Tracing evolutionary footprints to identify novel gene functional linkages.
Tracing evolutionary footprints to identify novel gene functional linkages.
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追踪进化足迹以识别新的基因功能联系
DOI：
10.1371/journal.pone.0066817
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Liu P
中科院分区：
文献类型：
--
作者：
Chen Y;Yang L;Ding Y;Zhang S;He T;Mao F;Zhang C;Zhang H;Huo C;Liu P
系统测定基因功能是充分了解每个基因对细胞中分子功能正确执行的精确贡献的重要步骤。基因功能连锁被定义为描述一组具有相似功能的基因之间的关系。随着数千个基因组的测序，出现了利用基因进化信息来识别基因功能联系的绝佳机会。为此，我们建立了一种计算方法（称为TRACE），通过由341个原核生物基因组构建的基因功能网络来追踪基因足迹。 TRACE 性能经过验证并成功测试，可预测酶功能以及途径组分。迄今为止尚未描述的产油细菌红球菌属的染色体分配样蛋白 ro03654。 RHA1（RHA1）被预测并通过实验验证，其缺失突变体与RHA1野生型相比显示出生长抑制。此外，四种蛋白质被预测充当原核 SNARE 样蛋白质，其中两种被证明位于质膜上。因此，我们相信TRACE是一种通过追踪进化事件来推断原核基因功能联系的有效新方法。
Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme functions as well as components of pathway. A so far undescribed chromosome partitioning-like protein ro03654 of an oleaginous bacteria Rhodococcus sp. RHA1 (RHA1) was predicted and verified experimentally with its deletion mutant showing growth inhibition compared to RHA1 wild type. In addition, four proteins were predicted to act as prokaryotic SNARE-like proteins, and two of them were shown to be localized at the plasma membrane. Thus, we believe that TRACE is an effective new method to infer prokaryotic gene functional linkages by tracing evolutionary events.
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