escherichia coli. MBio 8. Schirmer, T. 2016. C-di-GMP synthesis: structural aspects of evolution, catalysis and regulation. Journal of Molecular Biology 428:3683-3701. Schirmer, T., and Jenal, U. 2009. Structural and mechanistic determinants of c-di-GMP signalling. Nature Reviews Microbiology 7:724-735. Schmidt-Eisenlohr, H., Domke, N., and Baron, C. 1999. TraC of IncN Plasmid pKM101 Associates with Membranes and Extracellular High-Molecular-Weight Structures in Escherichia coli. Journal of Bacteriology 181:5563-5571. Shimoda, N., Toyoda-Yamamoto, A., Aoki, S., and Machida, Y. 1993. Genetic evidence for an interaction between the VirA sensor protein and the ChvE sugar-binding protein of Agrobacterium. Journal of Biological Chemistry 268:26552-26558. Smith, E. F., and Townsend, C. O. 1907. A plant-tumor of bacterial origin. Science 25:671-673. Stachel, S. E., Messens, E., Van Montagu, 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. Stachel, S. E., Timmerman, B., and Zambryski, P. 1986. Generation of single-stranded T-DNA molecules during the initial stages of T-DNA transfer from Agrobacterium tumefaciens to plant cells. Nature 322:706-712. Stachel, S. E., and Zambryski, P. C. 1986. virA and virG control the plant-induced activation of the T-DNA transfer process of A. tumefaciens. Cell 46:325-333. Steck, T. R., Morel, P., and Kado, C. I. 1988. Vir box sequences in Agrobacterium tumefaciens pTiC58 and A6. Nucleic Acids Research 16:8736. Su, J., Zou, X., Huang, L., Bai, T., Liu, S., Yuan, M., Chou, S.-H., He, Y.-W., Wang, H., and He, J. 2016. DgcA, a diguanylate cyclase from Xanthomonas oryzae pv. oryzae regulates bacterial pathogenicity on rice. Scientific Reports 6:25978. Sundberg, C., Meek, L., Carroll, K., Das, A., and Ream, W. 1996. VirE1 protein mediates export of the single-stranded DNA-binding protein VirE2 from Agrobacterium tumefaciens into plant cells. Journal of Bacteriology 178:1207-1212. Sundriyal, A., Massa, C., Samoray, D., Zehender, F., Sharpe, T., Jenal, U., and Schirmer, T. 2014. Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger cyclic di-GMP. Journal of Biological Chemistry 289:6978-6990. Takashi, A., Takashi, H., Satoshi, T., and Atsuhiro, O. 1989. Putative start codon TTG for the regulatory protein VirG of the hairy-root-inducing plasmid pRiA4. Gene 78:173-178. Thompson, M. A., Onyeziri, M. C., and Fuqua, C. 2018. Function and regulation of Agrobacterium tumefaciens cell surface structures that promote attachment. Pages 143-184 in: Agrobacterium Biology. Springer. Tomlinson, A. D., Ramey-Hartung, B., Day, T. W., Merritt, P. M., and Fuqua, C. 2010. Agrobacterium tumefaciens ExoR represses succinoglycan biosynthesis and is required for biofilm formation and motility. Microbiology 156:2670. Tomlinson, A. D., and Fuqua, C. 2009. Mechanisms and regulation of polar surface attachment in Agrobacterium tumefaciens. Current Opinion in Microbiology 12:708-714. Toro, N., Datta, A., Carmi, O., Young, C., Prusti, R., and Nester, E. W. 1989. The Agrobacterium tumefaciens virC1 gene product binds to overdrive, a T-DNA transfer enhancer. Journal of Bacteriology 171:6845-6849. Tsai, Y.-L., Wang, M.-H., Gao, C., Klüsener, S., Baron, C., Narberhaus, F., and Lai, E.-M. 2009. Small heat-shock protein HspL is induced by VirB protein (s) and promotes VirB/D4-mediated DNA transfer in Agrobacterium tumefaciens. Microbiology 155:3270. Tzfira, T., and Citovsky, V. 2007. Agrobacterium: from biology to biotechnology. Springer Science Business Media. Tzfira, T., Frankman, L. R., Vaidya, M., and Citovsky, V. 2003. Site-specific integration of Agrobacterium tumefaciens T-DNA via double-stranded intermediates. Plant Physiology 133:1011-1023. Valentini, M., and Filloux, A. 2019. Multiple roles of c-di-GMP signaling in bacterial pathogenesis. Annual Review of Microbiology 73:387-406. Van Kregten, M., de Pater, S., Romeijn, R., van Schendel, R., Hooykaas, P. J., and Tijsterman, M. 2016. T-DNA integration in plants results from polymerase-θ-mediated DNA repair. Nature Plants 2:1-6. Vergunst, A. C., Schrammeijer, B., den Dulk-Ras, A., de Vlaam, C. M., Regensburg-Tuınk, T. J., and Hooykaas, P. J. 2000. VirB/D4-dependent protein translocation from Agrobacterium into plant cells. Science 290:979-982. Vergunst, A. C., van Lier, M. C., den Dulk-Ras, A., Stüve, T. A. G., Ouwehand, A., and Hooykaas, P. J. 2005. Positive charge is an important feature of the C-terminal transport signal of the VirB/D4-translocated proteins of Agrobacterium. Proceedings of the National Academy of Sciences 102:832-837. Wang, C., Ye, F., Chang, C., Liu, X., Wang, J., Wang, J., Yan, X.-F., Fu, Q., Zhou, J., and Chen, S. 2019. Agrobacteria reprogram virulence gene expression by controlled release of host-conjugated signals. Proceedings of the National Aca……… | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/81843 | - |
| dc.description.abstract | "農桿菌會在植物上造成癌腫病，同時也被廣泛應用於基因轉殖與科學研究上。農桿菌在植物上受到酚類化合物刺激後，會誘導毒力基因表現，將細胞內的T-DNA經由第四型分泌系統送入植物細胞，造成癌腫病。cyclic-di-GMP為一種細菌的第二信使因子，已被提出可以調控細菌蛋白質分泌系統，並改變農桿菌的表徵，包含生物膜形成、胞外多醣體合成與泳動能力，然而其調控毒力的角色及機制並未被深入研究。先前的研究中已篩選cyclic-di-GMP的合成蛋白—二鳥苷酸環化酶(diguanylate cyclase, DGC)，發現在過量表現DGC Atu1207或Atu5372時，會顯著降低農桿菌毒力基因表現與轉殖能力。在本篇研究中，我們構築Δatu1207及Δatu5372之單突變株、雙突變株、與過量表現株，以探討Atu1207及Atu5372於農桿菌C58菌株之性狀分析。研究結果顯示，過量表現Atu1207或Atu5372顯著降低農桿菌於番茄上產生之腫瘤重量，而Δatu1207Δatu5372雙突變株則提升其腫瘤重量。除此之外，過量表現Atu1207或Atu5372顯著抑制農桿菌之virB及virE之毒力基因啟動子活性，而Δatu1207Δatu5372雙突變株則提升，且毒力mRNA及蛋白質表現量皆支持此結果，顯示DGC Atu1207及Atu5372負調控毒力基因啟動子以影響轉殖及產生腫瘤之表現。在生理特性的觀察中，過量表現Atu1207或Atu5372顯著降低細胞生長及泳動能力並提升生物膜之形成能力，然而突變株卻無顯著影響。值得注意的是，過量表現Atu5372相較Atu1207有更顯著的生物膜形成；而過量表現Atu1207則相較Atu5372更顯著的抑制毒力基因表現。綜合上述結果，Atu1207及Atu5372可能藉由不同的機制調控毒力基因啟動子及生理特性的改變，並負面影響農桿菌之轉殖效率及毒力。此外，親緣分析結果顯示Atu1207在不同農桿菌分類群中較為同源；而Atu5372則較為獨特。此研究闡述DGC如何調控農桿菌之轉殖能力及毒力，並奠定利用DGC提升農桿菌轉殖能力或控制癌腫病的基礎及研究方向。" | zh_TW |
| dc.description.provenance | Made available in DSpace on 2022-11-25T03:04:52Z (GMT). No. of bitstreams: 1 U0001-1307202110582500.pdf: 6338650 bytes, checksum: a369ee223166565f902dac836e7272c5 (MD5) Previous issue date: 2021 | en |
| dc.description.tableofcontents | VERIFICATION i ACKNOWLEDGEMENT ii 中文摘要 iii ABSTRACT iv TABLE OF CONTENTS vii LIST OF FIGURES x LIST OF TABLES xii LIST OF APPENDIX FIGURES xiii LIST OF APPENDIX TABLES xiv INTRODUCTION 1 1. Characteristics and taxonomy of Agrobacterium genus 1 2. Pathogenesis of crown gall disease and pathogenic mechanism 4 3. Overview and regulation of cyclic diguanylate (c-di-GMP) 16 4. Biological processes regulated by c-di-GMP 21 5. C-di-GMP studies in A. tumefaciens C58 24 6. Aim of this study 28 MATERIALS AND METHODS 30 1. Bacterial strains and growth condition 30 2. Techniques of molecular biology 30 3. Virulence assay 37 4. Gene expression analysis 40 5. Protein expression analysis 44 6. Physiological properties analyses 47 7. Comparative analysis 49 RESULTS 50 1. Overexpression of DGC Atu1207 and Atu5372 in A. tumefaciens C58 decreased the transient transformation effici ency and tumorigenicity 50 2. A. tumefaciens C58 Δatu1207Δatu5372 double mutant increased the tumorigenicity 52 3. Overexpression of Atu1207 or Atu5372 negatively regulates virulence gene expression at the transcriptional levels 54 4. A. tumefaciens C58 Δatu1207Δatu5372 double mutant has increased virulence gene expression 57 5. Overexpression of Atu1207 and Atu5372 in A. tumefaciens C58 but not mutants changed the physiological properties 59 6. Atu1207 is conserved across A. tumefaciens genomospecies while Atu5372 is unique to C58 62 DISCUSSION 64 1. Expression level of overexpressed DGC Atu1207 and Atu5372 in A. tumefaciens C58 65 2. Effect of DGC Atu1207 and Atu5372 on transformation of A. tumefaciens C58 65 3. Effect of DGC Atu1207 and Atu5372 on virulence gene expression in A. tumefaciens C58 67 4. DGC Atu1207 and Atu5372 modulate the physiological properties of A. tumefaciens C58 69 5. Evolutionary insights of DGC Atu1207 and Atu5372 70 6. Conclusion and future works 71 FIGURES 75 TABLES 105 REFERENCES 114 APPENDICES 145 1. Medium used in this study 145 2. Appendix figures 147 3. Appendix tables 158 4. Abbreviation list 183 | |
| dc.language.iso | en | |
| dc.subject | 二鳥苷酸環化酶 | zh_TW |
| dc.subject | Atu5372 | zh_TW |
| dc.subject | Atu1207 | zh_TW |
| dc.subject | cyclic-di-GMP | zh_TW |
| dc.subject | 生物膜 | zh_TW |
| dc.subject | 毒力 | zh_TW |
| dc.subject | 農桿菌 | zh_TW |
| dc.subject | biofilm | en |
| dc.subject | Agrobacterium tumefaciens | en |
| dc.subject | diguanylate cyclases | en |
| dc.subject | Atu1207 | en |
| dc.subject | virulence | en |
| dc.subject | Atu5372 | en |
| dc.subject | cyclic-di-GMP | en |
| dc.title | 農桿菌C58菌株diguanylate cyclases Atu1207與Atu5372之功能研究 | zh_TW |
| dc.title | Functional characterizations of diguanylate cyclases Atu1207 and Atu5372 in Agrobacterium tumefaciens C58 | en |
| dc.date.schoolyear | 109-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.author-orcid | 0000-0002-6515-2641 | |
| dc.contributor.advisor-orcid | 賴爾珉(0000-0003-3630-8683) | |
| dc.contributor.oralexamcommittee | 黃皓瑄(Hsin-Tsai Liu),鄭秋萍(Chih-Yang Tseng),郭志鴻 | |
| dc.subject.keyword | 農桿菌,毒力,生物膜,cyclic-di-GMP,二鳥苷酸環化酶,Atu1207,Atu5372, | zh_TW |
| dc.subject.keyword | Agrobacterium tumefaciens,virulence,biofilm,cyclic-di-GMP,diguanylate cyclases,Atu1207,Atu5372, | en |
| dc.relation.page | 183 | |
| dc.identifier.doi | 10.6342/NTU202101430 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2021-07-13 | |
| dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
| dc.contributor.author-dept | 植物病理與微生物學研究所 | zh_TW |
| dc.date.embargo-lift | 2026-07-01 | - |
| 顯示於系所單位： | 植物病理與微生物學系 | |
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