Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan.
Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6382-7. doi: 10.1073/pnas.1002036107. Epub 2010 Mar 22.
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.
人们普遍认为原核生物翻译是通过 mRNA5'UTR 中的 Shine-Dalgarno（SD）序列与 16S 核糖体 RNA3' 端的反 SD 序列相互作用而启动的。然而，有两种特殊的机制不需要 SD 序列即可启动翻译：一种是由核糖体蛋白 S1（RPS1）介导的，另一种是使用没有 5'UTR 的无领袖 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起始的有效启动子的普遍性。我们从 277 个物种（249 个真细菌和 28 个古细菌）中鉴定出 SD 序列。我们还设计了一个 SD 指数，该指数是包含 SD 序列的基因的比例，其中考虑了 GC 含量的差异。我们发现 SD 指数在原核生物物种之间存在差异，但在每个门内相似。尽管反 SD 序列在物种之间是保守的，但 SD 序列的缺失似乎已经独立地在不同的门中多次发生。对于这些门，RPS1 介导或无领袖 mRNA 用于翻译起始的机制被认为更为有效。此外，我们还发现一些物种，如蓝细菌，可能获得了新的翻译起始机制。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必不可少的，但它的机制在进化过程中已经发生了动态变化。
