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研究生(中)周淑玲
研究生(英)Sue-Lin Chou
論文名稱(中)對Xanthomonas arboricola具專一性的qumA-qumB gene cluster序列及座落位置分析
論文名稱(英)Sequence and locational analysis of qumA-qumB gene cluster specific to Xanthomonas arboricola
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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)Xanthomonas arboricola qumA-qumB基因群組
關鍵字(英)Xanthomonas arboricola qumA-qumB gene cluster quinate dehydrogenase porin peptidase probable membrane protein
摘要(中)中文摘要 先前研究發現在Xanthomonas中,只有X. arboricola的5個病原小種 (X. arboricola pv. carotae、X. arboricola pv. celebensis、X. arboricola pv. corylina、X. arboricola pv. juglandis以及X. arboricola pv. pruni) 具有代謝quinate的能力,我們並且也從X. arboricola pv. juglandis strain XJC5中,選殖出一22.1 kb的SQ2 clone,能使原本不能代謝quinate (SQ(-)) 的X. arboricola pv. celebensis strain XC143具有代謝quinate的能力。在SQ2 clone中,發現一個qumA (quinate dehydrogenase gene),此qumA也只存在於受測試Xanthomonas中的X. arboricola,本實驗室進一步以SQ2 clone內的其它片段為探針,進行Southern hybridization,發現和其有相同轉錄方向的qumB (porin gene) 同樣也是Xanthomonas中能夠代謝quinate的5個受檢測X. arboricola病原小種所特有的,而在其它不能代謝quinate的30多個Xanthomonas病原小種中,則無此兩個基因。由於qumA與qumB只存在於Xanthomonas中能夠代謝quinate的X. arboricola中,因此我們根據qumA和qumB的內部片段分別設計兩組引子,SQ-F2+SQ-R2以及Porin-F2+Porin-R,利用PCR的方式可以快速區分出X. arboricola以及其它Xanthomonas strains。繼續根據qumA的3’端以及qumB的5’端序列,設計一Q-F’+Porin-R’的引子組合,對於能代謝quinate的5個X. arboricola病原小種基因組DNA進行PCR檢測,結果都能擴增出預期的PCR產物,顯示qumA和qumB不但是Xanthomoans中能夠代謝quinate的X. arboricola所特有的,且在X. arboricola的5個病原小種中,qumA與qumB是相聚在一起的,形成 qumA-qumB gene cluster。在SQ2 clone中的qumA-qumB兩側,分別還發現mem (encode membrane protein)、一個未確定的ORF (暫命名為unknown) 及pep (encode peptidase protein),其都和qumA-qumB有相同的轉錄方向,排列位置為:mem-unknown-qumA-qumB-pep。經由Southern hybridization發現mem、unknown ORF以及pep並不是X. arboricola所獨有的,而是大多數的Xanthomonas所共有的。因此,同樣利用PCR檢測的方法,確定Xanthomonas的 5個病原小種中,qumA-qumB不但前後相鄰,並且都位在unknown ~ pep之間。因此, qumA-qumB gene cluster可能源自於其它生物,經由水平轉移 (horizontal transfer) 至Xanthomonas中。 利用Southern hybridization的結果發現mem、unknown ORF以及pep雖然是大多數Xanthomonas所共有的,不過還是有一些例外,因此我們可以mem、unknown ORF、qumA、qumB以及pep的內部片段為探針,將測試的33株Xanthomonas (30個病原小種) 大致分為六類 (I~VI):第I類是皆不會與這5個探針出現雜合反應訊息的X. hortorum pv. pelargonii strain XP15(T)以及X. punicae strain XP177(T);第II類是只能與unknown ORF的探針出現雜合反應訊息的X. campestris. pv. mangiferaeindicae strain XCM28-2;第III類是只能與mem和pep的探針出現雜合反應訊息者,且都是屬於X. campestris的DNA homology group 3的X. arrhenatheri strain XA(T)、X. poae strain XP(T)以及X. phlei strain XP(T);第IV類是能和mem以及unknown的探針有雜合反應訊息的X. eucalypti strain XE104(T);其它只能和mem、unknown以及pep的探針出現雜合反應訊息的18株Xanthomonas病原小種則都歸於第V類,第VI類是皆會與這5個探針出現雜合反應訊息的9株能代謝quinate的X. arboricola (5個病原小種)。藉mem、unknown ORF、qumA、qumB以及pep 5種探針進行Southern hybridization的結果,即可從這些Xanthomonas中辨別出XCM28-2和XE104(T),延續這個方法,若我們再累積更多的探針,或許繼續可以利用Southern hybridization或dot blot的方法,分辨出每一Xanthomonas的病原小種。 由於qumA與qumB只存在於Xanthomonas中能代謝quinate的X. arboricola (5個病原小種),而非其它多數不能代謝quinate的Xanthomonas所有,因此qumA與qumB可能是藉由其它細菌以horizontal transfer的方式傳至X. arboricola,因此,本實驗室以SQY培養基,先測試了Xanthomonas屬以外的植物病原細菌,如Erwinia及Pseudomonas屬,以了解這些細菌是否也具有代謝quinate的能力。其中,屬於Erwinia cluster I的E. ananas、E. herbicola以及E. herbicola pv. millettiae與屬於Erwinia cluster II的E. rhapontici以及E. cypripedii在SQY培養基中,會有和X. arboricola類似的變色反應 (深綠色);另外,有些P. syringae在SQY培養基中也會有變色反應,但顏色不同 (偏黃色)。分別以qumA與qumB的內部片段為探針進行Southern hybridization,發現Erwinia cluster I以及II的菌株均會和qumA的探針有雜合反應訊息,另外,還有2株P. syringae也會和qumA的探針有雜合反應訊息,而只有E. rhapontici strain ER1會與qumB的探針有雜合反應訊息。顯示qumA或qumB至少存在於X. arboricola、Erwinia以及Pseudomonas的基因組DNA中,因此,可能在這三種植物病原菌之間,有進行horizontal transfer的現象。
摘要(英)英文摘要 The five pathovars (X. arboricola pv. carotae、X. arboricola pv. celebensis、X. arboricola pv. corylina、X. arboricola pv. juglandis以及X. arboricola pv. pruni)of Xanthomonas arboricola that metabolize quinate were discovered. A gene involved in quinate metabolism had been cloned from X. arboricola pv. juglandis strain XJC5. The gene, qumA, located on 22.1 kb SQ2 clone from X. arboricola pv. juglandis strain XJC5, conferred quinate metabolic activity to X. arboricola pv. celebensis XC143 (SQ(-)strains). In this report, another gene-qumB, nearing the 3’-end of qumA, had the same transcriptional direction with qumA and showed specific to the five X. arboricola pathovars in Xanthomonas. Therefore, the nucleotide sequence of qumA and qumB were used to design two kinds of specific primer pairs(SQ-F2+SQ-R2 and Porin-F2+Porin-R) to distinguish X. arboricola from the other Xanthomonas genomic DNA. On the other hand, we also used two primer pairs (Q-F’+Porin-R’) to prove that qumA and qumB got together (qumA-qumB gene cluster) in the five X. arboricola pathovars by PCR (polymerase chain reaction). On the both sides of qumA-qumB, we found mem (membrane protein gene)、unknown ORF (uncertainly gene) and pep (peptidase gene)were together clustered in the order mem-unknown-qumA-qumB-pep and they had the same transcriptional direction in X. arboricola pv. juglandis strain XJC5. The genes homology to mem、unknown ORF and pep from X. arboricola pv. juglandis strain XJC5 existed not only in X. arboricola by Southern hybridization. In other words, almost all of the Xanthomonas had the three genes homology to mem、unknown ORF and pep in X. arboricola pv. juglandis strain XJC5. Therefore, we designed the other two kinds of primer pairs (X-F’+Q-R’ and Porin-F’+Pep-R’) to ensure that qumA-qumB in the five Xanthomonas pathovars were all between unknown and pep. This result indicated qumA-qumB gene cluster was so specific to X. arboricola that it is possible came from foreign biology into Xanthomonas. According to the five probes, the internal fragments of mem、unknown ORF 、qumA、qumB and pep, we could division 33 pathovars of Xanthomonas into six classes:class I contained X. hortorum pv. pelargonii strain XP15(T) and X. punicae strain XP177(T) which could not hybrid to all of the five probes;class II contained X. campestris pv. mangiferaeindicae strain XCM28-2 which could only hybrid to unknown probe;class III contained X. arrhenatheri strain XA(T)、X. poae strain XP(T) and X. phlei strain XP(T) (belong to X. campestris DNA homology group 3) which could only hybrid to mem and pep probes;class IV contained X. eucalypti strain XE104(T) which could only hybrid to mem and unknown probes;the other which could only hybrid to mem、unknown and pep probes were called class V;class VI was the X. arboricola which could hybrid to all of the five probes. Using the five probes, we could distinguish XCM28-2 and XE104(T) from the other 31 pathovars of Xanthomonas genomic DNA by Southern hybridization. If we collect enough probes in the future, maybe we can use this method to distinguish all of the Xanthomonas pathovars. Because of qumA-qumB was specific to the five X. arboricola pathovars and was not found in the other Xanthomonas species, we suspected that the qumA-qumB gene cluster came from other plant pathogens. To understood whether other plant pathogens also had the ability to metabolize quinate. Our laboratory tested some plant pathogens of Erwinia and Pseudomonas. We found that E. ananas、E. herbicola、E. herbicola pv. millettiae、E. rhapontici以及E. cypripedii (belong to Erwinia cluster I and cluster II) have the same color change in SQY medium (dark green) and P. syringae have the different color change in SQY medium (yellowwish). Moreover, the qumA probe could hybrid to all the test Erwinia belong to Erwinia cluster I、cluster II strains and two pathovars of P. syringae and qumB probe could only hybrid to E. rhapontici strain ER1 (belong to Erwinia cluster II) alone so far tested. So that qumA or qumB at least existed between the three kinds of plant pathogens, and might be took place horizontal transfer between them.
論文目次目 錄 中文摘要 英文摘要 前言 材料與方法 菌種及培養條件 qumA兩側序列的次選殖 核酸序列之定序與分析 設計PCR引子組合以確認X. arboricola中qumA-qumB的座落位置 植物病原細菌代謝quinate能力的測試 基礎分生技術 實驗結果 估計包含qumA且只存在於X. arboricola pv. juglandis strain XJC5的核 酸片段大小 qumA在Xanthomonas中的存在情形 靠近qumA 3’端方向序列的分析 分析X. arboricola中不同病原小種的qumA與qumB的相對位置 qumA-qumB兩旁的基因種類、排列順序以及在Xanthomonas和其他植 物病原菌中的存在情形 分析X. arboricola中不同病原小種的qumA-qumB的座落位置 qumA基因在其他植物病原菌中的存在情形 討論 參考文獻 圖表 英文縮寫表
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