贾第虫核仁蛋白基因组的鉴定及真核生物SSU Processome 的起源演化
文献类型：学位论文
| 作者 | 冯金梅 |
| 学位类别 | 博士 |
| 答辩日期 | 2012-05 |
| 授予单位 | 中国科学院研究生院 |
| 授予地点 | 北京 |
| 导师 | 文建凡 |
| 关键词 | 蓝氏贾第虫 核仁蛋白基因组 5S rRNA 系统 SSU processome 进化 |
| 其他题名 | Identification of the Nucleolar Protein Genome in Giardia lamblia and the Origin and Evolution of Eukaryotic SSU Processome |
| 学位专业 | 细胞生物学 |
| 中文摘要 | 核仁是真核细胞间期核中最明显的结构，其主要功能是作为rRNA转录、加工和核糖体亚基组装的场所。迄今，有关核仁的研究主要是在高等的真核生物上进行的，且已获得了三种高等真核生物的核仁蛋白质组数据，然而在单细胞原生生物中，有关核仁的研究较少。蓝氏贾第虫是一种单细胞原生生物，曾因其“还不具核仁结构”等一系列“原始性”特征而一度被认为是“最原始”的真核生物，而近年来也有观点认为其各种所谓的“原始”特征可能是高度适应寄生生活而“次生性退化”所致。本文首先运用生物信息学方法鉴定了贾第虫的核仁蛋白基因组，从而建立了第一个原生生物的核仁蛋白基因组；并将其与已知的真核生物基本的核仁蛋白基因组（Eukaryotic Basic Nucleolar Protein Genome, EBNPG）进行比较分析，对贾第虫的确切进化地位进行了探讨；其次，以研究得十分清楚的5S rRNA系统为对象，通过不同生物（特别是不同生活方式的掘食类）之间的系统比较分析进一步对贾第虫的“原始性”和“寄生退化性”进行了甄别性研究；最后，对核仁中负责核糖体小亚基pre-rRNA加工的SSU processome复合体的起源进化进行全面系统的研究。获得了如下的结果和结论： （1）贾第虫的核仁蛋白基因组含有255个核仁蛋白基因，包括216个已知真核生物核仁蛋白的直系同源物和39个贾第虫特异的核仁蛋白基因。GO注释分析表明这些核仁蛋白的主要功能是‘与核糖体相关’，而参与其它功能的蛋白数目极少。定位实验结果表明其有的蛋白只定位于核仁，也有的定位到核仁以外的区域。贾第虫核仁蛋白基因组与EBNPG有200个共同的蛋白，它们主要参与‘与核糖体相关’功能。仅存在于EBNPG的核仁蛋白（以人的数据为例）中，‘与核糖体相关’的蛋白比例降低，而其它功能类群的蛋白比例显著增多。这些研究结果不仅首次鉴定了单细胞原生生物贾第虫的核仁蛋白基因组，还表明其可能代表了真核生物分化前所共有的核仁蛋白基因组的情形，从而揭示了其核仁可能的“原始性”特征。此外，还表明核仁在真核生物进化早期的主要功能是‘与核糖体相关’，而其它各种功能可能是在贾第虫从真核生物底部分化后才逐渐发展起来。 （2）通过系统地收集、验证及鉴定工作，获得了贾第虫的三个分离株以及与贾第虫亲缘关系较近、同属掘食类的两种寄生和一种自由生活的原生生物的较为完整的5S rRNA系统的相关数据，进而系统比较分析了它们之间以及它们与古细菌、一般高等真核生物的5S rRNA系统。结果发现：1）不同株系的贾第虫均具有相同且简单的5S rRNA系统——不仅与一般真核生物典型的5S rRNA系统相比是最简单的，而且在这几种掘食类原生生物中也是最简单的；2）贾第虫的5S rRNA系统与古细菌的5S rRNA系统惊人的相似；3）寄生性物种的5S rRNA系统并不一定比自由生活物种的5S rRNA系统更为简单，相反，自由生活物种的5S rRNA系统的某些方面甚至比寄生性物种的更为简单。这些研究结果表明：贾第虫简单的5S rRNA系统是其原始性而非寄生退化性特征，其5S rRNA系统可能代表了从古细菌向真核生物典型的5S rRNA系统进化的早期阶段。贾第虫在其作为真核细胞的基本结构功能方面保留了其原始性，而在其一些与寄生生活密切相关的方面则可能因寄生而发生了次生性退化。因此，贾第虫应该是结合了“原始性”和“寄生次生退化性”于一身的一种“嵌合体”真核生物。 （3）基于基因组数据的系统调查分析表明：酵母SSU procesome的绝大多数组分广泛分布于现存所有真核生物类群中。仅有1-3个核糖体蛋白同源物存在于1375个调查的细菌基因组中，而有14个酵母的SSU processome 蛋白具有11个同源物广泛分布在67个调查的古细菌基因组中。分子系统分析和蛋白结构域组成分析的结果进一步显示：在原核生物进化为真核生物的过程中，这11个古细菌蛋白垂直遗传给真核生物，且其中的6个在真核生物的最近共同祖先（LECA）中经历了古老的基因重复。LECA中产生了大量真核特异的SSU processome蛋白，其中近一半仅由真核型的蛋白结构域组成，而另一半通过招募原核来源的蛋白结构域参与其形成。因此，本研究表明LECA可能已经具有了较为完善的与现存真核生物SSU processome接近的SSU processome。同时，首次描绘了SSU processome的起源与进化历史：SSU processome的雏形在古细菌中就已经出现；然后通过古老的基因重复、从头合成、招募原核来源的蛋白结构域来形成真核特异的蛋白等机制，在LECA中就已形成了复杂的SSU processome；在LECA分化成不同真核生物类群的过程中，通过不同水平的基因重复、丢失，以及谱系特异性的获得等多种进化方式，SSU processome在真核生物不同谱系中发生了进一步的复杂化和分化。此外，本研究还提示LECA已是一个复杂的真核细胞，它不仅已经具有复杂的SSU processome，甚至可能已经具有了核仁结构。 |
| 英文摘要 | Nucleolus is the most prominent subnuclear compartment in the interphase nucleus of a eukaryotic cell, and ribosomal biogenesis is its primary function. Until now, researches on nucleolus are mainly carried out on the higher eukaryotes, and three nucleolar protein genomes are available in higher eukaryotes, however, very few studies regarding to the nucleolus have been done in the unicellular protists. This greatly impedes the research on the evolution of nucleolus. Giardia lamblia is a unicellular protozoan, and it was considered to be the most primitive extant eukaryote by some researchers while a highly evolved parasite by others. Here, we identified the first nucleolar protein genome in G. lamblia, and established the first nucleolar protein genome in protist; then we compared it with the Eukaryotic Basic Nucleolar Protein Genome (EBNPG) to reveal the real evolutionary position of G. lamblia. Then, by comparing the well-studied 5S rRNA system among different organisms (especially for excavates which have different lifestyles), we have distinguished the primitive from the secondary parasitically-degenerated feature in G. lamblia. Finally, we comprehensively investigated the origin and evolution of the SSU processome which is a ribonucleoprotein complex required for the biogenesis of the 18S rRNA in nucleolus. The results and conclusions are as follows: (1) Using a combined computational program, we identified the nucleolar protein genome of G. lamblia, which has 255 nucleolar protein genes, including 216 orthologs of eukaryotic nucleolar proteins and 39 Giardia-specific nucleolar protein genes. Gene Ontology annotation indicated that the main function of giardial nucleolar proteins is ‘ribosome related’, and proteins involved in other functions are few. Localization experiment showed that several giardial nucleolar proteins uniquely localize in the nucleolus, while others localize in regions beyond the nucleolus. Two hundred nucleolar proteins are shared by the giardial nucleolar protein genome and EBNPG, and the primary function of them is ‘ribosome related’. Among the human nucleolar proteins which are present in EBNPG but absent in giardial nucleolar protein genome, the ration of proteins involved in the ‘ribosome related’ function decrease, while ratios of proteins involved in the other functional classes increase sharply. All these results indicated that we have not only established the nucleolar protein genome in unicellular protist G. lamblia for the first time, but also suggested that it may represent the common nucleolar protein genome in the ancestral of all eukaryotes, so we revealed the probably primitive feature of nucleolus in G. lamblia. Moreover, our results indicated that ‘ribosome related’ is the primary function of nucleolus in the early eukaryotes, and various other nucleolar functions arose at later point after the divergence of G. lamblia from the eukaryotic trunk. (2) By collecting and confirming pre-existing data and identifying new data, we obtained almost complete datasets of the system of three isolates of G. lamblia, two other parasitic excavates (Trichomonas vaginalis, Trypanosoma cruzi), and one free-living one (Naegleria gruberi). After comprehensively comparing each aspect of the system among these excavates and also with those of archaea and common eukaryotes, we found all the three Giardia isolates to harbor a same simplified 5S rRNA system, which is not only much simpler than that of common eukaryotes but also the simplest one among those of these excavates, and is surprisingly very similar to that of archaea; we also found among these excavates the system in parasitic species is not necessarily simpler than that in free-living species, conversely, the system of free-living species is even simpler in some respects than those of parasitic ones. The simplicity of Giardia 5S rRNA system should be considered a primitive rather than parasitically-degenerated feature. Therefore, Giardia 5S rRNA system might be a primitive system that is intermediate between that of archaea and the common eukaryotic model system, and it may reflect the evolutionary history of the eukaryotic 5S rRNA system from the archaeal form. Our results also imply G. lamblia might be a primitive eukaryote with secondary parasitically-degenerated features. (3) By phylogenetic distribution investigations, we found that the majority of yeast SSU processome proteins are widely distributed in all extant eukaryotic clades, and at most 1-3 ribosomal protein homologs of four of the yeast SSU processome proteins were found in 1375 bacteria, while 11 archaeal homologs to 14 of the yeast SSU processome proteins were observed in almost all 67 investigated archaea. Phylogenetic analysis showed that these 11 archaeal protein genes were vertically inherited by eukaryotes during the origin of eukaryotes from prokaryotes, and six of them underwent ancient gene duplication events that produced not only SSU processome proteins but also non-SSU processome ones in the Last Eukaryotic Common Ancestor (LECA). Protein domain composition analysis revealed that about half of eukaryote-specific SSU processome proteins are built up only with Eukaryotic protein domains, and the others are formed largely or only by recruiting prokaryote-original protein domains. Therefore, our results indicated that a rather perfect and nearly-modern SSU processome might have already formed in LECA. Besides, we have charted the picture of the origin and evolutionary history of SSU processome for the first time: a rudimentary SSU processome had likely arisen in archaea; then during the evolutionary origin of eukaryotes from prokaryotes, a complex SSU processome had formed in LECA through ancient gene duplication, de novo eukaryotic protein innovations, and recruiting prokaryote-original protein domains to form novel proteins; finally, during the divergence of various eukaryotic lineages from LECA, lineage-specific and species-specific gene duplications, lineage-specific gene innovations, and lineage-specific and species-specific gene losses, have complicated this complex further in diverse extant eukaryotes. Moreover, our study implied that LECA is a complex eukaryotic cell which had not only possessed the complicated SSU processome but also even harbored the nucleolus. |
| 语种 | 中文 |
| 公开日期 | 2012-06-07 |
| 源URL | [http://159.226.149.42:8088/handle/152453/6965]  |
| 专题 | 昆明动物研究所_真核细胞进化基因组 |
| 推荐引用方式 GB/T 7714 | 冯金梅. 贾第虫核仁蛋白基因组的鉴定及真核生物SSU Processome 的起源演化[D]. 北京. 中国科学院研究生院. 2012. |
入库方式： OAI收割
来源：昆明动物研究所
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