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研究生:王秀娟
研究生(外文):Hsiu-Chuan Wang
論文名稱:藉伯克氏類鼻疽菌基因體洞析tRNA基因副本與密碼捕捉的爭議
論文名稱(外文):INSIGHT INTO AN ISSUE OF tRNA GENE COPIES AND CODON CAPTURE BY A GENOMIC VIEW OF Burkholderia pseudomallei
指導教授:陳亞雷
指導教授(外文):Chen Ya-Lei
學位類別:碩士
校院名稱:國立高雄師範大學
系所名稱:生物科技系
學門:生命科學學門
學類:生物科技學類
論文種類:學術論文
論文出版年:2010
畢業學年度:99
語文別:中文
論文頁數:125
中文關鍵詞:tRNA基因密碼使用擺動解碼tRNA合成酶後轉譯修飾前轉錄修飾
外文關鍵詞:tRNA genescodon usageWobblephenomenatRNA synthetasePost-transcription modificationPre-translational modification
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tRNA的主要功能是扮演蛋白質合成時的“轉接”角色,在mRNA-ribosome複合物中,tRNA反密碼位於34-36(3-2-1)鹼基位置,與mRNA密碼(1-2-3)呈反向互補的識別。密碼與反密碼之間的關係是屬於“共同演化”,因此tRNA基因數目受mRNA密碼的搖擺現象及charged-tRNA發生前轉錄修飾所影響,但至今尚未有研究顯示利用基因體的生物資訊法去驗證之間的關係。Burkholderia pseudomallei在所有的原核基因體中擁有最多TRS序列,顯示其基因體在演化過程中經過多次改變,如此可以凸顯密碼的使用性與tRNA基因數目之間的關連性。本研究係將B. pseudomallei基因體,重新以tRNAScan-SE分析,並定義出59個具有功能性的tRNA基因。研究排除A34、G34、U34、I34-containing tRNAs的密碼搖擺影響、tRNAMetf基因、tRNASec isoaccepator gene及Q-containing tRNA的干擾,實際上參與tRNA捕捉的密碼總數共有22個與56個tRNA基因,建立密碼使用性與tRNA gene copies間的相關性(r2 > 0.87)。另外分析tRNA合成酶的Km值、Kcat值及Kcat/ Km與tRNA gene copies間的相關性,顯示並無關聯(r2 <0.01)。證實了B. pseudomallei密碼使用的出現頻率與tRNA gene copeis呈正相關性,並排除了tRNA合成酶催化能力對捕捉tRNA基因的影響。


The major function of tRNA was “Transfer” as protein combination. In mRNA-ribosome complex, the anticodon of tRNA was at 34-36 (3-2-1) base, and was the opposite complementary identification in mRNA code (1-2-3). The relation between codon and anticodon was coevolution, so the number of tRNA gene was impacted by wobble phenomena and charged-tRNA induced pre-translational modification. However, till now we didn’t have any research to verify this relation via genomic bio-information. Burkholderia pseudomallei had the most TRS serials in the genomes of prokaryotes, and it shown the multi-modification in gene evolution and could illustrate the relationship between the codon usage and the number of tRNA gene. In this research, we analyzed the gene of B. pseudomallei with tRNAScan-SE and define 59 functional tRNA gene. We excluded the wobble effect of A34, G34, U34 and I34-containing tRNAs and the interference of tRNAMetf gene, tRNASec isoaccepator gene, Q-containing tRNA in this research. Moreover, the physically codon number caught by tRNA was 22, and 56 tRNA gene, and established the relationship between codon usage and tRNA gene copies (r2 > 0.87). Besides, we also analyzed the relationship among Km value, Kcat value, Kcat/ Km of tRNA synthetase and tRNA gene copies, and this result demonstrates they didn’t have any relationship (r2< 0.01). This research pointed out that the positive relationship between the frequency of B. pseudomallei codon usage and tRNA gene copies, and excluded the effect to tRNA synthetase catalysis caught tRNA gene.
目 錄
誌謝 ....................................................I
中文摘要 ................................................III
英文摘要 ................................................IV
目錄 ....................................................V
第一章  前言 ............................................01
第二章  研究動機、目的與限制因素 ........................06
第三章  材料與方法 ......................................07
 生物資訊處理 ....................................07
 統計分析 ........................................08
第四章  結果 ............................................09
B. pseudomallei 基因體中tRNA基因數與分佈...........09
B. pseudomallei 基因體上的tRNA分佈 .................11
Codon usage與tRNA gene間的相關性 .................11
tRNAMet isoaccepator gene ............................12
A34- or G34- containing tRNAs ........................13
U34- containing tRNAs ..............................13
I34- containing tRNAs ................................14
tRNAsec isoaccepator gene .............................14
Q-family tRNA .....................................15
Codon usage與tRNA gene copies的線性相關 ...........16
B. pseudomallei 基因體上的tRNA synthetase ...........16
tRNA synthetase酵素活性 ...........................18
tRNA isoaccepators in viable B. pseudomallei ...........19
第五章  討論 ............................................21
第六章  參考文獻 ........................................28

表目錄
表一、 不同Burkholderia pseudomallei菌株之基本資料........34
表二、 同Burkholderia pseudomallei 菌株其Aminoacyl-tRNA
cluster之表現 .....................................35
表三、 不同菌種之間的Aminoacyl-tRNA cluster表現 ..........36
表四、 Burkholderia pseudomallei inter strain各遺傳密碼子
所對應胺基酸及密碼被使用頻率 ....................37
表五、 After wobble effect :Codon usage and tRNA content for
Burkholderia pseudomallei inter-strain .................41
表六、 Burkholderia pseudomallei inter strain post-transcription ....44
表七、 不同Burkholderia pseudomallei之tRNA synthetase .......46
表八、 tRNA synthetase之催化能力..........................50


圖目錄
圖一、Burkholderia pseudomallei於Chromosome 1及Chromosome 2
的tRNA排列 .......................................51
圖二、Burkholderia pseudomallei K96243 Aminoacyl-tRNA反轉模式
....................................................52
圖三、Aminoacyl-tRNA於Burkholderia pseudomallei inter strain
基因上的分佈 ......................................53
圖四、Burkholderia pseudomallei tRNAIls及tRNAAla位在16S-23S
RNA中間的inter-space基因聚集模式 ...................54
圖五、Burkholderia pseudomallei特有的inter-strain tRNA gene cluster
....................................................55
圖六、Burkholderia pseudomallei inter-strain各個胺基酸的所有密碼組與tRNAaa gene種類相關性分析 ........................56
圖七、分析Burkholderia pseudomallei inter strain tRNAMet 的二級結構
....................................................57
圖八、分析Burkholderia pseudomallei inter strain tRNASer的二級結構
.....................................................58
圖九、Burkholderia pseudomallei inter-strain各個胺基酸的所有
密碼組與tRNAaa gene種類,相關性分析 ................59
圖十、Burkholderia pseudomallei aminoacyl- tRNA Biosynthesis ....60
圖十一、 leucyl -tRNA synthetase二級結構分析 .................61
圖十二、isoleucyl -tRNA synthetase二級結構分析...............62
圖十三、 tryptophanyl -tRNA synthetase二級結構分析 ............63
圖十四、alanyl -tRNA synthetase二級結構分析 .................64
圖十五、glycyl-tRNA synthetase二級結構分析 .................65
圖十六、 phenylalanyl-tRNA synthetase二級結構分析 ...........66
圖十七、Burkholderia pseudomallei inter-strain各個胺基酸的所有
密碼組與tRNA gene經tRNA synthetase催化能力捕捉的影響
...................................................67

附 錄
附錄ㄧ、Burkholderia pseudomallei Genome Distribution of tRNAs
...........................................................................68
附錄二、Burkholderia pseudomallei tRNAs structure ............................76
附錄三、Burkholderia pseudomallei inter-species中有20個
tRNA gene存在基因體之位置有所不同 ............................116


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