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標題: 台灣傳染性支氣管炎病毒核殼基因重組與正向天擇之探討
Characterization of recombination and positive selection in nucleocapsid gene of Taiwanese infectious bronchitis viruses
作者: 郭淑明
Kuo, Shu-Ming
關鍵字: infectious bronchitis virus;傳染性支氣管炎病毒;nucleocapsid gene;recombination;positive selection;RNA-binding capacity;coronavirus;surface plasmon resonance;核殼基因;重組;正向天擇;RNA結合能力;冠狀病毒;表面電漿共振
出版社: 生命科學系所
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雞傳染性支氣管炎由冠狀病毒第三群的傳染性支氣管炎病毒所引起,成為危害全世界養雞業的主要禽病之一。在台灣雖然已經廣泛使用進口疫苗株 (大多為美國麻州血清型之H120),但仍無法控制疫情、造成巨大的經濟損失。為了研究台灣傳染性支氣管炎病毒基因之親緣關係,在本研究中我們將台灣本土傳染性支氣管炎病毒株TW2575/98 首次全基因組解序 (GenBank DQ646405),並與其他傳染性支氣管炎病毒的基因序列進行親緣、重組與天擇分析。親緣分析所有非結構與結構基因,發現台灣傳染性支氣管炎病毒除了核殼基因以外,其他基因皆與中國較近、與美國較遠,這也許能夠解釋進口疫苗一直難以控制台灣傳染性支氣管炎病毒爆發之情形;而台灣傳染性支氣管炎病毒之核殼基因親緣分析則與美國較近、與中國較遠,獲得與其他大多數基因親緣不一致的結果。進一步偵測到台灣傳染性支氣管炎病毒核殼基因的5’端,也就是對應到核殼蛋白質氮端功能區域的序列與美國株發生重組,此情形發生在所有測試的台灣傳染性支氣管炎病毒,因此認為遠在台灣祖先的傳染性支氣管炎病毒之核殼基因就已經發生重組。為了更進一步了解台灣傳染性支氣管炎病毒在面臨普遍施用進口疫苗的免疫壓力下,還重組為與美國株近似的核殼基因序列之意義,藉由PAML 4軟體分析,發現核殼蛋白質第64 與123 個胺基酸預測為選擇性壓力造成的正向天擇位點,而這兩個正向天擇位點除了恰位於前述核殼基因重組的區域內,並且根據冠狀病毒核殼蛋白質胺基酸序列的結構排比,亦位司RNA結合的核殼蛋白質氮端功能區域。因此將這兩個正向天擇位點的胺基酸定點突變後進行表面電漿共振分析,結果發現T64P、T64N與T123V突變的核殼蛋白質與RNA結合能力顯著降低,兩個正向天擇位點的突變可能減弱核殼蛋白質與病毒RNA的辨識能力,並進一步間接影響RNA複製與轉錄。換言之,台灣傳染性支氣管炎病毒核殼蛋白質的氮端功能區域透過正向天擇增強RNA結合能力以提高演化適應度以利在台灣長期使用進口疫苗從而產生的免疫壓力之環境下生存。總結本研究,由台灣傳染性支氣管炎病毒核殼基因的親緣不一致與正向天擇的結果,推論以免疫雞隻為宿主的RNA病毒經由5’端核殼基因重組與兩個胺基酸位點之正向天擇,而演化成一個具演化優勢的本土演化族群之發現是首次被提出。

Infectious bronchitis (IB) is currently one of the major diseases affecting the poultry industry around the world; it is caused by the avian infectious bronchitis virus (IBV), a member of the group 3 coronaviruses (CoVs). IBV has caused tremendous economic losses in Taiwan (TW) and has even affected flocks that had been extensively immunized with the Massachusetts (Mass)-serotype (mostly H120) vaccines. To investigate the genomic features of TW IBV and to further infer its phylogeny, we first sequenced the complete genome of the Taiwanese IBV field isolate TW2575/98 (GenBank DQ646405) and compared it to the genomes of other IBV strains and conducted phylogenetic, recombination, and selection analyses. Based on phylogenetic analysis of all of the nonstructural and most of the structural genes, we found that TW IBVs are genetically distinct from the IBVs of the United States of America (US) but similar to those in China (CH). This finding may explain why Mass-serotype vaccines fail to control IBV outbreaks in Taiwan. In contrast, only the nucleocapsid (N) gene of TW IBV showed phylogenetic incongruence. Using recombination programs, we indicated that putative RNA recombination between the TW and US IBVs at the 5' end of the N gene that corresponds to the N-terminal domain (NTD) of the N protein is responsible for this phylogenetic incongruence. Surprisingly, the recombinant N gene was found in all of the TW IBV isolates that were tested, suggesting that a recombination event might have led to the establishment of a founder lineage. To further understand the significance of TW IBVs evolving into a US-like genotype under the immune stress of the Mass-serotype vaccines, we further performed an adaptive evolutionary analysis using the PAML 4 package and identified two positively selected sites at the amino acids 64 and 123 in the putative crossover region of the N protein. According to the structure-based alignment of the CoV N amino acid sequences, these two residues are located in the N-terminal RNA-binding domain of the N protein. We speculated that the positive selection in the NTD of the N protein (N-NTD) of TW IBVs might act to increase its RNA-binding capacity. To evaluate the interaction of the N protein with viral RNA at the positively selected sites using surface plasmon resonance (SPR), we found that the RNA-binding capacity of the N-NTDs of T64P, T64N, and T123V mutants generated by site-directed mutagenesis significantly decreased, indicating impaired viral RNA recognition by these mutants that may further indirectly affect RNA replication and transcription. In other words, our experimental results supported the functional significance of the positively selected sites in RNA-binding capacity, indicating that the N-NTD of TW IBV lineages might been evolved under the adaptive selection through indirectly increased efficiency of RNA replication and transcription for increasing evolutionary fitness, therefore benefiting their survival. In conclusion, the unique phylogenetic incongruence and positively selected sites in the N-NTD of TW IBVs provide insights for the first time into the mechanism by which a recombinant RNA virus with evolutionally selected residues can emerge as a local dominant population in immunized flocks.
其他識別: U0005-2701201116413100
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