| 其他摘要 | 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. |
修改评论