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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 沈湯龍 | |
| dc.contributor.author | Ru-Ying Fang | en |
| dc.contributor.author | 方如瑩 | zh_TW |
| dc.date.accessioned | 2021-06-17T08:08:57Z | - |
| dc.date.available | 2029-12-31 | |
| dc.date.copyright | 2019-08-29 | |
| dc.date.issued | 2019 | |
| dc.date.submitted | 2019-08-16 | |
| dc.identifier.citation | Adkar-Purushothama, C., Brosseau, C., Giguère, T., Sano, T., Moffett, P., and Perreault, P. 2015. Small RNA derived from the virulence modulating region of the Potato spindle tuber viroid silences callose synthase senes of tomato plants. Plant Cell 27:2178-2194.
Alazem, M., He, M., H., Moffett, P., and Lin, N. S. 2017. Abscisic acid induces resistance against Bamboo mosaic virus through Argonaute 2 and 3. Plant Physiol. 174:339-355. Andika, I., Maruyama, K., Sun, L., Kondo, H., Tamada, T., and Suzuki, N. 2015. Different Dicer-like protein components required for intracellular and systemic antiviral silencing in Arabidopsis thaliana. Plant Signal Behav 10:e1039214. Bai, M., Yang, G., Chen, W., Mao, Z., Kang, H., Chen, G., Yang, Y., and Xie, B. 2012. Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNApolymerase gene families and their expression analyses in response to viralinfection and abiotic stresses in Solanum lycopersicum. Gene 501:52-62. Baumberger N., B. D. 2005. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci U S A. 106:11928-11933. Carthew, R., and Sontheimer, E. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell 136:642-655. Chen, X. 2009. Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21-44. Di Serio, F., Flores, R., Verhoeven, J., Li, S., Pallás, V., Randle, J., Sano, T., Vidalakis, G., and Owens, R. 2014. Current status of viroid taxonomy. Arch Viro 159:3467-3478. Ding, B. 2009. The biology of viroid-host interactions. Annu Rev Phytopathol 47:105-113. Duran-Vila, N. 2019. Viroids as companions of a professional career. Viruses 11:245. Duranvila, N., Roistacher, C. N., Riverabustamante, R., and Semancik, J. S. 1988. A definition of citrus viroid groups and their relationship to the exocortis disease. J. Gen. Virol 69:3069–3080. Flores, R., Hernandez, C., de Alba AE, M., Daròs, J. A., and and Di Serio, F. 2005. Viroids and viroid-host interactions. Annu Rev Phytopathol 43:117-139. Flores, R., Minoia, S., Carbonell, A., Gisel, A., Delgado, S., López-Carrasco, A., Navarro, B., and Di Serio, F. 2015. Viroids, the simplest RNA replicons: How they manipulate their hosts for being propagated and how their hosts react for containing the infection. Virus Res 2:136-145. Hadidi, A., Flores, R., Candresse, T., and Barba, M. 2016. Next-generation sequencing and genome editing in plant virology. Front Microbiol 7:1325. Itaya, A., Folimonov, A., Matsuda, Y., Nelson, R., and Ding, B. 2001. Potato spindle tuber viroid as inducer of RNA silencing in infected tomato. Mol Plant Microbe Interact 14:1332-1334. Itaya, A., Zhong, X., Bundschuh, R., Qi, Y., Wang, Y., Takeda, R., Harris, A., Molina, C., Nelson, R., and Ding, B. 2007. A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation. J Virol 81:2980-2994. Keese, P., and Symons, R. 1985. Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc Natl Acad Sci U S A. 82:4582-4586. Mallory, A., and Vaucheret, H. 2010. Form, function, and regulation of ARGONAUTE proteins. Plant Cell 22:3879-3889. Markarian, N., Li, H., Ding, S., and Semancik, J. 2004. RNA silencing as related to viroid induced symptom expression. Arch Virol 149:397-406. Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., Wu, L., Li, S., Zhou, H., Long, C., Chen, S., Hannon, G., and Qi, Y. 2008. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell 133:116-127. Minoia, S., Carbonell, A., Di Serio, F., Gisel, A., Carrington, J., Navarro, B., and Flores, R. 2014. Specific Argonautes selectively bind small RNAs derived from Potato spindle tuber viroid and attenuate viroid accumulation In vivo. J Virol 88:11933-11945. Mishra, M. D., Hammond, R. W., Owens, R. A., Smith, D. R., and Diener, T. O. 1991. Indian bunchy top disease of tomato plants is caused by a distinct strain of citrus exocortis viroid. J. Gen. Virol:1781. Molnár, A., Csorba, T., Lakatos, L., Várallyay, E., Lacomme, C., and Burgyán, J. 2005. Plant virus-derived small interfering RNAs originate predominantly from highly structured single-stranded viral RNAs. J Virol 79:7812-7818. Navarro, B., Pantaleo, V., Gisel, A., Moxon, S., Dalmay, T., Bisztray, G., Di Serio, F., and Burgyan, J. 2009. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PloS one 4:e7686. Papaefthimiou, I., Hamilton, A., Denti, M., Baulcombe, D., Tsagris, M., and Tabler, M. 2001. Replicating potato spindle tuber viroid RNA is accompanied by short RNA fragments that are characteristic of post-transcriptional gene silencing. Nucleic Acids Res 29:2395-2400. Roistacher, C. N., Calavan, E. C., Blue, R. L., Navarro, L., and Gonzales, R. 1977. A new more sensitive citron indicator for detection of mild isolates of Citrus exocortis viroid (CEV). Plant Dis. Rep 61:135–139. Serra, P., Messmer, A., Sanderson, D., James, D., and Flores, R. 2018. Apple hammerhead viroid-like RNA is a bona fide viroid: Autonomous replication and structural features support its inclusion as a new member in the genus Pelamoviroid. Virus Res 249:8-15. Szittya, G., Moxon, S., Pantaleo, V., Toth, G., Rusholme Pilcher, R., Moulton, V., Burgyan, J., and Dalmay, T. 2010. Structural and functional analysis of viral siRNAs. PLoS Pathog 6:e1000838. Verniere, C., Perrier, X., Dubois, C., Dubois, A., Botella, L., Chabrier, C., Bove, J. M., and and Vila, N. D. 2006. Interactions between citrus viroids affect symptom expression and field performance of clementine trees grafted on trifoliate orange. Phytopathology 96:356-368. Wang, M., Bian, X., Wu, L., Liu, L., Smith, N., Isenegger, D., Wu, R., Masuta, C., Vance, V., Watson, J., Rezaian, A., Dennis, E., and Waterhouse, P. 2004. On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proc Natl Acad Sci U S A. 101:3275-3280. Wang, X., Zhou, C., Tang, K., Zhou, Y., and and Li, Z. 2009. A rapid one-step multiplex RT-PCR assay for the simultaneous detection of five citrus viroids in China. European Journal of Plant Pathology 124:175-180. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/73731 | - |
| dc.description.abstract | 類病毒為裸露、單股的環狀RNA分子，大小約為246至433個核苷酸，且不轉譯任何蛋白質。類病毒影響病徵產生之機制尚未明瞭。研究顯示，21至24個核苷酸大小的類病毒小片段RNA (viroid-derived small RNA, vd-sRNA) 會以寄主的messenger RNA (mRNA) 作為目標並切割，引起寄主mRNA的RNA靜默 (RNA silencing)。有一假說推定：vd-sRNA會抑制寄主mRNA的表現，進而產生病徵。柑橘鱗砧類病毒 (Citrus exocortis viroid, CEVd) 為主要危害柑橘的類病毒，其亦可感染茄科作物番茄。CEVd於番茄上可造成植株矮化、葉片黃化、扭曲無法伸展及向下捲曲之病徵。本研究自行製備番茄 (Solanum lycopersicum) Argonaute蛋白1a (SlAGO1a) 及番茄Argonaute蛋白1b (SlAGO1b) 之抗體，並自健康及感染CEVd之番茄植株進行SlAGO1a之免疫沈澱 (immunoprecipitation, IP)。於IP產物中萃取RNA，並與健康及感染CEVd之總量RNA (total RNA) 一同進行小RNA次世代定序，藉以得知CEVd是否會產生vd-sRNA及vd-sRNA是否會進入AGO蛋白中進行RNA靜默。我們於感病植株之total RNA及SlAGO1a-IP產物中皆發現序列與CEVd基因組相同的小片段RNA。SlAGO1a-IP中發現22,216種小片段RNA共讀取4,303,121次 (reads)，其中有950種，409,550讀取次數的小片段來自CEVd的基因組。比較total RNA與SlAGO1a-IP之vd-sRNA可發現兩者熱點分佈並不完全相同。此外，以psRNATarget軟體預測，950種的vd-sRNA可產生1,540個候選標靶基因。降解組定序 (Degradome sequencing) 將可證明這些候選標靶基因是否確實被vd-sRNA切割，而體外RNA誘導沈默複合體 (RNA-induced silencing complex, RISC) 活性分析將可為vd-sRNA調控寄主基因表現提供直接的證據。 | zh_TW |
| dc.description.abstract | Viroids are a 246- to 433-nts of non-coding, naked, single-stranded circular RNA. How viroid causes symptoms that remains unclear. A hypothesis proposes viroid-derived small RNAs (vd-sRNAs) (21- to 24-nts in length) might target and cleavage host mRNAs, resulting in gene silencing and leading to symptom development. CEVd-infected tomatoes show stunting, epinasty, and leaf distortion symptoms. We generated antibodies of tomato Solanum lycopersicum Argonaute 1a (SlAGO1a) and SlAGO1b. We performed immunoprecipitation with SlAGO1a IgG from CEVd-infected tomato plants and identified vd-sRNAs by small RNA deep sequencing. There are 4,303,121 reads in 22,216 species of small RNAs were found in SlAGO1a-IP profile, whereas 409,550 reads in 950 species belong to vd-sRNAs of CEVd. The hot-spot distributions of the vd-sRNAs between total small RNA and SlAGO1a-IP indicated that the critical vd-sRNAs which were loaded into SlAGO1a have different hot-spots. Based on the target prediction, 1,540 mRNAs of tomato plants are predicted by 950 species of vd-sRNAs. We are performing the degradome assay to evaluate these candidate targets and the in vitro RISC activity assay will perform with these IP SlAGO1s to confirm the vd-sRNA-mediated host gene cleavage. Uncovering predicted target mRNAs and the interaction between small RNAs will provide more insight information on the pathogenic CEVd-derived small RNAs. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-17T08:08:57Z (GMT). No. of bitstreams: 1 ntu-108-R05633024-1.pdf: 2645298 bytes, checksum: 48fe5600075573912d2d0046641d0d0a (MD5) Previous issue date: 2019 | en |
| dc.description.tableofcontents | 中文摘要 II
Abstract III Content V List of Figures VIII Table of contents XI Introduction 1 Viroid 1 RNA silencing and viroid pathogenesis 2 Deep sequencing for virology and AGOs biology study 4 Materials and Methods 6 Plant materials, growth conditions and viroid source 6 In vitro transcription and inoculation 6 Total RNA extraction and cDNA synthesis 7 RT-PCR detection 7 SlAGO1a and SlAGO1b recombinant protein purification and antibody generation 8 SlAGO1a and SlAGO1b immunoprecipitation (IP) and small RNA deep sequencing 9 High-throughput sequencing of small RNA and data analysis 10 RNA Induced Silencing Complex (RISC) activity assay 11 Results 12 The symptoms of CEVd-infected tomato plants 12 Selection of N-terminal SlAGO1a and SlAGO1b for recombinant protein production 13 Recombinant protein purification 13 Evaluation of SlAGO1a IgG IP efficiency and Identification of SlAGO1a-derived small RNAs 14 The vd-sRNA distribution on CEVd genomic RNA 16 The first-nt of vd-sRNAs 17 Identification of target genes of vd-sRNA 18 The in vitro AtAGO1- and SlAGO1a-mediated RISC activity assay 19 Discussion 21 SlAGO1a antibody performing AGO1-containing small RNA identification 21 SlAGO1a-IP profile enhances target gene prediction 22 Application of in vitro RISC activity assay 23 Conclusion 24 Reference 25 Figure and tables 31 List of Figures Figure 1. Symptoms of CEVd-infected tomato. 32 Figure 2. The gene structure and alignment of AGO amino acid sequences.. 33 Figure 3. N terminals of SlAGO1a and SlAGO1b recombinant protein purification and antibody generation. 34 Figure 4. Evaluation of SlAGO1a IgG IP efficiency.. 35 Figure 5. The hotspots of distribution of vd-sRNAs on CEVd genomic RNA.. 37 Figure 6. The statistic of the first-nt of vd-sRNAs. 38 Figure 7. The in vitro AtAGO1- and SlAGO1a-mediated RISC activity assay. 39 Table of contents Table 1. The small RNAs deep sequencing results from healthy and CEVd-infected plants. 28 Table 2. The list of predicted vd-sRNA target genes. 29 Table 3. The vd-siRNAs target gene silencing relative genes. 31 Supplementary Table 1. The list for SlAGO1a-IP products that identified by LC-MS/MS. 40 Supplementary Table 2. The list of predicted vd-sRNA target genes that the counts are over than 5000. 41 | |
| dc.language.iso | en | |
| dc.subject | Argonaute蛋白 | zh_TW |
| dc.subject | RNA靜默 | zh_TW |
| dc.subject | 類病毒病程發展 | zh_TW |
| dc.subject | 柑橘鱗砧類病毒 | zh_TW |
| dc.subject | 類病毒小片段RNA | zh_TW |
| dc.subject | Citrus exocortis viroid (CEVd) | en |
| dc.subject | viroid pathogenesis | en |
| dc.subject | RNA silencing | en |
| dc.subject | Argonaute (AGO) | en |
| dc.subject | viroid-derived small RNA (vd-sRNA) | en |
| dc.title | 柑橘鱗砧類病毒小片段RNA於番茄上病程進展和機制探討 | zh_TW |
| dc.title | Pathogenic effects and mechanisms of CEVd-derived small RNAs on Citrus exocortis viroid infected tomato plants | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 107-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 張雅君,洪挺軒,林詩舜,林崇熙 | |
| dc.subject.keyword | 柑橘鱗砧類病毒,類病毒病程發展,RNA靜默,Argonaute蛋白,類病毒小片段RNA, | zh_TW |
| dc.subject.keyword | Citrus exocortis viroid (CEVd),viroid pathogenesis,RNA silencing,Argonaute (AGO),viroid-derived small RNA (vd-sRNA), | en |
| dc.relation.page | 47 | |
| dc.identifier.doi | 10.6342/NTU201903803 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2019-08-17 | |
| 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 |
| 顯示於系所單位： | 植物病理與微生物學系 | |
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