人類多核苷酸磷酸酶降解核醣核酸的結構研究

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研究生：	林佳良 Lin, Chia Liang
論文名稱：	人類多核苷酸磷酸酶降解核醣核酸的結構研究 Structural insights into RNA degradation by human polynucleotide phosphorylase
指導教授：	袁小琀 Yuan, Hanna S. 呂平江
口試委員:	袁小琀呂平江林淑端孫玉珠殷献生詹迺立
學位類別：	博士 Doctor
系所名稱：	生命科學暨醫學院 - 生物資訊與結構生物研究所 Institute of Bioinformatics and Structural Biology
論文出版年：	2012
畢業學年度：	100
語文別：	英文
論文頁數：	77
中文關鍵詞：	多核苷酸磷酸酶
外文關鍵詞：	polynucleotide phosphorylase
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多核苷酸磷酸酶 (polynucleotide phosphorylase, PNPase) 是一種在演化上具有高度保留性的酵素，存在於各種生物體內，包含細菌、植物到哺乳動物，主要參與在核醣核酸的代謝與降解。人類多核苷酸磷酸酶 (hPNPase) 不只負責降解特定的訊息核醣核酸 (mRNA) 和微核醣核酸 (miRNA)，也負責輸送核醣核酸進入粒線體內，因此它調控廣泛的生理功能，包含細胞衰老 (cellular senescence) 以及細胞內的動態平衡 (homeostasis)。人類多核苷酸磷酸酶可以和hSUV3解旋酶 (helicase) 形成複合體，hSUV3解旋酶能夠幫助人類多核苷酸磷酸酶降解含有二級結構的核醣核酸。然而人類多核苷酸磷酸酶如何利用它的各種功能區和核醣核酸進行結合與降解，以及hSUV3解旋酶如何和人類多核苷酸磷酸酶進行結合，並且幫助其降解核醣核酸的詳細機制依然不清楚。
在本論文中我們解析出切除S1功能區之人類多核苷酸磷酸酶和hSUV3解旋酶的晶體結構，其解析度分別為為2.1 Å及3.3 Å。人類多核苷酸磷酸酶擁有一個 α-helical、一個KH、一個S1以及兩個RNase PH功能區 (domain)，根據先前的研究，KH和S1功能區是參與核醣核酸的結合，而RNase PH功能區則是活性中心負責核醣核酸的降解。我們測定的晶體結構顯示三聚體的人類多核苷酸磷酸酶具有一個由六個RNase PH功能區所形成的類六環結構，其頂端則被三個KH功能區所形成的KH孔洞所覆蓋。我們的生化以及點突變實驗證明對於人類多核苷酸磷酸酶而言，S1功能區並不是和核醣核酸結合的關鍵區域，反而KH功能區上的保留性GXXG模體 (motif) 是直接參與核醣核酸的結合。我們的結構研究提供對於人類多核苷酸磷酸酶功能的新見解，其利用KH功能區所形成的KH孔洞來抓住具有較長3'端的核醣核酸，再將它傳送通過由RNase PH功能區形成的通道，最後進行降解的步驟。另一方面，具有較短3'端且有二級結構的核醣核酸則可以被人類多核苷酸磷酸酶輸送而不會被降解。
我們也發現人類多核苷酸磷酸酶能夠和hSUV3解旋酶形成3:3或3:2的複合體。hSUV3解旋酶的晶體結構顯示出其具有四個功能區，分別是N端功能區、兩個RecA-like功能區以及C端功能區。再者C端功能區不只參與核酸的結合，也參與了人類多核苷酸磷酸酶的結合。因此hSUV3解旋酶的晶體結構提供了我們研究其和人類多核苷酸磷酸酶之作用的起點。總和來說，此研究增進了我們對人類多核苷酸磷酸酶在降解和輸送核醣核酸的分子結構和機制上的瞭解。

PNPase (polynucleotide phosphorylase) is an evolutionarily conserved enzyme that participates in RNA processing and degradation in almost all species from bacteria to plants and higher mammals. Human PNPase (hPNPase) not only degrades specific mRNA and miRNA, but also imports RNA into mitochondria, and thus it regulates diverse physiological processes, including cellular senescence and homeostasis. It has been shown that hPNPase forms a complex with the helicase hSUV3 which promotes the activity of hPNPase in the digestion of structural RNA. However, how hPNPase binds and cleaves RNA using its various domains, as well as how hSUV3 interacts and works with hPNPase in RNA degradation are mostly unknown.
Here we determined the crystal structures of an S1 domain-truncated hPNPase and hSUV3 at a resolution of 2.1 Å and 3.3 Å, respectively. hPNPase contains one α-helical, one KH, one S1, and two RNase PH domains. Based on previous studies, the KH and S1 domain are involved in RNA binding and RNase PH domain is the active center for RNA degradation. We showed here that the trimeric hPNPase has a hexameric ring-like structure formed by six RNase PH domains, capped with a trimeric KH pore. Our biochemical and mutagenesis studies suggest that the S1 domain is not critical for RNA binding, and conversely, that the conserved GXXG motif in the KH domain directly participates in RNA binding in hPNPase. Our studies thus provide structural and functional insights into hPNPase, which uses a KH pore to trap a long RNA 3' tail that is further delivered into an RNase PH channel for the degradation process. Structural RNA with short 3' tails are, on the other hand, transported but not digested by hPNPase.
Moreover, we found that hPNPase forms a 3:3 and 3:2 complex with hSUV3. The crystal structure of hSUV3 reveals a four domain structure, the N-terminal domain, two RecA-like domains, and the C-terminal domain which is not only involved in nucleic acids binding, but also in interacting with hPNPase. The crystal structure of hSUV3 thus offers a starting point for the future study of its interactions with hPNPase. In summary, our studies provide structural insights for the role of hPNPase in RNA degradation and transportation.

CONTENTS
CONTENTS                                               I
CONTENT OF TABLES                                   III
CONTENT OF FIGURES                                  IV
論文摘要    1
ABSTRACT    3
1. INTRODUCTION    5
1.1 PNPase in bacteria and plant chloroplasts is involved in mRNA   degradation    5
1.2 PNPase in mammals is a multifunctional enzyme    7
1.3 Structure of bacterial PNPase    8
1.4 Eukaryotic exosomes share similar functions to bacterial PNPase    9
1.5 Structure of exosome is similar to PNPase    10
1.6 PNPase forms complex with helicase in the degradation of structural    RNA    12
1.7 Exosomes work with helicase in the degradation of structural RNA    13
1.8 Specific aims    14
2. MATERIALS AND METHODS    16
2.1 Cloning, protein expression, and purification of hPNPase    16
2.2 Cloning, protein expression, and purification of hSUV3    17
2.3 Nuclease activity assays    17
2.4 RNA-binding assays    18
2.5 Crystallization and crystal structure determination of ∆S1 hPNPase    18
2.6 Crystallization and crystal structure determination of hSUV3    19
2.7 Complex formation of hPNPase and hSUV3    20
3. RESULTS    21
3.1 hPNPase is a trimeric exoribonuclease digesting ssRNA up to ~4  nucleotides    21
3.2 Crystal structure of ∆S1 hPNPase    21
3.3 A KH pore is formed in hPNPase    23
3.4 The C-terminal S1 domain of hPNPase is not critical for RNA binding    and cleavage    24
3.5 hPNPase digests the long 3' tail of structured RNA    25
3.6 The KH pore is responsible for RNA binding in hPNPase    26
3.7 hPNPase forms a 3:3 and 3:2 complex with hSUV3    27
3.8 Crystal structure of hSUV3    27
4. DISCUSSION    30
4.1 KH pore in PNPase versus S1 pore in exosomes    30
4.2 A constricted channel in hPNPase for efficient RNA binding    31
4.3 RNA degradation or translocation by hPNPase    32
5. REFERENCES    34

CONTENT OF TABLES
Table 1. X-ray data collection and refinement statistics for ∆S1 hPNPase    45
Table 2. X-ray data collection and refinement statistics for hSUV3    46

CONTENT OF FIGURES
Figure 1-1. PNPase acts as a 3'-to-5' exoribonuclease.    47
Figure 1-2. Messanger RNA turnover in E. coli.    48
Figure 1-3. A model of the structure of the RNA degradosome.    49
Figure 1-4. Schematic representation of the diversified functions of hPNPase.    50
Figure 1-5. Domain structures of bacterial and eukaryotic PNPases.    51
Figure 1-6. Crystal structure of S. antibioticus PNPase.    52
Figure 1-7. Crystal structure of E. coli PNPase.    53
Figure 1-8. Diverse functions of the eukaryotic exosome    54
Figure 1-9. Architectures and structures of PNPase and exosome complex    55
Figure 3-1. Recombinant human PNPase is a trimeric protein.    57
Figure 3-2. Recombinant human PNPase is a functional phosphorylase   capable of digesting RNA.    58
Figure 3-3. Crystals of human PNPase    59
Figure 3-4. Crystal packing of ∆ S1 hPNPase.    60
Figure 3-5. Crystal structure of ∆S1 hPNPase.    61
Figure 3-6. The citrate ions bind at the active site in the second RNase PH domain in hPNPase.    62
Figure 3-7. The electrostatic surface potential of the trimeric hPNPase reveals  a basic central channel for RNA binding and degradation.    63
Figure 3-8. Superimposition of the structure of three different PNPases.    64
Figure 3-9. Structure model of full-length hPNPase.    65
Figure 3-10. Comparison of the S1 pore in exosomes and the KH pore in hPNPase.    66
Figure 3-11. Structural model of RNA bound at the KH domain of hPNPase.    67
Figure 3-12. Structural model of RNA bound at the KH pore of hPNPase.    68
Figure 3-13. RNA binding and cleavage assays for full-length (FL) and ∆S1 hPNPase.    69
Figure 3-14. hPNPase can digest the long 3' overhang of a structured RNA    up to ~12 nucleotides.    70
Figure 3-15. Structure-based sequence alignment of PNPase and Rrp40 and Rrp4 exosome subunits.    71
Figure 3-16. The GXXG motif in the KH domain of PNPase participates in  RNA binding.    72
Figure 3-17. hPNPase trimer and hSUV3 trimer form heterohexamers in high-salt condition.    73
Figure 3-18. hPNPase trimer and hSUV3 dimer form heteropentamers in low-salt condition.    74
Figure 4-1. The RNA-binding central channel in PNPase and exosomes.    76
Figure 4-2. Structural model of hPNPase bound with a structured RNA.    77

                                

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