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研究生：	陳乃齊 Chen, Nai-Chi
論文名稱：	石斑魚神經壞死病毒之晶體結構與功能研究 Structural and functional studies of the betanodavirus grouper nervous necrosis virus
指導教授：	陳俊榮 Chen, Chun-Jung 陳宗嶽 Chen, Tzong-Yueh
學位類別：	博士 Doctor
系所名稱：	生物科學與科技學院 - 生物科技研究所 Institute of Biotechnology
論文出版年：	2016
畢業學年度：	104
語文別：	英文
論文頁數：	114
中文關鍵詞：	野田病毒科、神經壞死病毒、鈣離子結合突出單元
外文關鍵詞：	Nodaviridae, nervous necrosis virus, calcium-associated protrusion domain
相關次數：	點閱：154 下載：7
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臺灣為海洋性島嶼，同時也是現今國際遠洋漁業和水產養殖之生產國。有關野田病毒科（Nodaviridae）的兩個主要屬為alphanodaviruses及betanodaviruses。病毒性神經壞死症（viral nervous necrosis, VNN）由betanodaviruses屬中的神經壞死病毒（nervous necrosis virus, NNV）所引起，主要造成魚苗及幼魚產生病毒性腦炎與視網膜病變且伴隨極高的死亡率。我們利用全始演算法（ab initio method）搭配非結晶學對稱性（non-crystallographic symmetry averaging）完成T=3石斑魚神經壞死累病毒（grouper necrosis virus-like particle, GNNV-LP）結構解析，其解析度為3.6埃（Å）。另外，兩種T=1石斑魚神經壞死次病毒顆粒（subviral particle），包括解析度為3.1埃之突出單元剔除型（delta-P-domain mutant）與N端多精胺酸序列剔除型（N-ARM deletion mutant）也完成其結構分析。除此之外，超高解析度1.2埃之鈣離子結合突出單元（truncated P-domain）呈現石斑魚神經壞死病毒之突出單元具有特異性之DxD序列與鈣金屬離子進行鍵結並且於病毒外殼組裝期間促進三聚體外鞘蛋白之形成且扮演重要角色於專一性宿主感染。經由上述結構及功能性分析，石斑魚神經壞死病毒之突出單元於病毒外鞘組裝及宿主感染皆扮演重要角色。

關鍵字: 野田病毒科、神經壞死病毒、鈣離子結合突出單元。

Structural and functional studies of the betanodavirus grouper nervous necrosis virus

Nai-Chi Chen
Chun-Jung Chen and Tzong-Yueh Chen
Institute of Biotechnology
College of Bioscience and Biotechnology

SUMMARY

Betanodaviruses belong to the family Nodaviridae and cause the mortality of numerous larval-stage fish species. Here we report protein crystal structures of a piscine betanodavirus, the grouper nervous necrosis virus, in four different forms. Highlights are two structural features that contribute to the viral molecular mechanisms of the T=3 and T=1 capsid assembly: a calcium-associated protrusion domain and a functional arginine-rich motif. These results also shed insights into the structural basis for evolutionary lineage of the family Nodaviridae.

Key words: Nodaviridae, nervous necrosis virus, calcium-associated protrusion domain.

INTRODUCTION

Aquaculture is one of the major global economic activities, such as cultivation of marine fish and prawn, in many countries. In fact, Taiwan, an island surrounded by sea, is one of the major distant water fisheries and aquaculture producers in the world. In terms of production and value, aquaculture has long been far ahead of offshore and coastal fisheries combined, and been just the second to distant water fisheries (Chen and Qiu, 2014). Today, aquaculture in Taiwan, including island and marine cultures, is well correlation with Taiwanese economy and society, such as income generation, food source and food supply. Furthermore, several species, such as oyster, farmed fishes and grass carp, have long been reared as an important food source in Taiwan. Currently, the major farmed fishes include milkfish, tilapia, grouper, giant freshwater prawn and pacific white shrimp with the export economic importance in Taiwan (Chen and Qiu, 2014).

The stressful and crowded conditions of aquaculture might cause these most problematic impacts in infectious diseases. Since the first half of the 20th century, the more significant viral pathogens of finfish, including aquabirnaviruses within the family Birnaviridae, infectious hematopoietic necrosis virus (IHNV) and viral hemorrhagic septicemia virus (VHSV) within the family Rhabdoviridae, infectious salmon anemia virus (ISAV) within the family Orthomyxoviridae, epizootic hematopoietic necrosis virus (EHNV) within the family Iridoviridae and betanodavirus making up the family Nodaviridae are reported (Crane and Hyatt, 2011).

The family Nodaviridae is further classified as the two major genera including alphanodaviruses and betanodaviruses. (Thiery et al., 2004) and displays T=3 symmetry (180 subunits in the capsid) of approximately ~29−35 nm in diameter. Basically, one CP exhibits the typical canonical 8-stranded jelly roll β-barrel fold, which consists of two pairs of antiparallel β-sandwich (Cheng and Brooks, 2013). To elucidate the structural information and mechanisms of capsid conformation, capsid assembly and viral infection by the genus betanodavirus of largely uncharacterized, we have determined the crystal structures of the grouper nervous necrosis virus (GNNV).

MATERIALS AND METHODS

A DNA sequence corresponding to the full-length of orange-spotted grouper nervous necrosis virus (OSGNNV) RNA2 (GenBank accession no KT071606) was amplified with specific primers by PCR and cloned into the artificial vector between SfoI and XhoI restriction sites for the production of N-terminal hexa-histidine-SUMO-tagged fusion protein (Lee et al., 2008).

All constructs were transformed and over-expressed in Escherichia coli (E. coli) BL21-CodonPlus(DE3)-RIL cells (Stratagene). Overexpression of the full-length GNNV CP were induced with 0.5 mM IPTG (isopropyl β-D-thio-galactopyranoside) for overnight at 18°C. The SUMO-tag GNNV CP was then purified from the soluble supernatant by Ni2+-affinity chromatography (HiTrap HP, Amersham Biosciences).

Initial crystallization screening for the GNNV-LP was performed using the hanging-drop vapor diffusion method with a Mosquito liquid-handling robot (TTP Labtech) for high-throughput crystallization condition screening. Crystals appeared within 1−2 weeks under the initial reservoir condition of 0.2 M sodium formate (pH 7.2) and 20% (w/v) PEG3350. The ab initio method by using icosahedral non-crystallographic symmetry (NCS) averaging with phase extension was performed to determine the initial phases of the T=3 GNNV-LP (Taka et al., 2005).

Finally, the coordinates of the T=3 GNNV-LP were refined to a crystallographic Rcryst of 0.257 and Rfree of 0.295 at 3.6 Å resolution. In the current model, 97% of all residues were in the most favored region of the Ramachandran plot and 3% of that was in the allowed regions using MolProbity (Chen et al., 2010).

RESULTS AND DISCUSSION

We determine the 3.6 Å resolution ab initio crystal structure of the T=3 GNNV-LP with non-crystallographic symmetry (NCS) averaging. The manually modeling of residues 52−338 for subunits A and B, and residues 34−338 for subunit C were fitting into the electron density of the icosahedral asymmetric unit (iASU) of the T=3 GNNV-LP. One T=3 GNNV-LP consists of sixty trimeric S-domains that participate in inter-subunit contacts to form a continuous shell of the capsid with an empty inner cavity. Three neighboring P-domains per iASU constitute the predominantly β-strand portion of the protein at the quasi three-fold (Q3) axes to form 60 protrusions on the particle surface. The 180 neighboring monomeric S-domains from subunits A, B and C make up the icosahedral shell in dimeric, trimeric and pentameric interactions along the I2, I3 and icosahedral five-fold (I5) axes (Fig. 1).

The present structures of the genus betanodavirus GNNV provides the important mechanistic insights into the processes of capsid assembly and viral infection. Actually, despite conservations about a viral genome encoding three major proteins and a compatible geometry of the T=3 architecture in the family Nodaviridae, the atomic striking features of the GNNV-LP described here facilitate to delineate the key structural components that trigger the CP oligomerization and stabilize the capsid assembly. The molecular organizations and assembly mechanisms of the genus betanodavirus GNNV reveal that the family Nodaviridae may lead to the novel viral evolutional approaches among the Tombusviridae, Caliciviridae and Birnaviridae families, which are compatible with the independent evolution linage previously. Structural mapping of the GNNV P-domain might facilitate the engineering of the vaccine development in the fish aquaculture industry.

Figure 1. Surface domain-colored diagram (left) and central cavity (right) representations of the T=3 GNNV-LP.
The tip-to-tip distance is ~350 Å, the diameter of the central cavity is ~228 Å, and the spike protrusion on the capsid surface is ~47 Å. The S-domains of the subunits A, B and C are shown in orange, blue and red, respectively, and the P-domains are shown in cyan. The structure of the GNNV-LP is viewed along the I2, I3 and I5 axes.

CONCLUSION

In this study, we report the ab initio structure of a T=3 grouper nervous necrosis virus-like particle (GNNV-LP) at 3.6 Å resolution determined by non-crystallographic symmetry averaging method. In summary, this work provides several important structural insights into the genus betanodavirus GNNV. Despite conservation of a viral genome encoding three major proteins and a compatible geometry of the T=3 architecture in the family Nodaviridae, the structure of the GNNV-LP obtained here allows us to delineate the key structural components that trigger the oligomerization and stabilize the capsid assembly. Furthermore, structural mapping of the GNNV P-domain might be useful for the development of vaccine strategies in the fish aquaculture industry.

Table of Contents
Chinese Abstract (中文摘要)	 I
Abstract	 II
Acknowledgements	 VI
Table of Contents	 VII
Contents of Tables	 X
Contents of Figures	 XI
Abbreviation List	 XV
Chapter 1 Research Background	 1
1-1 Classification of virus	 1
1-2 Viral nucleocapsid correlated with viral infection	 4
1-3 Aquaculture and viral diseases	 5
1-4 The family Nodaviridae	 7
1-5 The capsid structures of the family Nodaviridae	 9
1-6 Virus-like particle and its applications	 10
1-7 Thesis purpose	 11
Chapter 2 Materials and Methods	 13
2-1 Expression vector constructions of the full length and the different truncated domains of GNNV CP	 13
2-2 	Purification and characterizations of the T=3 GNNV-LP, T=1 subviral particles (SVPs) and the truncated P-domain	 13
2-3 Size characterizations of the T=3 GNNV-LP and T=1 SVPs by size-exclusion chromatography and negative-staining electron microscopy	 15
2-4 Crystallization and data collection of T=3 GNNV-LP, T=1 SVPs and the truncated P-domain	 16
2-5 Structure determinations of T=3 GNNV-LP, T=1 SVPs and the truncated P-domain…..	 19
2-6 Cell culture and virus infection	 25
2-7 qPCR analysis of GNNV RNA and statistics	 26
Chapter 3 Results	 27
3-1 The purity of viral CPs and particle assembly trials of the T=3 GNNV-LP, T=1 SVPs and the truncated P-domain	 27
3-2 T=3 icosahedral structure of the GNNV-LP	 27
3-3 Structural characterization of the N-terminus of the CP	 29
3-4 The icosahedral scaffold of the S-domain with Ca2+ ions incorporation	 31
3-5 The overall structure of the trimeric P-domains	 33
3-6 Calcium ions, water molecules and amino-acid variations on the P-domain	 34
3-7 Enhancement of GNNV infection by polyethylene glycol	 36
3-8 Particle polymorphism and subunit organization in T=3 and T=1 GNNV assembly	 37
Chapter 4 Discussion	 40
4-1 Structural insights into the β-annulus and the N-arm in GNNV	 41
4-2 Ca2+ binding and cysteine residues in the S-domain	 42
4-3 Topologies of the S-, P-domains and linker region on betanodavirus	 44
4-4 The calcium-incorporating trimeric P-domains	 45
4-5 	Functional P-domain for trimerization of CPs, host-cell binding and specificity	.  46
4-6 N-ARM and particle polymorphism in GNNV assembly	 49
Chapter 5 Conclusion	 52
References	 54
Tables	 65
Figures	 70
Related Paper Publications	 114

Contents of Tables
Table 1. Selected protein constructs and PCR primers	 66
Table 2. Primers used in quantitative RT-PCR	 67
Table 3. Data collection, phase extension and refinement statistics of the GNNV-LP and various truncated forms	 68
Table 4. Data collection, phase extension and refinement statistics of the truncated P-domain	 69

Contents of Figures
Figure 1. Phylogenetic tree analysis of CPs of the family Nodaviridae	 71
Figure 2. The over-expression and purification of the GNNV CP	 72
Figure 3. Domain organization and SDS-PAGE analyses of oligomerization of three various length GNNV CPs in solution	 73
Figure 4. The over-expression and purification of the truncated P-domain	 74
Figure 5. Size-exclusion chromatography elution profiles for the T=3 GNNV-LP	 75
Figure 6. EM, crystal images, dehydration process and diffraction collection of the GNNV-LP	 76
Figure 7. The different crystal conformations of the truncated P-domain	 77
Figure 8. The different crystal conformations of the delta-P-domain mutant	 78
Figure 9. The self-rotation function analysis of the T=3 GNNV-LP crystal	 79
Figure 10. The crystal packing of the T=3 GNNV-LP	 80
Figure 11. The ab initio phasing with NCSA of the T=3 GNNV-LP	 81
Figure 12. Ab initio phase determination of the T=3 GNNV-LP using NCS averaging with phase extension	 83
Figure 13. Structural determination of the T=3 GNNV-LPs by the ab initio method with NCSA	 84
Figure 14. Sequence alignment of CPs of the family Nodaviridae	 86
Figure 15. Overall structure and the topology diagram of the GNNV CP	 87
Figure 16.	Surface domain-colored diagram (left) and central cavity (right) representations of the T=3 GNNV-LP	 88
Figure 17. The structural comparison of the trimeric GNNV CPs and FHV CPs	 89
Figure 18. Structural organizations of the N-arm and the β-annulus	 90
Figure 19. The 5-fold interface of T=3 GNNV-LP	 92
Figure 20. Structural organization of the S-domain	 93
Figure 21. The inner surface of the pentamer subunit color-coded according to the computed electrostatic potential	 94
Figure 22. Trimeric interactions of the P-domain with Ca2+ ions	 95
Figure 23. Structural comparison of the P-domains among GNNV, Orsay virus, HEV and Calicivirus	 98
Figure 24. Specific arrangement of water molecules in the P-domain	 99
Figure 25. The orientations of the linker region between viral capsids	 100
Figure 26. Evolutionary lineages of GNNV	 101
Figure 27. The flexible phenomenon of the T=3 GNNV-LP and linker region	 102
Figure 28. The ligand-binding pockets of the P-domain	 103
Figure 29. Improvement of GNNV infection by PEG treatment	 104
Figure 30. The particle polymorphism of the GNNV capsid correlated with N-ARM	 105
Figure 31. EM images of GNNV-LPs with different capsid organizations	 106
Figure 32. Crystal packing and self-rotation function of the T=1 N-ARM deletion mutant..	 107
Figure 33. The structural comparison of the T=1 delta-P-domain and SeMV SVPs	 108
Figure 34. The structural insights of the T=1 delta-P-domain mutant	 109
Figure 35. The equilibrium properties of the monomeric and trimeric P-domains	112
Figure 36. Diagram showing the putative self-assembly process of the T=3 and the T=1 GNNV capsids	 113
S1 Fig.    Structural determination of the T=3 GNNV-LPs by the ab initio method with NCSA
S2 Fig.    EM images of GNNV-LPs of different capsid organization
S3 Fig.    Crystal packing and self-rotation function of the T=1 N-ARM deletion mutant
S4 Fig.    Structural organization of the S-domain
S5 Fig.    Structural comparison of the P-domains among GNNV, Orsay virus, HEV and Calicivirus
S6 Fig.    Specific arrangement of water molecules in the P-domain and the Ca2+-mediated oligomerization of GNNV CP
S7 Fig.    The Ca2+-binding and ligand-binding pockets of the P-domain
S8 Fig.    Phylogenetic tree and sequence alignment of CPs of the family Nodaviridae

                                    

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