跳到主要內容

臺灣博碩士論文加值系統

(18.97.9.172) 您好!臺灣時間:2025/02/14 04:07
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果 :::

詳目顯示

我願授權國圖
: 
twitterline
研究生:林建廷
研究生(外文):Chien-Ting Lin
論文名稱:Agrobacterium vitis之基因體學探討及與Agrobacterium tumefaciens之比較基因體學分析
論文名稱(外文):Genomic characterization of Agrobacterium vitis and comparative analysis with Agrobacterium tumefaciens
指導教授:黃皓瑄郭志鴻郭志鴻引用關係
指導教授(外文):Hau-Hsuan HwangChih-Horng Kuo
口試委員:賴爾珉
口試委員(外文):Erh-Min Lai
口試日期:2017-07-24
學位類別:碩士
校院名稱:國立中興大學
系所名稱:生命科學系所
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2017
畢業學年度:105
語文別:英文
論文頁數:48
中文關鍵詞:農桿菌基因體學
外文關鍵詞:Agrobacterium vitisAgrobacterium tumefaciensGenomics
相關次數:
  • 被引用被引用:0
  • 點閱點閱:502
  • 評分評分:
  • 下載下載:0
  • 收藏至我的研究室書目清單書目收藏:0
農桿菌(Agrobacterium)是一種常見於土壤中,且可跨界(kingdom)轉移遺傳物質至其他真核生物中的一種植物病原菌,其中最常見的一種農桿菌是根瘤農桿菌(Agrobacterium tumefaciens),可以感染的宿主以雙子葉植物為主。A. tumefaciens的基因體組成主要有一條環狀和一條線狀的染色體,其中使農桿菌能感染其他宿主的主因是Ti質體(tumor-inducing plasmid)。Ti質體上有一段T-DNA (transfer DNA)會透過第四型分泌系統(type IV secretion system、T4SS)將其轉移至植物細胞內,並鑲嵌進植物細胞的染色體上。野生種T-DNA上含有細胞分裂素(cytokinin)和植物生長素(auxin)的生合成基因,當T-DNA嵌入植物的染色體中,這些基因便可大量表現,導致植物細胞產生不正常的增生並造成冠癭狀腫瘤(crown gall tumor)。Agrobacterium vitis與A. tumefaciens最大的差異在於,A. vitis只會造成葡萄產生冠癭狀腫瘤,當其感染其他植物時則會產生植物過敏反應(hypersensitive response、HR)。A. vitis的基因體組成主要有兩條環狀的染色體,並且具有Ti質體。本研究主要針對四株A. vitis菌株(CG678、CG78、CG412、 F2/5)進行全基因體定序,藉以瞭解其種內的遺傳變異,並藉由與已發表的A. tumefaciens基因體序列進行比較,進而探討種間的遺傳變異。分析結果顯示此四株新菌株在主要的兩條染色體與A. vitis S4有極大的相似度。其中A. vitis F2/5並不具有Ti質體,而A. vitis CG678和A. vitis CG78的Ti質體幾乎與A. vitis S4相同。此外,分子演化樹和基因組成分析的結果顯示A. vitis CG678與A. vitis CG78之間的歧異度極低,其所共有的同源基因間僅有0.3% 蛋白質序列差異。而A. vitis CG412的Ti質體、T-DNA及第四型分泌系統的基因組成,卻與A. tumefaciens Ach5 具有較高的相似度。然而與A. tumefaciens Ach5比較之下,A. vitis CG412缺少第四型分泌系統中的VirB7基因。針對A. vitis與A. tumefaciens的種間比較結果顯示,此二個物種各有約500-600的物種特有基因。其中A. vitis特有的基因有較多屬於訊息傳導的功能,而A. tumefaciens則有較多的無機離子運輸基因。綜合而論,此研究結果可增進學界對農桿菌屬內,物種的種內及種間之基因體多樣性之了解。
Agrobacterium is a genus of plant pathogenic bacteria, which are commonly found in soil and could perform trans-kingdom DNA transfer to other eukaryotes. The most notable species is Agrobacterium tumefaciens, which naturally infects dicot hosts. The genome of A. tumefaciens contains one circular chromosome and one linear chromosome. The major season that Agrobacterium could infect their eukaryotic host is the presence of a Ti plasmid (tumor-inducing plasmid). There is a DNA region on Ti plasmid called T-DNA (transfer DNA) that could be transferred into host cells by the type IV secretion system (T4SS) and integrated into the chromosome of the host plant. There are oncogenes on the T-DNA of wild-type Agrobacterium, for example: the biosynthesis genes of cytokinin and auxin. When T-DNA was integrated into the host chromosome, these oncogenes would express and cause abnormal plant cell growth to generate the crown gall tumor. The most notable difference between A. vitis and A. tumefaciens is that A. vitis only can cause crown gall tumor on grapevines. A. vitis infection in other host plants would only cause hypersensitive response (HR). The genome of A. vitis contains two circular chromosomes, and some strains also have a Ti plasmid. This study focused on the genome characterization of four wild-type A. vitis strains to study the genetic variation within the species, as well as to investigate the inter-specific genetic variations by comparative analysis with the available genome sequences of A. tumefaciens strains. The results demonstrated that the two major chromosomes of all four newly characterized A. vitis strains are similar to A. vitis S4. The Ti plasmid of A. vitis CG678 and A. vitis CG78 is almost identical with that of A. vitis S4, and A. vitis F2/5 does not have a Ti plasmid. The phylogenetic and gene content analysis demonstrated that the genetic variation between A. vitis CG678 and A. vitis CG78 is very low. There is only 0.3% divergence in amino acid sequences of their shared homologous genes. The Ti plasmid, T-DNA content, and T4SS genes of A. vitis CG412 is more similar to A. tumefaciens Ach5. In comparison with A. tumefaciens Ach5, A. vitis CG412 lacks VirB7 gene. Comparative analysis of between A. vitis and A. tumefaciens indicated that both have approximately 500-600 species-specific genes. A. vitis has more signal transduction genes, and A. tumefaciens has more genes for the transport of inorganic ions. In conclusion, this study improved our knowledge about the genome diversity of Agrobacterium at the inter- and intra-species levels.
摘要 i
Abstract ii
Tables directory vi
Figures directory vii
Introduction 1
1. Agrobacterium overview 1
1.1. The tumor-inducing plasmid (Ti plasmid) 2
1.2. The properties and gene contents of the T-DNA 3
1.3. Agrobacterium transfer T-DNA and Vir proteins to the plant cells by T4SS 4
2. Agrobacterium vitis 4
2.1. Species characteristics 4
2.2. Genomic study of the Agrobacterium vitis S4 5
3. Development of Next Generation Sequencing (NGS) and comparative genomics 6
3.1. Development of Next Generation Sequencing (NGS) 6
3.2. Genomics studies of the wild-type Agrobacterium strains 7
4. The goal of this study 8
Materials and Methods 9
1. Strains information (Table, strain geographic location, host reference) 9
2. Whole genome sequencing 9
3. Genome assembly, and annotation 9
4. Comparative genomics analyses 10
5. Molecular phylogenetic inference 11
Results 12
1. Characteristics of genome assemblies 12
2. Genome alignment 12
3. Phylogenetic analyses 13
4. Ti plasmid organization 13
5. Gene content comparison 14
6. Comparison of secretion system genes among the Agrobacterium strains 15
Discussion 17
1. Genome features of four A. vitis strains 17
2. Phylogenetic analyses of four A. vitis strain 17
3. The Ti plasmid features of four A. vitis strains and comparison with A. tumefaciens 17
4. Comparative analyses of gene content 18
5. Comparison of secretion system among Agrobacterium strains 19
References 20
1.Akiyoshi, D.E., Klee, H., Amasino, R.M., Nester, E.W., and Gordon, M.P. (1984). T-DNA of Agrobacterium tumefaciens encodes an enzyme of cytokinin biosynthesis. Proc Natl Acad Sci U S A 81, 5994-5998.
2.Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1997). Basic local alignment search tool. J Mol Biol 215, 403-410.
3.Ananiadou, S., Sullivan, D., Black, W., Levow, G.A., Gillespie, J.J., Mao, C., Pyysalo, S., Kolluru, B., Tsujii, J., and Sobral, B. (2011). Named entity recognition for bacterial Type IV secretion systems. PLoS one 6, e14780.
4.Baron, C., and Zambryski, P.C. (1995). The plant response in pathogenesis, symbiosis, and wounding: variations on a common theme? Annu Rev Genet 29, 107-129.
5.Benson, D.A., Karsch-Mizrachi, I., Clark, K., Lipman, D.J., Ostell, J., and Sayers, E.W. (2012). GenBank. Nucleic Acids Res 40, D48-D53.
6.Bevan, M.W., and Chilton, M.D. (1982). T-DNA of the Agrobacterium Ti and Ri plasmids. Annu Rev Genet 16, 357-384.
7.Bourras, S., Rouxel, T., and Meyer, M. (2015) Agrobacterium tumefaciens gene transfer: how a plant pathogen hacks the nuclei of plant and nonplant organisms. Phytopathology 105, 1288-1301.
8.Brencic, A., and Winans, S.C. (2005). Detection of and response to signals involved in host-microbe interactions by plant-associated bacteria. Microbiol Mol Biol Rev 69, 155-194.
9.Burr, T.J., and Reid, C.L. (1994). Biological control of grape crown gall with non-tumorigenic Agrobacterium vitis strain F2/5. Am J Enol Vitic 45, 213-219.
10.Burr, T.J., Bazzi, C., Sule, S., and Otten, L. (1998). Crown gall of grape: biology of Agrobacterium vitis and the development of disease control strategies. Plant Dis 82, 1288-1297.
11.Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T. (2009). BLAST+: architecture and applications. BMC Bioinformatics. 10, 421.
12.Caplan, A.B., Van Montagu, M., and Schell, J. (1985). Genetic analysis of integration mediated by single T-DNA borders. J Bacteriol 161, 655-664.
13.Cascales, E., and Christie, P.J. (2004). Definition of a bacterial type IV secretion pathway for a DNA substrate. Science 304, 1170-1173.
14.Cavara, F. (1897). Tuberculosi della vite. Intorno alla eziologia di alcune malattie di piante cultivate. Le Stazioni Sperimentale Agraric Itliana 30, 483-487.
15.Cho, S.T., Chang, H.H., Egamberdieva, D., Kamilova, F., Lugtenberg, B., and Kuo, C.H. (2015). Genome analysis of Pseudomonas fluorescens PCL1751: a rhizobacterium that controls root diseases and alleviates salt stress for its plant host. PLoS ONE 10, e0140231.
16.Christie, P.J. (1997). Agrobacterium tumefaciens T-complex transport apparatus: aparadigm for a new family of multifunctional transporters in eubacteria. J Bacteriol 179, 3085-3094.
17.Christie, P.J. (2004). Type IV secretion: the Agrobacterium VirB4/D4 and related conjugation systems. Biochim Biophys Acta 1694, 219-234.
18.Christie, P.J. (2016). The mosaic type IV secretion systems. EcoSal Plus 7, 1-22.
19.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.
20.Christie, P.J., and Cascales, E. (2005). Structural and dynamic properties of bacterial type IV secretion systems. Mol Membr Biol 22, 51-61.
21.Christie, P.J., Whitaker, N., and González-Rivera, C. (2014). Mechanism and structure of the bacterial type IV secretion systems. Biochim Biophys Acta 1843, 1578-1591.
22.Citovsky, V., Guralnick, B., Simon, M.N., and Wall, J.S. (1997). The molecular structure of Agrobacterium VirE2-single stranded DNA complexes involved in nuclear import. J Mol Biol 271, 718-727.
23.Darling, A.C.E., Mau, B., Blattner, F.R., and Perna, N.T. (2004). Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14, 1394-1403.
24.DeCleene, M., and DelLey, J. (1976). The host range of crown gall. Bot Rev 42, 389-466.
25.Diaz, J., Bernal, A., Pomar, F., and Merino, F. (2001). Induction of shikimate dehydrogenase and peroxidase in pepper (Capsicum annum L.) seedlings in response to copper stress and its relation to lignification. Plant Sci 161, 179-188.
26.Duban, M.E., Lee, K., and Lynn, D.G. (1993). Strategies in pathogenesis: mechanistic specificity in the detection of generic signals. Mol Microbiol 7, 637-645.
27.Durrenberger, F., Cameri, A., Hohn, B., and Koukolikova-Nicola, Z. (1989). Covalently bound VirD2 protein of Agrobacterium tumefaciens protects the T-DNA from exonucleolytic degradation. Proc Natl Acad Sci U S A 86, 9154-9158.
28.Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792-1797.
29.Engstrom, P., Zambryski, P., Van Montagu, M., and Stachel, S. (1987). Characterization of Agrobacterium tumefaciens virulence proteins induced by the plant factor acetosyringone. J Mol Biol 197, 635-645.
30.Escobar, M.A., and Dandekar, A.M. (2003). Agrobacterium tumefaciens as an agent of disease. Trends Plant Sci 8, 380-386.
31.Felsenstein, J. (1989). PHYLIP-phylogeny inference package (version 3.2). Cladistics 5, 164-166.
32.Fuller, C.W., Middendorf, L.R., Benner, S.A., Church, G.M., Harris, T., Huang, X., Jovanovich, S.B., Nelson, J.R., Schloss, J.A., Schwartz, D.C., Vezenov, D.V. (2009). The challenges of sequencing by synthesis. Nat Biotechnol 27, 1013–1023.
33.Fullwood, M.J, Wei, C.L., Liu, E.T., and Ruan, Y. (2009). Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res 19, 521-532.
34.Gelvin, S.B. (2003). Agrobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool. Microbiol Mol Biol Rev 67, 16-23.
35.Gelvin, S.B. (2010). Plant proteins involved in Agrobacterium-mediated genetic transformation. Annu Rev Phytopathol 48, 45-68.
36.Gelvin, S.B. (2014). Traversing the cell: Agrobacterium T-DNA journey to the host genome. Front Plant Sci 3, 52.
37.Gietl, C., Koukolikova-Nicola, Z., and Hohn, B. (1987). Mobilization of T-DNA from Agrobacterium to plant cells involves a protein that binds single-stranded DNA. Proc Natl Acad Sci U S A 84, 9006-9010.
38.Gohlke, J., and Deeken, R. (2014). Plant responses to Agrobacterium tumefaciens and crown gall development. Front Plant Sci 5, 155.
39.Guindon, S., and Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696-704.
40.Guyon, P., Chilton, M.D., Petit, A., and Tempe, J. (1980). Agropine in "null-type" crown gall tumors: evidence for generality of the opine concept. Proc Natl Acad Sci U S A 77, 2693-2697.
41.Hepburn, A.G., White, J., Pearson, L., Maunders, M.J., Clarke, L.E., Prescott, A.G., and Blundy, K.S. (1985). The use of pNJ5000 as an intermediate vector for the genetic manipulation of Agrobacterium Ti-plasmids. J Gen Microbiol 131, 2961-2969.
42.Herlache, T.C., and Triplett, E.W. (2002). Expression of a crown gall biological control phenotype in an avirulent strain of Agrobacterium vitis by addition of the trifolitoxin production and resistance genes. BMC Biotechnol 2, 2.
43.Herlache, T.C., Zhang, H.S., Ried, C.L., Carle, S.A., Basaran, P., Thaker, M., Burr, A.T., and Burr, T.J. (2001). Mutations that affect Agrobacterium vitis induced grape necrosis also alter its ability to cause a hypersensitive response on tobacco. Phytopathology 91, 966-972.
44.Howard, E.A., Winsor, B.A., De Vos, G., and Zambryski, P. (1989). Activation of the T-DNA transfer process in Agrobacterium results in the generation of a T-strand-protein complex: Tight association of VirD2 with the 5’ends of T-strands. Proc Natl Acad Sci U S A 86, 4017-4021.
45.Hu, X., Zhao, J., Degrado, W.F., and Binns, A.N. (2013). Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals. Proc Natl Acad Sci U S A 110, 678-683.
46.Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. (2010). Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119-130.
47.Jataswal, R.K., Veluthambi, K., Gelvin, S.B., and Slightom, J.L. (1987). Double-stranded cleavage of T-DNA and generation of single-stranded T-DNA molecules in Escherichia coli by a virD-encoded border-specific endonuclease from Agrobacterium tumefaciens. J Bacteriol 169, 5035-5045.
48.Kanehisa, M., and Goto, S. (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28, 27-30.
49.Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M. (2010). KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38, D355-D360.
50.Kanehisa, M., Sato, Y., and Morishima, K. (2016). BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428, 726-731.
51.Klee, H., Montoya, A., Horodyski, F., Lichtenstein, C., Garfinkel, D., Fuller, S., Flores, C., Peschon, J., Nester, E., and Gordon, M. (1984). Nucleotide sequence of the tms genes of the pTiA6NC octopine Ti plasmid: two gene products involved in plant tumorigenesis. Proc Natl Acad Sci U S A 81, 1728-1732.
52.Koboldt, D.C., Steinberg, K.M., Larson, D.E., Wilson, R.K., and Mardis, E.R. (2013). The next-generation sequencing revolution and its impact on genomics. Cell 155, 27-38.
53.Krenek, P., Samajova, O., Luptovciak, I., Doskocilova, A., Komis, G., and Samaj, J. (2015). Transient plant transformation mediated by Agrobacterium tumefaciens: principles, methods and applications. Biotechnol Adv 33, 1024-1042.
54.Ku, C., Lo, W.S., Chen, L.L., and Kuo, C.H. (2013). Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in Spiroplasma. Genome Biol Evol 5, 1151-1164.
55.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.
56.Lacroix, B., Kozlovsky, S.V., and Citovsky, V. (2008). Recent patents on Agrobacterium-mediated gene and protein transfer, for research and biotechnology. Recent Pat DNA Gene Seq 2, 69-81.
57.Lagesen, K., Hallin, P., AndreasRodland, E., Staerfeldt, H.H., Rognes, T., and Ussery, D.W. (2007). RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35, 3100-3108.
58.Lai, E.M., Shih, H.W., Wen, S.R., Cheng, M.W., Hwang, H.H., and Chiu, S.H. (2006). Proteomic analysis of Agrobacterium tumefaciens response to the vir gene inducer acetosyringone. Proteomics 6, 4130-4136.
59.Lang, J., Vigouroux, A., Planamente, S., El Sahili, A., Blin, P., and Aumont-Nicaise, M. (2014) Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host. PLoS Pathog 10, e1004444.
60.Lehoczky, J. (1968). Spread of Agrobacterium tumefaciens in the vessels of the grapevine after natural infection. Phytopathology 63, 239-246.
61.Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25, 1754-1760.
62.Li, Y., Gronquist, M.R., Hao, G., Holden, M.R., Eberhard, A., Scott, R.A., Savka, M.A., Szegedi, E., Sule, S., and Burr, T.J. (2006). Chromosome and plasmid-encoded N-acyl-homoserine lactones produced by Agrobacterium vitis wild type and mutants that differ in their interactions with grape and tobacco. Physiol Mol Plant Pathol 67, 284-290.
63.Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079.
64.Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., Lin, D., Lu, L., and Law, M. (2012). Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012, 251364.
65.Li, L., Stoeckert, C.J., and Roos, D.S. (2003). OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res 13, 2178-2189.
66.Lo, W.S., Chen, L.L., Chung, W.C., Gasparich, G., and Kuo, C.H. (2013). Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. BMC Genomics 14, 22.
67.Loman, N.J., Constantinidou, C., Chan, J.Z., Halachev, M., Sergeant, M., Penn, C.W., Robinson, E.R., and Pallen, M.J. (2012). High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10, 599-606.
68.Lo, W.S., Gasparich, G.E., and Kuo, C.H. (2015). Found and lost: the fates of horizontally acquired genes in arthropod-symbiotic Spiroplasma. Genome Biol Evol 7, 2458-2472.
69.Lowe, T.M., and Eddy, S.R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25, 955-964.
70.Mandouri, H., Petit, A., Oger, P., and Dessaux, Y. (2002). Engineered rhizosphere: the trophic bias generated by opine-inducing plants is independent of the opine type, the soil origin, and the plant species. Appl Environ Microbiol 68, 2562-2566.
71.Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., Dewell, S.B., Du, L., Fierro, J.M., Gomes, X.V., Godwin, B.C., He, W., Helgesen, S., Ho, C.H., Irzyk, G.P., Jando, S.C., Alenquer, M.L., Jarvie, T.P., Jirage, K.B., Kim, J.B., Knight, J.R., Lanza, J.R., Leamon, J.H., Lefkowitz, S.M., Lei, M., Li, J., Lohman, K.L., Lu, H., Makhijani, V.B., McDade, K.E., McKenna, M.P., Myers, E.W., Nickerson, E., Nobile, J.R., Plant, R., Puc, B.P., Ronan, M.T., Roth, G.T., Sarkis, G.J., Simons, J.F., Simpson, J.W., Srinivasan, M., Tartaro, K.R., Tomasz, A., Vogt, K.A., Volkmer, G.A., Wang, S.H., Wang, Y., Weiner, M.P., Yu, P., Begley, R.F., and Rothberg, J.M. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380.
72.Miranda, A., Janssen, G., Hodges, L., Peralta, E.G., and Ream, W. (1992). Agrobacterium tumefaciens transfers extremely long T-DNAs by a unidirectional mechanism. J Bacteriol 174, 2288-2297.
73.Montoya, A.L., Chilton, M.D., Gordon, M.P., Sciaky, D., and Nester, E.W. (1977). Octopine and nopaline metabolism in Agrobacterium tumefaciens and crown gall tumor cells: role of plasmid genes. J Bacteriol 129, 101-107.
74.Montoya, A.L., Moore, L.W., Gordon, M.P., and Nester, E.W. (1978). Multiple genes coding for octopine-degrading enzymes in Agrobacterium. J Bacteriol 136, 909-915.
75.Moore, L. W., and G. Warren. (1979). Agrobacterium radiobacter strain K84 and biological control of crown gall. Annu Rev Phytopathol 17, 163-179.
76.Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., and Kanehisa, M. (2007). KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35, W182-W185.
77.Nester, E.W. (2014). Agrobacterium: nature’s genetic engineer. Font Plant Sci 5, 730
78.Newell, C.A. (2000). Plant transformation technology. Developments and applications. Mol Biotechnol 16, 53-65.
79.Ormeño-Orrillo, E., Servín-Garcidueñas, L.E., Rogel, M.A., González, V., Martínez-Romero, J., and Martínez-Romero, E. (2015). Taxonomy of Rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics. Syst Appl Microbiol 38, 287-291.
80.Otten, L., de Ruffray, P., Momol, E.A., Momol, M.T., and Burr, T.J. (1996). Phylogenetic relationships between Agrobacterium vitis isolates and their Ti plasmid. Mol Plant Microbe Interact 9, 782-786.
81.Pitzschke, A., and Hirt, H. (2010). New insights into an old story: Agrobacterium-induced tumour formation in plants by plant transformation. EMBO J 29, 1021-1032.
82.Reinhardt, J.A., Baltrus, D.A., Nishimura, M.T., Jeck, W.R., Jones, C.D., and Dangl, J.L. (2009). De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 19, 294-305.
83.Robinson, J.T., Thorvaldsdottir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G., and Mesirov, J.P. (2011). Integrative genomics viewer. Nat Biotech 29, 24-26.
84.Sanger, F., and Coulson, A.R. (1975). A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94, 441-448.
85.Shendure, J., and Ji, H. (2008). Next-generation DNA sequencing. Nat Biotechnol 26, 1135-1145.
86.Shendure, J., Mitra, R.D., Varma, C., and Church, G.M. (2004). Advanced sequencing technologies: Methods and goals. Nat Rev Genet 5, 335-344.
87.Shi, Y., Lee, L.Y., and Gelvin, S.B. (2014). Is VIP1 important for Agrobacterium-mediated transformation? Plant J 79, 848-860.
88.Singer, K., Shiboleth, Y.M., Li, J., and Tzfira, T. (2012). Formation of complex extrachromosomal T-DNA structures in Agrobacterium tumefaciens-infected plants. Plant Physiol 160, 511-522.
89.Slater, S.C., Goldman, B.S., Goodner, B., Setubal, J.C., Farrand, S.K., Nester, E.W., Burr, T.J., Banta, L., Dickerman, A.W., Paulsen, I., Otten, L., Suen, G., Welch, R., Almeida, N.F., Arnold, F., Burton, O.T., Du, Z., Ewing, A., Godsy, E., Heisel, S., Houmiel, K.L., Jhaveri, J., Lu, J., Miller, N.M., Norton, S., Chen, Q., Phoolcharoen, W., Ohlin, V., Ondrusek, D., Pride, N., Stricklin, S.L., Sun, J., Wheeler, C., Wilson, L., Zhu, H., and Wood, D.W. (2009). Genome sequences of three Agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol 191, 2501-2511.
90.Smith, E.F., and Townsend, C.O. (1907). A plant tumor of bacterial origin. Science 25, 671-673.
91.Srinivasan, R., and Gothandam, K.M. (2016). Synergistic action of D-glucose and acetosyringone on Agrobacterium strains for efficient Dunaliella transformation. PLoS One 11, e0158322.
92.Stachel, S.E., and Zambryski, P.C. (1989). Bacteria-yeast conjugation. Generic trans-kingdom sex? Nature 340, 190-191.
93.Staphorst, J.L., van Zyl, F.G.H., Strijdom, B.W., and Groenewold, Z.E. (1985). Agrocinproducing pathogenic and nonpathogenic biotype-3 strains of Agrobacterium tumefaciens active against biotype-3 pathogens. Curr Microbiol 12, 45-52.
94.Sule, S., Cursino, L., Zheng, D., Hoch, H.C., and Burr, T.J. (2009). Surface motility and associated surfactant production in Agrobacterium vitis. Lett Appl Microbiol 49, 596-601.
95.Suzuki, K., Hattori, Y., Uraji, M., Ohta, N., Iwata, K., Murata, K., Kato, A., and Yoshida, K. (2000). Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene 242, 331-336.
96.Swain, M.T., Tsai, I.J., Assefa, S.A., Newbold, C., Berriman, M., and Otto, T.D. (2012). A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc 7, 1260-1284.
97.Tatusov, R.L., Fedorova, N., Jackson, J., Jacobs, A., Kiryutin, B., Koonin, E., Krylov, D., Mazumder, R., Mekhedov, S., Nikolskaya, A., Rao. B.S., Smirnov, S., Sverdlov. A., Vasudevan, S., Wolf, Y., Yin, J., and Natale, D. (2003). The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41.
98.Tatusov, R.L., Koonin, E.V., and Lipman, D.J. (1997). A genomic perspective on protein families. Science. 278, 631-637.
99.Toro, N., Datta, A., Yanofsky, M., and Nester, E. (1988). Role of the overdrive sequence in T-DNA border cleavage in Agrobacterium. Proc Natl Acad Sci U S A 85, 8558-8562.
100.Treangen, T.J., and Salzberg, S.L. (2011). Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13, 36-46.
101.Trokter, M., Felisberto-Rodrigues, C., Christie, P. J., and Waksman, G. (2014). Recent advances in the structural and molecular biology of type IV secretion systems. Curr Opin Struct Biol 27, 16-23.
102.Tzfira, T., and Citovsky, V. (2006). Agrobacterium-mediated genetic transformation of plants; biology and biotechnology. Curr Opine Biotechnol 17, 147-154.
103.Van Dijk, E.L., Auger, H., Jaszczyszyn, Y., and Thermes, C. (2014). Ten years of next-generation sequencing technology. Trends Genet 30, 418-426.
104.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.
105.Wang, K. Stachel, S.E., Timmerman, B., Montagu, V.M., and Zambryski, P.C. (1987). Site-specific nick in the T-DNA border sequence as a result of Agrobacterium vir gene expression. Science 235, 587-591.
106.Yang, Y.L., Li, J.Y., Wang, J.H., and Wang, H.M. (2009). Mutations affecting chemotaxis of Agrobacterium vitis strain E26 also alter attachment to grapevine roots and biocontrol of crown gall disease. Plant Pathol 58, 594-605.
107.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.
108.Young, C., and Nester, E.W. (1988). Association of the VirD2 protein with the 5’ end of T-strand in Agrobacterium tumefaciens. J Baceriol 170, 3367-3374.
109.Zerbino, D.R., and Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18, 821-829.
110.Zheng D., and Burr T.J. (2013). An Sfp-type PPTase and associated polyketide and nonribosomal peptide synthases in Agrobacterium vitis are essential for induction of tobacco hypersensitive response and grape necrosis. Mol Plant Microbe Interact 26, 812-822.
111.Ziemienowicz, A. (2014). Agrobacterium-mediated plant transformation: Factors, applications and recent advances. Biocatal Agric Biotechnol 3, 95-102.
連結至畢業學校之論文網頁點我開啟連結
註: 此連結為研究生畢業學校所提供,不一定有電子全文可供下載,若連結有誤,請點選上方之〝勘誤回報〞功能,我們會盡快修正,謝謝!
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top