Computational inference of scenarios for α-proteobacterial genome evolution
Computational inference of scenarios for α-proteobacterial genome evolution
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DOI：
10.1073/pnas.0400975101
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发表时间：
2004-06-29
影响因子：
11.1
通讯作者：
Andersson, SGE
中科院分区：
文献类型：
--
作者：
Boussau, B;Karlberg, EO;Andersson, SGE
α -变形菌被认为是线粒体的起源，显示出10倍的基因组大小变异，为研究细菌基因组大小进化提供了一个很好的模型系统。在这里，我们使用计算方法来推断祖先的基因集，并量化基因沿着α -变形细菌物种树的分支的通量。我们的研究表明，在使植物相关细菌多样化的分支上，基因大量扩增，而在分离动物和人类细胞内细菌的分支上，基因极度缺失。基因数量的改变主要影响与调节、运输和小分子代谢相关的功能类别，其中许多是由位于辅助染色体上的同源基因家族编码的。结果表明，a-变形菌祖先含有3000 - 5000个基因，是一种自由生活的、需氧的、可运动的细菌，具有用于宿主细胞和环境相互作用的毛和表面蛋白。大约三分之一的祖先基因在真核生物中没有同源物。超过40%没有真核对应物的基因编码的蛋白质在α -变形细菌中是保守的，但尚未确定其功能。这些基因从未进入真核生物，但广泛分布于细菌中，可能代表细菌的药物靶点，应该是未来功能表征的主要候选者。
The alpha-proteobacteria, from which mitochondria are thought to have originated, display a 10-fold genome size variation and provide an excellent model system for studies of genome size evolution in bacteria. Here, we use computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree. Our study reveals massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches separating intracellular bacteria of animals and humans. Alterations in gene numbers have mostly affected functional categories associated with regulation, transport, and small-molecule metabolism, many of which are encoded by paralogous gene families located on auxiliary chromosomes. The results suggest that the a-proteobacterial ancestor contained 3,000-5,000 genes and was a free-living, aerobic, and motile bacterium with pili and surface proteins for host cell and environmental interactions. Approximately one third of the ancestral gene set has no homologs among the eukaryotes. More than 40% of the genes without eukaryotic counterparts encode proteins that are conserved among the alpha-proteobacteria but for which no function has yet been identified. These genes that never made it into the eukaryotes but are widely distributed in bacteria may represent bacterial drug targets and should be prime candidates for future functional characterization.