臺灣博碩士論文加值系統

三域生物都可能被病毒感染，許多細菌噬菌體與真核生物病毒都是顯學，但有關古菌病毒的描述卻僅佔少數。好氧極端高鹽古菌因較易培養，其相關噬菌體型態病毒被報導與研究的較早。近年來，泉太古生物門的高溫古菌多樣化病毒形態與病毒離開宿主後於高溫環境下的形態結構變化與適應演化，是目前相當被關注的主題研究。然而在過去二十年間幾乎沒有關於甲烷古菌病毒的研究發表。賴美津教授實驗室執行科技部天然氣水合物計畫，研究生翁杰愔自台灣西南海域變形前緣區取得活塞岩心底泥樣品分離純化出甲烷囊菌屬新種菌株Methanoculleus taiwanensis CYW4T，以穿透式與掃描式電子顯微鏡均觀察到病毒及CYW4T細胞於後對數期被病毒裂解現象。本論文研究進一步測量CYW4T於不同生長期的細胞密度OD、甲烷產量與顯微觀察，確認病毒於後對數期與平穩期間裂解釋出，菌量下降，菌液澄清。甲烷古菌病毒VMta (Virus of Methanoculleus taiwanensis)，病毒顆粒為球形，有二十面體衣殼蛋白(capsid protein)，外部還有外套膜(envelope)包覆，直徑大小約為100 nm。VMta病毒具雙股DNA含70,262個鹼基對，G+C含量為54.5%，有101個開放讀序框架(ORFs)。VMta基因體序列經BLASTX及HHpred比對，顯示可能利用穿刺蛋白將DNA送入宿主中，並以滾環型複製機制(rolling cycle replication, RCR)複製DNA，經由終端酶將DNA包裝進空的衣殼蛋白，最後由裂解性酵素，例如內溶素(endolysin)破壞宿主而出。
本研究亦自台灣西南海域好景海脊取得岩心樣品純化出新甲烷菌株Methanoculleus sp. CWC-02，經由親緣關係比對，菌株CWC-02與Methanoculleus marisnigri JR1T 有98.4%相似度，而兩株菌的平均核苷酸一致性(ANI)為86.81%；且基因組對基因組距離計算(GGDC)分析結果為32.50%，顯示菌株CWC-02應為Methanoculleus屬下之新 “種” 菌株。菌株CWC-02能利用甲酸及H2/CO2及2-propanol、2-butanol等二級醇為基質行甲烷化作用，最適生長溫度為37℃。菌株CWC-02生長至平穩期於TEM的觀察下，也發現有許多的VPL (virus-like particle)自細胞裂解而出，推測菌株CWC-02也被裂解病毒感染。於天然氣水合物潛力區以甲烷為主的生態系中，碳源與營養的加速循環，對此生態系的影響與可能的甲烷天然氣累積值得進一步探討。

Viruses infect all Three Domains of lifes, however the knowledge of archaeal viruses is limited. Lately, the diverse virus morphology and the independent virus development outside the extreme thermophilic/acidophilic archaeal host attracted the attention on archaeal virus investigations. Currently, over 100 archaeal viruses have been discovered, most related to thermophilic Crenarchaea and extreme halophilic Euryarchaea. However, almost none methanoarchaeal virus was reported for the past two decades. From the core sediment on the top of gas hydrate habitat in the deformation front site offshore south-western Taiwan, Methanoculleus taiwanensis CYW4T was enriched, isolated and characterized. Cell lysis was observed at stationary phase and a lytic virus which caused the lysis of strain CYW4T was observed under TEM. The spherical shape virion, about 100 nm, with the icosahedral capsids and envelope was named as VMta (Virus of Methanoculleus taiwanensis). VMta is a dsDNA virus which contained 70,262 bp with a mol% G+C content of 54.5 and 101 putative open reading frames (ORFs). Base on the VMta genome information and analysis through BLASTX and HHpred, it was suggested that the VMta may injected the DNA into the host by the puncture protein and replicated their genomes through the rolling-circle replication (RCR) mechanism. The viral DNAs were packed into the empty capsid by the terminase enzymes and virons left host cell with the endolysin disruption.
Methanoculleus sp. CWC-02 were enriched from the marine sediment of the Good weather ridge. Phylogenetic analysis revealed that strain CWC-02 was closely related to Methanoculleus marisnigri JR1T (98.4% 16S rRNA gene sequence similarity). Genome relatedness between strain CWC-02 and Methanoculleus marisnigri JR1T was computed using both average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC) with values of 86.81% and 32.50%, respectively. According to genomic data, it is patent the strain CWC-02 may the novel new species. Strain CWC-02 used H2 plus CO2, formate, 2-propanol and 2-butanol as catabolic substrates. The optimum growth temperature was 37℃. The stationary phase growth of strain CWC-02 cells also observed virus-like particles under TEM. The occurrence of methanoarchaeal viruses at the methane (gas) hydrate ecosystems indicated that viruses may play a role in acceleration of the carbon and nutritional cycling.

摘要 i
Abstract ii
目錄 iii
表目錄 vii
圖目錄 viii
壹、前言 1
貳、前人研究 4
一、甲烷古菌(太古生物) (Methanogen) 4
二、自甲烷天然氣水合物潛力區純化的甲烷古菌發現甲烷古菌病毒 5
三、原核生物病毒 6
(一) 病毒分類 6
(二) 細菌病毒 6
(三) 古菌病毒 7
(四) 好氧極端高鹽古菌病毒 8
1. 雙股DNA (dsDNA)好氧極端高鹽古菌病毒 8
2. 單股DNA好氧極端高鹽古菌病毒 9
(五) 高溫古菌病毒 10
1. 泉太古生物門病毒(Crenarchaeal virus) 10
2. 廣域太古生物門病毒(Euryarchaeal virus) 13
(六) 甲烷古菌病毒 13
四、病毒感染作用及複製過程 14
(一) DNA病毒複製機制 15
(二) 滾環型複製(Rolling-circle replication, RCR) 15
參、材料與方法 17
第一部分-古菌病毒純化及特性分析 17
一、甲烷古菌培養與病毒純化 17
(一)台灣甲烷囊菌(Methanoculleus taiwanensis CYW4T)培養 17
(二) PEG沉澱 17
(三) 蛋白質層析儀(Fast performance liquid chromatography, FPLC) 18
(四) 病毒溶液濃縮 19
二、穿透式電子顯微鏡(Transmission electron microscopy, TEM)觀察 19
三、甲烷古菌病毒DNA萃取 19
四、核酸酶作用 20
五、蛋白質電泳 20
(一) VMta病毒樣品處理 20
(二) SDS-PAGE 20
(三) 銀染色法(Silver stain) 21
六、脂質之萃取及分析 22
(一) 甲烷古菌細胞膜與甲烷古菌病毒脂質萃取 22
七、病毒基因體定序與序列分析比對 23
(一) 核酸與蛋白質序列分析 23
(二) HHpred分析 24
(三) CDD (Conserved domain database)比對分析 24
第二部分-甲烷古菌純化及特性分析 25
一、採樣時間地點與樣品甲烷古菌增殖進度 25
二、藥劑與培養基 25
(一) 除氧操作系統(Hungate station) 25
(二) MB/W與MM/W液態培養基配製 25
(三) 還原劑及碳源配製 26
(四) 抗生素溶液配製 27
(五) TGC (thioglycollate)培養基配製 27
三、甲烷古菌增殖培養與厭氧轉殖接種 28
(一) 接菌 28
(二) 氣相層析儀偵測樣品甲烷氣體 28
(三) 抗生素添加 28
(四) 連續稀釋法(serial dilution) 29
(五) Roll-tube 29
四、微生物形態觀察 30
(一) 位相差顯微鏡觀察細胞 30
(二) 穿透式電子顯微鏡(Transmission electron microscopy, TEM)觀察細胞 30
(三) 場發射掃描式電子顯微鏡(Field-emission scanning electron microscope, FE-SEM)觀察細胞 30
五、生長與生理生化特性分析 31
(一) 碳源利用測試 31
(二) 抗生素抗性測試 32
(三) 生長曲線測量 32
(四) 溫度生長範圍測試 33
六、甲烷古菌染色體DNA萃取 33
七、核酸純度與定量分析 34
八、聚合酶連鎖反應(Polymerase chain reaction, PCR) 34
九、核酸電泳分析 35
十、PCR增幅樣品切膠純化回收 35
十一、質體轉型作用 36
(一) 勝任細胞的製備 36
(二) 質體轉形作用 37
(三) 質體抽取與純化 37
十二、核酸定序與序列分析 38
(一) 16S rRNA基因定序與序列分析 38
(二) 染色體DNA定序與序列分析 38
肆、結果與討論 40
一、病毒VMta 40
(一)病毒VMta與台灣甲烷囊菌CYW4T的關係 40
(二) VMta病毒純化 41
(三) VMta為雙股DNA病毒 41
(四) VMta病毒結構分析 41
(五) VMta病毒脂質組成分析 42
(六) VMta病毒蛋白組成分析 42
(七) 病毒基因體分析 43
1. VMta病毒序列與蛋白功能預測 43
2. 病毒結構相關序列分析 43
3. DNA複製相關序列分析 44
4. 病毒組裝與釋出宿主相關功能序列分析 45
(八) VMta病毒的生命週期 45
二、深海底泥甲烷古菌之增殖培養與純化 47
(一) 自好景海脊(Good weather ridge)純化的Methanoculleus sp. CWC-02之細胞形態、系統演化分類與生理生化特性分析 47
(二) 細胞型態 47
(三) 系統演化分類分析 48
(四) 生理生化與生長特性分析 49
伍、結論與展望 51
陸、表與圖 52
柒、參考文獻 89
捌、附錄 99

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