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研究生(英)Ling-Ya Chiu
論文名稱(中)青枯病菌基因組中插入序列IS1405的特性分析與應用
論文名稱(英)The analysis and application of endogenous IS1405s of Ralstonia solanacearum
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指導教授(中)李永安
指導教授(英)Yung-An Li
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關鍵字(中)插入序列 青枯病菌
關鍵字(英)insertion sequemce Ralstonia solanacearum
摘要(中)IS1405和IS5 family中的11個IS成員,使用maximum parsimony analysis建構親緣關係圖,結果顯示在IS5 family的六個subgroups:IS1031、IS427、ISL2、ISH1、IS903和IS5 subgroups中,IS1405屬於IS5 subgroup。同時發現屬於IS5 subgroup的IS成員中,來自相同菌種的IS,在親緣關係圖中位於較近的分支,顯示IS5 subgroup中的IS成員親緣關係和菌種來源的分類地位相同。同屬於IS5 subgroup的IS成員:IS1405、IS1384、IS1051、IS1479a、ISPSMC和IS1646的核酸序列比對中,在coding region相同度由51-60%不等,5''和3'' non-coding region中相同度降至22-30%不等,顯示5''和3'' non-coding region核酸序列的變異大於coding region。利用IS1405 的5''和3'' non-coding region和其他IS5 subgroup成員差異大的核酸序列,設計polymerase chain reaction (PCR)反應的引子對,利用此引子對對來自七個不同寄主的26株青枯病菌菌株進行PCR擴增反應,皆有預期的1.1 kb片段產生,靈敏度達70 cfu/ml和1.6×10-3ng/ml。但對其他植物病原菌,如Erwinia和Xanthomonas等進行PCR反應,則無任何預期的片段產生,因此利用IS1405序列所設計的此組引子對,對青枯病菌具有專一性的檢測功用,並證實IS1405只存在於青枯病菌中,所以IS1405是一個species-specific的插入序列。 自青枯病菌基因組中,以inverted PCR和直接選殖含有IS1405的EcoRI片段這兩種方式,取得七個含有IS1405的核酸片段,分析這七個IS1405在青枯病菌基因組中,座落位置兩旁的核酸序列。在目標位置(target site)分析方面,有五個IS1405的 target site為CTAG,另有兩個為CTAA,綜合以上可知IS1405具有高度專一性的target site選擇,序列為CTAR (R = A或G);其中有五個IS1405是以和target site相同的方向插入,另外兩個則以和target site相反的方向插入,顯示IS1405在辨認位置後,可用不同的方向插入目標位置中;在IS1405插入位置兩旁序列比對中,排列在IS1405左旁邊為5''-CCT(2)T(3)CAC(3)CGC(3)T(4)T(6)G(13) TAG-3''的保守序列;在IS1405右旁邊的序列,則為5''-AG(3)T(14)T(2)ATA(13)T-3''的保守序列。 另以IS1405兩端的inverted repeat (IR)序列設計引子,藉由PCR方式對青枯病菌基因組中含有IS1405的不同EcoRI片段,擴增出七個isoIS1405核酸序列,加上之前選殖的三個isoIS1405核酸序列,共十個進行分析。這十個isoIS1405核酸序列,有五個來自青枯病菌菌株PS-CTW31的不同片段,三個來自青枯病菌菌株PS68,另外兩個分別來自於青枯病菌菌株PS96和PS95。在序列長度分析,這十個isoIS1405的核酸序列皆為1,174 bp,在序列67-1,030 bp處可轉譯出長度為321個胺基酸的蛋白質序列,此段胺基酸中包含有跳躍酵素特有的序列。在核酸序列比對中,十個isoIS1405相同度由95%-99%不等,並可依據核酸序列的差異,將十個isoIS1405區分為一、二兩類,在同一類中核酸序列相同度為98-99%,在不同類間核酸序列相同度為95-97%不等;第一類的isoIS1405序列在29個地方具有相同,但和第二類的isoIS1405序列不同的核酸序列,也就是這兩類的isoIS1405核酸序列,是利用這29個核酸序列的差異作區別。在基因演化的過程中,29個核酸序列同時突變的機率接近於零,因此推測這兩類的isoIS1405的形成是個別獨立的,而不是經由隨機突變形成的。同時,在將isoIS1405的PCR擴增片段以AvaI處理後跑電泳的實驗結果中,也顯示isoIS1405可區分為AvaI-1和AvaI-2兩類,在AvaI-1中包含有和第一類isoIS1405相同的成員;AvaI-2中包含有和第二類相同的isoIS1405成員,因此使用PCR-RFLP的方式,可將isoIS1405在核酸序列的變異情形快速的呈現出來。在isoIS1405的分佈方面,青枯病菌菌株PS-CTW9和PS-ES10中只含有屬於AvaI-1類的isoIS1405,其他青枯病菌菌株如PS68、PS-CTW25等中,則同時存在有這兩類不同的isoIS1405。 以IS1405為探針,對來自七個不同寄主的26株青枯病菌菌株基因組,以EcoRI處理後進行南方氏雜合反應。依產生雜合片段的數目,可將青枯病菌區分成A、B兩大group,A group 中含有七個以內的雜合片段;B group中則有十二個以上的雜合片段,每一個group再依雜合型式的差異區分出多個subgroups (A1-A5和B1-B7)。在A1 subgroup的菌株中,共同擁有1.4 kb的核酸片段,以PCR方式擴增出屬於A1 subgroup的青枯病菌菌株PS68的1.4 kb片段,命名為IS1405BF,再以此片段3''端距離IS1405插入位置55個 bp處,設計引子PSIS-RA1,此引子和PSIS-F共同使用,對青枯病菌菌株進行PCR擴增反應,只有屬於A1 subgroup的青枯病菌能擴增出1,181 bp的預期片段。同時,選殖出青枯病菌菌株PS-CTW31和其他B1 subgroup中的菌株,都共同擁有的2 kb EcoRI核酸片段,命名為IS1405 FF,並以此片段3''端距離IS1405插入位置130個 bp處的序列設計引子PSIS-RB1,和PSIS-F共同使用,對青枯病菌菌株進行PCR擴增反應,只有屬於B1 subgroup的青枯病菌能擴增出1,256 bp的預期片段,因此使用PCR方式可快速區分出屬於A1和B1 subgroups的青枯病菌菌株。 以IS1405 5''和3'' non-coding region設計的引子對PSIS-F+PSIS-R,可專一性的檢測青枯病菌,而以IS1405在基因組中座落位置兩旁的片段IS1405BF和IS1405FF設計的引子對,可利用PCR方式快速區分出A1和B1兩大subgroups,所以利用IS1405對青枯病菌進行檢測和分類是實用且快速的方法。
摘要(英)IS1405 of Ralstonia solanacearum belongs to the IS5 subgroup of IS5 family based on phylogenetic tree analysis of nucleotide sequences using the maximum parsimony analysis and comparison of terminal nucleotide sequences. Further comparison of IS1405 with IS5 subgroup members, such as IS1384, IS1051, IS1479a, ISPSMC and IS1646, revealed that the nucleotide sequence of coding region (encodes transposase) shared identity from 51-60%, but the identity of 5'' and 3'' non-coding region ranged from 22 to 30%. Oligonucleotide primers (PSIS-F + PSIS-R) specific to IS1405 were designed for polymerase chain reaction (PCR) based on the nucleotide sequence of 5'' and 3''non-coding regions. The primers amplified a 1.1-kb PCR product only from R. solanacearum but not from other plant pathogenic bacteria, such as Erwinia and Xanthomonas spp. Accordingly, oligonucleotide primers (PSIS-F + PSIS-R) are specific not only to IS1405 but also to R. solanacearum. The analysis of flanking sequences of six endogenous isoIS1405s of R. solanacearum revealed that IS1405 has a preferred target site, CTAR(R=A or G), and can transpose into this target site at two different orientations. Further analysis of the 50-bp flanking sequences of endogenous IS1405s showed that there are consensus sequence of 5''-CCT(2)T(3)CAC(3)CGC(3)T(4)T(6)G(13) TAG-3'' at the left flanking sequence and that of 5''-AG(3)T(14)T(2)ATA(13)T-3'' at the right. In addition, nucleotide sequence of ten endogenous isoIS1405s isolated from 3 different strains of R. solanacearum were analyzed. The results indicated that all isoIS1405s are 1,174 bp nucleotide long and consisted of one open reading frame encoding a protein of 321 amino acids. The nucleotide sequences were highly conserved and shared 95-99% identity. Treatment of these IsoIS1405s with AvaI showed two different restriction fragment length polymorphism (RFLP) patterns, AvaI-1 and AvaI-2 types. Two types of IS1405s coexist in most strains of R. solanacearum. An internal fragment of IS1405 was used as a probe to hybridize EcoRI-treated total DNA of R. solanacearum. The results revealed that strains of R. solanacearum in Taiwan had an extensive genetic variability. The strains were classified into two distinct groups based on number of hybridized DNA fragments. The number of hybridized bands of group A varied from 4 to 7, and that of group B was more than 12. The strains in each group were further divided into subgroups (A1-A5 and B1-B7) according to hybridization patterns. Strains of A1 subgroup had a common 1.4-kb hybridized DNA fragment. The flanking sequence of IS1405 in 1.4-kb DNA fragment was determined and used to design a PCR primer, PSIS-RA1. PCR reaction using PSIS-RA1 and PSIS-F as primers amplified a specific PCR product only from the strains of A1 subgroup but not from those of other subgroups. The same strategy was also applied to the strains of B1 subgroup, which contained a common 2-kb hybridized DNA fragment. PSIS-RB1 was designed based on the flanking sequence of IS1405 in the fragment. A specific PCR product was amplified only from strains of B1 subgroup not from those of other subgroups using PSIS-RB1 and PSIS-F as primers.
論文目次中文摘要 英文摘要 前言 材料與方法 菌種及培養條件 IS1405和IS5 family成員的比較 分析青枯病菌菌株中IS1405座落位置兩旁的核酸序列 序列分析 IS1405在青枯病菌race 1各菌株中存在情形 isoIS1405的選殖 isoIS1405的定序分析 PCR-RFLP的方式 實驗結果 IS1405與IS5 family成員間的序列比對分析 IS5 supgroup間的核酸序列比對 利用PCR方式檢測青枯病菌 IS1405在青枯病菌基因組中插入位置兩旁序列的分析 (1)選殖青枯病菌基因組中帶有IS1405之DNA片段 (2)含有IS1405之青枯病菌DNA片段分析 (3)IS1405插入兩旁序列並列分析 isoIS1405的選殖及序列比對分析 (1)isoIS1405序列的選殖 (2)isoIS1405序列分析 (3)isoIS1405利用PCR-RFLP分類 以IS1405在青枯病菌race1各菌株中存在的情況 以IS1405座落位置區分青枯病菌subgroup 討論 參考文獻 圖表 英文縮寫表
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