Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).
复制标题
通过基因组注释，使用直系同源蛋白（COGS）的基因组注释来理解Crenarchaeon的第一个基因组序列。
DOI：
10.1186/gb-2000-1-5-research0009
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发表时间：
2000
期刊：
影响因子：
12.3
通讯作者：
中科院分区：
文献类型：
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作者：
标准档案序列数据库还没有被设计成基因组注释的工具，而且远不是最优的。我们利用COGs数据库重新标注了两种古细菌的基因组，分别是Aeropyrum pernix和Pyrococcus abyssi。Aeropyrum pernix是绿古细菌中第一个测序的成员。利用COGNITOR程序将A. pernix和P. abyssi蛋白分配给COGs；通过使用PSI-BLAST和TBLASTN程序进行额外的数据库搜索，对结果进行了逐案验证。利用保守的序列相似性阈值，我们预测了300多个羊角草蛋白的功能，与原始注释相比，预测结果提高了约50%。A. pernix与之前在Euryarchaeota中发现的大多数保守蛋白核心相同。基于COGs基因组共发生的聚类分析或距离矩阵树构建表明，尽管与两种焦球菌（Pyrococci）类群相似，但在古细菌中形成了一个不同的类群。在这些分析中，没有迹象表明绿古菌和真核生物之间存在特定的关系。在Euryarchaeota和大多数细菌中保守的几种蛋白质在a . pernix中意外地缺失，包括一整套从头合成嘌呤生物合成酶，GTPase FtsZ（细菌和Euryarchaeota细胞分裂机制的关键组成部分），以及trna特异性假尿嘧啶合成酶，以前被认为是普遍存在的。A. pernix在48个不包含任何euryarchaeal成员的COGs中表示。这些蛋白质中有许多是TCA循环酶和电子传递链酶，反映了A. pennix的有氧生活方式。在系统发育分析的基础上组织的专用数据库，并根据已知和预测的蛋白质功能进行精心策划，为基因组注释提供了显著的改进。差异基因组显示方法有助于系统地研究基因库的共同和独特特征，并在某些情况下揭示意想不到的联系，这些联系可能表明系统发育上遥远的生物体之间的功能相似性和侧基因交换。
Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (COGs) to reannotate the genomes of two archaea, Aeropyrum pernix, the first member of the Crenarchaea to be sequenced, and Pyrococcus abyssi. A. pernix and P. abyssi proteins were assigned to COGs using the COGNITOR program; the results were verified on a case-by-case basis and augmented by additional database searches using the PSI-BLAST and TBLASTN programs. Functions were predicted for over 300 proteins from A. pernix, which could not be assigned a function using conventional methods with a conservative sequence similarity threshold, an approximately 50% increase compared to the original annotation. A. pernix shares most of the conserved core of proteins that were previously identified in the Euryarchaeota. Cluster analysis or distance matrix tree construction based on the co-occurrence of genomes in COGs showed that A. pernix forms a distinct group within the archaea, although grouping with the two species of Pyrococci, indicative of similar repertoires of conserved genes, was observed. No indication of a specific relationship between Crenarchaeota and eukaryotes was obtained in these analyses. Several proteins that are conserved in Euryarchaeota and most bacteria are unexpectedly missing in A. pernix, including the entire set of de novo purine biosynthesis enzymes, the GTPase FtsZ (a key component of the bacterial and euryarchaeal cell-division machinery), and the tRNA-specific pseudouridine synthase, previously considered universal. A. pernix is represented in 48 COGs that do not contain any euryarchaeal members. Many of these proteins are TCA cycle and electron transport chain enzymes, reflecting the aerobic lifestyle of A. pernix. Special-purpose databases organized on the basis of phylogenetic analysis and carefully curated with respect to known and predicted protein functions provide for a significant improvement in genome annotation. A differential genome display approach helps in a systematic investigation of common and distinct features of gene repertoires and in some cases reveals unexpected connections that may be indicative of functional similarities between phylogenetically distant organisms and of lateral gene exchange.