Biased biological functions of horizontally transferred genes in prokaryotic genomes
Biased biological functions of horizontally transferred genes in prokaryotic genomes
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DOI：
10.1038/ng1381
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发表时间：
2004-07-01
期刊：
影响因子：
30.8
通讯作者：
Gojobori, T
中科院分区：
文献类型：
--
作者：
Nakamura, Y;Itoh, T;Gojobori, T
水平基因转移是促进微生物基因组多样化的主要机制之一（1-3）。为了阐明原核生物种间基因流的全貌，我们开发了一种新的方法，通过贝叶斯推断与训练模型的核苷酸组成检测水平转移的基因和它们可能的供体。我们的方法给出了每个基因序列的平均后验概率（水平转移指数），低水平转移指数表示最近的水平转移。我们发现，116个原核生物完整基因组中有14%的开放阅读框发生了最近的水平转移。基于此数据集，我们定量地确定了水平转移基因的生物学功能，除了移动的元件基因，偏向于三个类别：细胞表面，DNA结合和致病性相关的功能。因此，基因的可转移性似乎在很大程度上取决于它们的功能。
Horizontal gene transfer is one of the main mechanisms contributing to microbial genome diversification(1-3). To clarify the overall picture of interspecific gene flow among prokaryotes, we developed a new method for detecting horizontally transferred genes and their possible donors by Bayesian inference with training models for nucleotide composition. Our method gives the average posterior probability ( horizontal transfer index) for each gene sequence, with a low horizontal transfer index indicating recent horizontal transfer. We found that 14% of open reading frames in 116 prokaryotic complete genomes were subjected to recent horizontal transfer. Based on this data set, we quantitatively determined that the biological functions of horizontally transferred genes, except mobile element genes, are biased to three categories: cell surface, DNA binding and pathogenicity-related functions. Thus, the transferability of genes seems to depend heavily on their functions.