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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 袁小琀 | |
| dc.contributor.author | Che-Chuan Yang | en |
| dc.contributor.author | 楊哲權 | zh_TW |
| dc.date.accessioned | 2021-05-20T21:47:22Z | - |
| dc.date.available | 2012-09-09 | |
| dc.date.available | 2021-05-20T21:47:22Z | - |
| dc.date.copyright | 2010-09-09 | |
| dc.date.issued | 2010 | |
| dc.date.submitted | 2010-08-04 | |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/10656 | - |
| dc.description.abstract | Rrp46 原本是真核生物外切體(exosme)的組成蛋白之ㄧ；外切體複合物(exosome complex) 是一參與核醣核酸分解的重要的核醣核酸外切酶(exoribonuclease)，可從單股的核醣核酸之3'端往5'端逐一進行分解作用，同時調控細胞內各種核醣核酸的生成與降解，此功能維繫了細胞活性的正常。因此，Rrp46 也是組成外切體複合物及維持細胞正常生長所必需。
在蛋白質分類上，Rrp46 屬於RNase PH 外切酶家族。此類核醣核酸分解酵素(RNase)，廣泛保留在從原核生物(prokaryotes)到真核生物(eukaryotes)的各類生物體中，包括細菌、古代菌(archaea)、酵母菌，乃至於植物與人類。在線蟲(C.elegans)當中，CRN-5 是Rrp46 的同源蛋白質(homologue)；被發現可能另外當作細胞凋亡(apoptosis)時，參與分解染色體去氧核醣核酸(chromosomal DNA)的新功能。本篇論文即結合了生化分析、生物物理及蛋白質晶體結構等方法，來探討Rrp46 及CRN-5 降解DNA 及RNA 時的生化特性及生理功能，為此類RNase PH外切酶的新功能提出更有利的佐証。 在此篇論文中，我們提出了CRN-5 以及稻米Rrp46 (oRrp46)的蛋白質晶體結構，它們的最高解析度分別是3.9 Å 及2.0 Å。經由分析三個不同物種(人類、稻米及線蟲)的Rrp46 重組蛋白質發現，它們以二具體(homodimer)的形式存在於體外。除了已知與外切體複合物結合外，我們也首次觀察到此二具體形式的Rrp46亦同時存在人類與稻米細胞環境中。由生化生析的結果，發現稻米二具體oRrp46重組蛋白質除了具有磷酸分解(phosphorolysis)RNA 的活性外，更首次發現能水解(hydrolysis)DNA 的生化活性；人類的hRrp46 及線蟲的CRN-5 蛋白則只具有結合DNA，而不具分解DNA 的活性。藉由蛋白質晶體結構與突變技術，我們分析稻米oRrp46 活性區域以及受質結合區裡的重要胺基酸殘基所扮演的角色。發現E160Q 的突變會明顯抑制稻米oRrp46 的DNA 水解活性，對分解RNA 的影響則有限；但是K75E/Q76E 的突變，則同時抑制了稻米oRrp46 對DNA 及RNA 的結合與分解。CRN-5 本身雖沒有DNA 分解活性，但經實驗確認，它能與另一個細胞凋亡核酸水解酶 (apoptotic nuclease) CRN-4 有直接的結合作用，並且增強CRN-4 的DNA 水解活性。推測了這兩個蛋白質可能在細胞凋亡時分解DNA 有協同作用。 綜合以上強力的研究證據，我們推測Rrp46 蛋白質會穩定形成外切體複合物以外的二具體；此二具體可能依照不同的物種，或直接扮演有活性的組成份，或扮演結構性組成份，參與細胞凋亡時分解DNA 的重要生理機制。 | zh_TW |
| dc.description.abstract | Rrp46 was first identified as a protein component of the eukaryotic exosome, a protein complex involved in 3' processing of RNA during RNA turnover and surveillance. The C. elegans Rrp46 homologue, CRN-5, was subsequently characterized as a cell death-related nuclease, participating in DNA fragmentation during apoptosis.
Rrp46/CRN-5 has a conserved RNase PH domain, usually identified in 3'-to-5' exoribonucleases. To determine how an RNase PH protein could bind and digest DNA during apoptosis, we combined biochemical, biophysical and crystal structural approaches to study Rrp46/CRN-5 from various specises, including human, rice and C. elegans. We have determined the crystal structures of CRN-5 and rice Rrp46 (oRrp46) at a resolution of 3.9 Å and 2.0 Å, respectively. We found that recombinant human Rrp46 (hRrp46), oRrp46, and CRN-5 are homodimers, and that endogenous hRrp46 and oRrp46 also form homodimers in a cellular environment, in addition to their association with a protein complex. Dimeric oRrp46 had both phosphorolytic RNase and hydrolytic DNase activities, whereas hRrp46 and CRN-5 bound to DNA without detectable nuclease activity. Site-directed mutagenesis in oRrp46 abolished either its DNase (E160Q) or RNase (K75E/Q76E) activities, confirming the critical importance of these residues in catalysis or substrate binding. Moreover, CRN-5 directly interacted with the apoptotic nuclease CRN-4, and enhanced the DNase activity of CRN-4, suggesting that CRN-5 cooperates with CRN-4 in apoptotic DNA degradation. Taken together all these results strongly suggest that Rrp46 forms a homodimer separately from exosome complexes and, depending on species, is either a structural or catalytic component of the machinery that cleaves DNA during apoptosis. | en |
| dc.description.provenance | Made available in DSpace on 2021-05-20T21:47:22Z (GMT). No. of bitstreams: 1 ntu-99-D93442002-1.pdf: 9383501 bytes, checksum: 558cad553626a217f2adfb4f3bec962a (MD5) Previous issue date: 2010 | en |
| dc.description.tableofcontents | CONTENTS..................................................................................................................i
CONTENT OF TABLES............................................................................................iv CONTENT OF FIGURES...........................................................................................v 中文摘要.....................................................................................................................vii 英文摘要ABSTRACT.................................................................................................ix 1. INTRODUCTION................................................................................................1 1.1 Apoptotic DNA fragmentation by nucleases.................................................1 1.2 DFF40/CAD and Dicer are caspase-activated DNases in mammals and C. elegans, respectively.................................................................................2 1.3 Endonuclease G is a mitochondrial apoptotic nuclease.................................3 1.4 DNase II digestes apoptotic DNA fragments into nucleotides after phagocyte engulfment....................................................................................4 1.5 Cell death-related nucleases in C. elegans are also involved in apoptotic DNA degradation including CRN-5, a homologue of human hRrp46..........4 1.6 CRN-5 is an RNase PH protein homolougous to human hRrp46 protein.....6 1.7 Rrp46 is a component of exosome complex involved in RNA processing, quality control and turnover...........................................................................7 1.8 The structures of RNase PH proteins and exosome complex........................9 1.9 Recombinant human and yeast exosomes are inactive in phosphorolysis...10 1.10 Cofactors regulate and activate exosome’s activity.....................................11 1.11 hRrp46 is a broadly immunogenic antigen, which is overexpressed in tumor cells..............................................................................................................13 1.12 Auto-antibodies against hRrp46 are also found in patients with autoimmune diseases........................................................................................................13 1.13 Specific aims................................................................................................14 2 MATERIALS AND METHODS........................................................................16 2.1 Cloning, protein expression, and purification..............................................16 2.2 Dynamics light scattering (DLS) and analytical ultracentrifugation (AUC) .....................................................................................................................17 2.3 Fractionation of cell extracts and western blotting......................................18 2.4 DNA-binding and DNase activity assays....................................................18 2.5 RNA-binding and RNase activity assays.....................................................19 2.6 Crystallization and X-ray diffraction data collection..................................20 2.7 Structure determination and refinement......................................................21 2.8 His-tag pull-down assays.............................................................................22 3 RESULTS.............................................................................................................23 3.1 C. elegans’ CRN-5 is a homologue to human Rrp46..................................23 3.2 Overexpression and purification of CRN-5 and Rrp46 proteins.................23 3.3 Recombinant purified CRN-5/Rrp46 proteins form stable homodimer in vitro..............................................................................................................24 3.4 Endogenous Rrp46 forms a separated dimer in addition to associating with a protein complex in vivo.............................................................................25 3.5 CRN-5 and Rrp46 are DNA binding proteins, but only rice Rrp46 is a RNA binding protein.............................................................................................26 3.6 Dimeric rice oRrp46 shows metal-dependent DNase activity.....................26 3.7 Rice oRrp46 shows typical RNase PH activity...........................................27 3.8 Crystallization of CRN-5 and rice oRrp46 proteins....................................28 3.9 Overall structure of dimeric CRN-5 and momomeric rice oRrp46 proteins.........................................................................................................28 3.10 A metal binding residue is conserved in RNase PH family protein and critical to DNase activity of rice oRrp46.....................................................30 3.11 Substrate binding residues are variable in RNase PH family protein and important to both RNase and DNase activity of rice oRrp46......................31 3.12 CRN-5 interacts with another apoptotic nuclease CRN-4 and enhances CRN-4’s DNase activity..............................................................................32 4 DISCUSSIONS....................................................................................................34 4.1 RNA binding residues are critical for the enzyme activity of RNase PH proteins.........................................................................................................34 4.2 Dual roles of Rrp46 in RNA turnover and DNA degradation......................35 4.3 C. elegans uses functional-known proteins to accomplish apoptotic DNA degradation...................................................................................................38 5 FUTURE WORKS..............................................................................................38 5.1 The DNA hydrolysis mechanism of oRrp46................................................38 5.2 Critical roles of substrate binding residues in RNase PH proteins..............39 5.3 Cooperation between CRN proteins............................................................40 REFERENCES...........................................................................................................74 | |
| dc.language.iso | en | |
| dc.title | CRN-5與Rrp46參與核酸降解的結構及功能性研究 | zh_TW |
| dc.title | Structural and Functional Studies of CRN-5 and Rrp46 in Apoptotic DNA Degradation | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 98-2 | |
| dc.description.degree | 博士 | |
| dc.contributor.oralexamcommittee | 吳惠南,林淑端,梁博煌,呂平江,蕭傳鐙 | |
| dc.subject.keyword | 核醣核酸之轉化,去氧核醣核酸之降解,晶體結構,去氧核醣核酸分解酵素 PH,核醣核酸分解酵素,去氧核醣核酸分解酵素,細胞凋亡核酸水解酵素, | zh_TW |
| dc.subject.keyword | RNA turnover,DNA degradation,Crystal Structure,RNase PH,RNase,DNase,apoptotic nuclease, | en |
| dc.relation.page | 85 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2010-08-05 | |
| dc.contributor.author-college | 醫學院 | zh_TW |
| dc.contributor.author-dept | 生物化學暨分子生物學研究所 | zh_TW |
| 顯示於系所單位： | 生物化學暨分子生物學科研究所 | |
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