The nucleoli, including their proteomes, of higher eukaryotes have been extensively studied, while few studies about the nucleoli of the lower eukaryotes – protists were reported. Giardia lamblia, a protist with the controversy of whether it is an extreme primitive eukaryote or just a highly evolved parasite, might be an interesting object for carrying out the nucleolar proteome study of protists and for further examining the controversy. Using bioinformatics methods, we reconstructed G. lamblia nucleolar proteome (GiNuP) and the common nucleolar proteome of the three representative higher eukaryotes (human, Arabidopsis, yeast) (HEBNuP). Comparisons of the two proteomes revealed that: 1) GiNuP is much smaller than HEBNuP, but 78.4% of its proteins have orthologs in the latter; 2) More than 68% of the GiNuP proteins are involved in the “Ribosome related” function, and the others participate in the other functions, and these two groups of proteins are much larger and much smaller than those in HEBNuP, respectively; 3) Both GiNuP and HEBNuP have their own specific proteins, but HEBNuP has a much higher proportion of such proteins to participate in more categories of nucleolar functions. For the first time the nucleolar proteome of a protist - Giardia was reconstructed. The results of comparison of it with the common proteome of three representative higher eukaryotes -- HEBNuP indicated that the simplicity of GiNuP is most probably a reflection of primitiveness but not just parasitic reduction of Giardia, and simultaneously revealed some interesting evolutionary phenomena about the nucleolus and even the eukaryotic cell, compositionally and functionally.

中文翻译：

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贾第鞭毛虫核仁蛋白质组的鉴定和进化分析

已经对高等真核生物的核仁，包括其蛋白质组进行了广泛的研究，而关于低等真核生物的核仁的研究很少，仅报道了原生生物。对于是否是极端原始的真核生物还是只是高度进化的寄生虫，有争议的原虫Giardia lamblia，可能是进行原核生物的核仁蛋白质组学研究并进一步研究该争议的有趣对象。使用生物信息学方法，我们重建了G. lamblia核仁蛋白质组（GiNuP）和三个代表性的高等真核生物（人，拟南芥，酵母）（HEBNuP）的常见核仁蛋白质组。两种蛋白质组的比较显示：1）GiNuP比HEBNuP小得多，但78.4％的蛋白质在后者中具有直系同源物；2）超过68％的GiNuP蛋白参与“核糖体相关”功能，其他的参与其他功能，这两类蛋白质分别比HEBNuP中的蛋白质大得多和小得多；3）GiNuP和HEBNuP都有自己的特定蛋白质，但是HEBNuP含有更多比例的此类蛋白质，以参与更多类别的核仁功能。首次重建了原生生物贾第虫的核仁蛋白质组。将其与三种代表性的高等真核生物的常见蛋白质组进行比较的结果表明，GiNuP的简单性很可能反映了贾第虫的原始性，而不仅仅是寄生减少，同时还揭示了一些关于核仁和核仁的有趣的进化现象。甚至是真核细胞