A comparative analysis of ABC transporters in complete microbial genomes
A comparative analysis of ABC transporters in complete microbial genomes
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DOI：
10.1101/gr.8.10.1048
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发表时间：
1998-10-01
期刊：
影响因子：
7
通讯作者：
Kanehisa, M
中科院分区：
文献类型：
--
作者：
Tomii, K;Kanehisa, M
ABC转运蛋白是所有细菌物种中最大的同源基因编码的细胞易位机制的主要类别。在三种分子成分的基因中经常发现操纵子结构：atp结合蛋白、膜蛋白和底物结合蛋白。在这里，我们通过比较和分类七种微生物全基因组中已知和假定的ABC转运蛋白，建立了一个“同源类群表”。我们的程序是首先通过序列相似性搜索和分类最保守的atp结合蛋白组分，然后通过检查其他组分的相似性和操纵子结构的保守性对整个转运蛋白单元进行分类。由此得到的25个ABC转运蛋白同源群与已知功能密切相关。通过分析，我们可以为假设的转运蛋白分配底物特异性，预测额外的转运蛋白操纵子，并识别新型的假设转运蛋白。同源类群表也被用作另外四个基因组功能分配的参考数据集。一般来说，尽管在细菌进化过程中基因位置发生了广泛的洗牌，但ABC转运体操纵子是高度保守的。然而，在胞囊菌中，形成操纵子的倾向明显减少。我们的结果表明，祖先的ABC转运操纵子可能在细菌和古细菌形成之前的进化早期就出现了。
The ABC transporter is a major class of cellular translocation machinery in all bacterial species encoded in the largest set of paralogous genes. The operon structure is frequently found for the genes of three molecular components: the ATP-binding protein, the membrane protein, and the substrate-binding protein. Here, we developed an "ortholog group table" by comparison and classification of known and putative ABC transporters in the complete genomes of seven microorganisms. Our procedure was to first search and classify the most conserved ATP-binding protein components by the sequence similarity and then to classify the entire transporter units by examining the similarity of the other components and the conservation of the operon structure. The resulting 25 ortholog groups of ABC transporters were well correlated with known functions. Through the analysis, we could assign substrate specificity to hypothetical transporters, predict additional transporter operons, and identify novel types of putative transporters. The ortholog group table was also used as a reference data set For functional assignment in four additional genomes. in general, the ABC transporter operons were strongly conserved despite the extensive shuffling of gene locations in bacterial evolution. In Synechocystis, however, the tendency of forming operons was clearly diminished. Our result suggests that the ancestral ABC transporter operons may have arisen early in evolution before the speciation of bacteria and archaea.