Dynamic evolution of translation initiation mechanisms in prokaryotes
Dynamic evolution of translation initiation mechanisms in prokaryotes
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DOI：
10.1073/pnas.1002036107
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发表时间：
2010-04-06
影响因子：
11.1
通讯作者：
Gojobori, Takashi
中科院分区：
文献类型：
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作者：
Nakagawa, So;Niimura, Yoshihito;Gojobori, Takashi
通常认为，原核翻译是由mRNA的5' UTR中的Shine-Dalgarno（SD）序列与16 S核糖体RNA的3'末端中的抗SD序列之间的相互作用引发的。然而，有两种特殊的机制，它们不需要SD序列用于翻译起始：一种是由核糖体蛋白S1（RPS 1）介导的，另一种是使用缺乏其5' UTR的无前导mRNA。为了了解翻译起始机制的进化变化，我们研究了SD序列作为原核生物翻译的有效起始子的普遍性。我们从277个物种（249个真细菌和28个古细菌）中鉴定了SD序列。我们还设计了一个SD指数，这是一个比例的SD含有基因的GC含量的差异考虑在内。我们发现，SD指数各不相同的原核生物物种，但在每个门是相似的。虽然抗SD序列在物种之间是保守的，但SD序列的丢失似乎在不同的门中独立地发生了多次。对于这些门，RPS 1介导的或无前导mRNA使用的翻译起始机制被认为在更大程度上起作用。此外，我们还发现一些物种，如蓝藻，可能获得新的翻译起始机制。我们的研究结果表明，尽管翻译起始对于每个物种基因组中的所有蛋白质编码基因都是不可或缺的，但其机制在进化过程中动态变化。
It is generally believed that prokaryotic translation is initiated by the interaction between the Shine-Dalgarno (SD) sequence in the 5' UTR of an mRNA and the anti-SD sequence in the 3' end of a 16S ribosomal RNA. However, there are two exceptional mechanisms, which do not require the SD sequence for translation initiation: one is mediated by a ribosomal protein S1 (RPS1) and the other used leaderless mRNA that lacks its 5' UTR. To understand the evolutionary changes of the mechanisms of translation initiation, we examined how universal the SD sequence is as an effective initiator for translation among prokaryotes. We identified the SD sequence from 277 species (249 eubacteria and 28 archaebacteria). We also devised an SD index that is a proportion of SD-containing genes in which the differences of GC contents are taken into account. We found that the SD indices varied among prokaryotic species, but were similar within each phylum. Although the anti-SD sequence is conserved among species, loss of the SD sequence seems to have occurred multiple times, independently, in different phyla. For those phyla, RPS1-mediated or leaderless mRNA-used mechanisms of translation initiation are considered to be working to a greater extent. Moreover, we also found that some species, such as Cyanobacteria, may acquire new mechanisms of translation initiation. Our findings indicate that, although translation initiation is indispensable for all protein-coding genes in the genome of every species, its mechanisms have dynamically changed during evolution.