Birth and death of orphan genes in Rickettsia
Birth and death of orphan genes in Rickettsia
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DOI：
10.1093/molbev/msg175
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发表时间：
2003-10-01
影响因子：
10.7
通讯作者：
Andersson, SGE
中科院分区：
文献类型：
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作者：
Amiri, H;Davids, W;Andersson, SGE
数以千计的功能未知的物种特异性基因，即所谓的孤儿基因，其起源和进化一直是个谜。在这里，我们使用立克次体作为参考系统，研究了孤儿序列进化的速率和模式。在本研究中检查的康氏立克次体孤儿中，80%被发现是短基因片段或邻近基因短片段的融合体。我们重建了全长基因的推定序列，短孤儿片段被认为源自该序列。由此重建的基因之一显示出与锚蛋白重复蛋白家族的弱相似性，这一鉴定得到了比较分子模型的有力支持。对基因片段化模式的研究强调了短重复序列作为重组事件目标的重要性，重组事件导致序列丢失和短的、瞬时的开放阅读框的形成。我们的分析表明，即使在任何当代物种中不存在全长开放阅读框的情况下，也可以推断出共同祖先中存在的基因序列。这种重建支持识别丢失的蛋白质功能，并暗示重要的生活方式改变。
The origin and evolution of the thousands of species-specific genes with unknown functions, the so-called orphan genes, has been a mystery. Here, we have studied the rates and patterns of orphan sequence evolution, using the Rickettsia as our reference system. Of the Rickettsia conorii orphans examined in this study, 80% were found to be short gene fragments or fusions of short segments from neighboring genes. We reconstructed the putative sequences of the full-length genes from which the short orphan fragments are thought to have originated. One of the genes thus reconstructed displays weak similarity to the ankyrin-repeat protein family, an identification that is strongly supported by comparative molecular modeling. Studies of the patterns of gene fragmentation underscore the importance of short repeated sequences as targets for recombination events that result in sequence loss and the formation of short, transient open reading frames. Our analysis demonstrates that gene sequences present in the common ancestor can be inferred even in cases when no full-length open reading frame is present in any of the contemporary species. Such reconstructions support the identification of lost protein functions and hint at important lifestyle changes.