摘要
形态学以及分子生物学的证据表明文昌鱼是脊索动物中的基底生物,是研究脊椎动物形态、发育以及免疫系统的起源与进化的重要模式生物。随着比较免疫学的迅速发展,以及佛罗里达文昌鱼基因组测序的完成,关于文昌鱼免疫的研究越来越引起人们的关注。因此,本论文在文昌鱼EST数据库的基础上以文昌鱼免疫相关基因LITAF、 GNBP以及免疫相关microRNA为研究对象,通过分子克隆、实时定量、基因芯片、比较基因组学以及免疫生物学等检测手段得到以下几个方面的研究结果：
1.本论文首先系统的对文昌鱼五个发育阶段的EST序列进行了比较分析,通过聚类拼接在卵、原肠胚、神经胚、幼虫及成虫中分别得到3364、3230、10,299、4052、3866个contig序列以及193、183、933、178、151个singlet序列。在这些序列中共预测得到25796个ORF,其中有6529个预测的ORF能够与Uniprot数据库中已知的蛋白序列相匹配。同时也对不同发育阶段的基因进行了GO功能注释,结果显示在神经胚阶段的GO注释要明显高于其它发育阶段。同时从BLASTx的结果中找到20个可能与免疫相关的基因,为后续免疫基因功能的研究提供了数据基础。此外,我们还对这些基因进行了microRNA靶标分析。最后基于以上分析结果构建了文昌鱼EST数据库http://rich.yunda.org/test/amphioxusest/。
2.GNBP蛋白是一个重要的模式识别蛋白,能够驱使宿主抵御病原微生物的入侵。我们从白氏文昌鱼中克隆了一个GNBP基因,命名为AmphiGNBP,该基因编码558个氨基酸,序列分析表明该基因包含一个保守的p-1,3-葡聚糖识别与结合结构域,与其它物种不同的是该基因还包含两个额外的WSC结构域。对该基因的组织表达模式分析发现该基因主要是在文昌鱼的免疫组织肝盲囊及肠中高表达。脂多糖(LPS)刺激实验表明LPS能够诱导该基因的表达。这些研究揭示了文昌鱼AmphiGNBP基因与其它已知基因的共性与特性,为深入的研究GNBP基因的功能与进化提供了基础。
3.TNF-α是一个重要的细胞因子,在LPS刺激的条件下能够调节先天免疫反应。脂多糖诱导的]TNF-α因子(LITAF)是近年来新发现的一个转录因子能够调控TNF-α以及一些其它炎症因子的表达。本论文首次在白氏文昌鱼中克隆得到了一个LITAF基因,命名为AmphiLITAF,该基因的DNA序列长度大概有1.6kb左右,能够转录产生一个827个碱基的cDNA序列,编码127个氨基酸。序列分析表明该基因包含一个保守的LITAF结构域,与其它物种的氨基酸序列相似性在37%-60%之间。对该基因的空间表达模式分析发现,该基因在肝盲囊和肠中高表达,在肌肉、鳃及性腺中次之,而在脊索中的表达量最低。LPS刺激实验表明在文昌鱼中LPS能够在一定程度上诱导AmphiLITAF基因的表达。该实验为进一步弄清LITAF基因在文昌鱼免疫中的作用及对该基因深入的进化分析提供了线索。
4.采用小RNA深度测序的方法对白氏文昌鱼进行了小RNA测序,共得到568个microRNA (miRNA)。其中171个nicroRNA与佛罗里达文昌鱼中的nicroRNA一致,其余的497个microRNA则为在文昌鱼中新发现的microRNA,其中302个是在其它物种中存在的,而另外的95个microRNA则是在文昌鱼中特异存在的。利用芯片技术对PBS处理组及副溶血性弧菌处理组(PV)的文昌鱼microRNA进行定点检测,通过对不同处理组中microRNA转录组的比较分析找到差异表达的nicroRNA17个,进一步对这些nicroRNA基因进行靶标预测,发现其靶基因中可能与免疫相关的基因共31个,·为进一步开展文昌鱼中microRNA与免疫基因相互作用的研究提供了全新的数据。
本论文搭建了Windows平台的数据库,提供了可视化友好的用户界面,为文昌鱼的基因组学、分子进化及发育生物学研究提供了有效的工具。基于EST数据库的信息首次对文昌鱼AmphiGNBP及AmphiLITAF基因进行了功能分析,为更全面的阐述文昌鱼的免疫调控提供了数据基础。对文昌鱼免疫相关microRNA的筛选为研究文昌鱼的免疫调控补充了新鲜的数据,有利于揭示全新的免疫调控机制。
Both morphological and molecular evidence show that amphioxus is the basal chordate and is a crucial organism for understanding the chordate evolution including the origin of the immune system, morphology and development. With the rapid development of comparative immunology, as well as the completion of the Branchiostoma floridae genome sequencing, the attention was focused on amphioxus immune increasingly. In this study, based on the ESTs of amphioxus, using molecular cloning, real-time PCR, microarray, comparative genomics and immunobiology technology, we studied the immune-related gene LITAF, GNBP and microRNAs. The results as follows:
1. We have systematically compared amphioxus ESTs from five developmental stages. For the egg, gastrula, neurula, larva and adult stages, amphioxus ESTs were assembled, respectively, into3364,3230,10,299,4052and3866contigs, and193,183,933,178and151singlets.25,796ORFs were identified, of which6,529predicted ORFs have found matches from the UniProt database. The analysis suggested that there were significantly more GO terms assigned to the conreads of neurula stage. Meanwhile, we found20putative immune-related genes from these BLASTx results, providing the prilimilary data for functional study of amphioxus immunity. In addition, we also analyzed the target gene of these microRNAs. A web interface was developed for visualization of the contigs, miRNAs and annotations (http://www.rich.yunda.org/test/amphioxusest/).
2. Gram-negative bacteria-binding proteins (GNBPs) are important pattern recognition proteins (PRPs), which can initiate host defense in response to pathogen surface molecules. In this study, we identified and characterized an amphioxus GNBP gene (designated as AmphiGNBP). The AmphiGNBP encodes a putative protein with558aa, which contains a conserved β-1,3-glucan recognizing and binding domain. Interestingly, AmphiGNBP encodes two extra WSC (cell wall integrity and stress response component) domains, which are unique in AmphiGNBP and not found in those known GNBPs from other species. The AmphiGNBP was mainly expressed in immune tissues, such as hepatic cecum and intestine. The expression of AmphiGNBP was affected after LPS stimulation. These studies disclose the particularity and universality of AmphiGNBP and will provide profound insights into the function and evolution of GNBP.
3. TNF-a is an important cytokine that can be stimulated by Lipopolysaccharide (LPS) to regulate the innate immunity. The lipopolysaccharide-induced TNF-a factor (LITAF) functions as a transcription factor for regulating the expression of TNF-a as well as various inflammatory cytokines in response to LPS stimulation. In this study, we identified and characterized an amphioxus LITAF gene (designated as AmphiLITAF). First, we identified the AmphiLITAF from the amphioxus and found that AmphiLITAF gene with～1.6kb in length has a827bp cDNA transcription product which encodes a putative protein with127amino acids containing conserved LITAF-domain, the deduced amino acid of AmphiLITAF shared37-60%similarity with the LITAFs from other species; second, we uncovered the spatial distribution of the LITAF in different tissues, the expression level of AmphiLITAF mRNA was the highest in hepatic cecum and intestine, moderate in muscles, gills and gonad, and the lowest in notochord; finally, we discovered that the expression of AmphiLITAF was affected after LPS stimulation. Our findings provide an insight into the innate immune response in the amphioxus and the evolution of the LITAF family.
4. Using small RNA deep sequencing technology, a total of568microRNAs (miRNA) have been found in Branchiostoma belcheri.171microRNA sequences are consistent with those of Branchiostoma floridae, the rest of the497microRNAs are newly discovered in amphioxus. Among these newly discovered microRNAs,302microRNAs are conserved in other species, and95microRNAs are amphioxus specific microRNAs. We used microRNA microarray technology to analysis six microRNA transcriptomes prepared from amphioxus under PBS stimulation and amphioxus infection with Vibrio parahaemolyticus (PV) at different time points. By comparing the data from different treatment groups, we found18immune-related microRNAs. These microRNAs may be interaction with31immune-related genes. These results of our study suggest that miRNAs play an important role in the coordinated regulation of immune-related gene expression in the amphioxus.
In this thesis, we built amphioxus EST database under the windows operation system. A web interface was developed for visualization of the contigs, microRNAs and annotations. The constructed AmphiEST database may serve as an essential resource for future studies of the development and evolution of amphioxus. Based on the EST database, we firstly identified and characterized LITAF and GNBP gene homolog from amphioxus, and our findings provide an insight into the innate immune response in the amphioxus and the evolution of the LITAF and GNBP family. Screening of amphioxus immune-related microRNAs will help with the development of new immune mechanism to prevent or treat Vibrio parahaemolyticus infections in the amphioxus.
引文
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