Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine-Dalgarno sequence in prokaryotes.
Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine-Dalgarno sequence in prokaryotes.
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DOI：
10.1093/nar/gkx124
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发表时间：
2017-04-20
影响因子：
14.9
通讯作者：
Gojobori T
中科院分区：
文献类型：
--
作者：
Nakagawa S;Niimura Y;Gojobori T
在原核生物中，翻译起始被认为是通过16SRRNA的3΄尾部与其5΄非翻译区的相应Shine-Dalgarno(SD)序列之间的相互作用而发生的。然而，一些基因缺乏SD序列(非SD基因)，基因组中非SD基因的比例因原核生物物种的不同而不同。为了从进化的角度阐明原核生物中非SD基因的翻译起始机制，我们统计了260种原核生物(235个细菌和25个古生物)非SD基因起始密码子周围的核苷酸频率。我们在细菌和古菌中发现了起始密码子上游明显的核苷酸频率偏差，这可能是因为存在缺乏5΄非编码区的无领导mRNAs。此外，我们观察到所有被研究的门中起始密码子的上游和下游区域的核苷酸模式总体上相似。对称的核苷酸频率偏差可能通过阻止起始密码子周围二级结构的形成来促进翻译起始。这些特征在含有大量非SD序列的物种基因组中更为突出，这表明起始密码子周围的稳定性降低对于原核生物有效的翻译起始是重要的。
In prokaryotes, translation initiation is believed to occur through an interaction between the 3΄ tail of a 16S rRNA and a corresponding Shine–Dalgarno (SD) sequence in the 5΄ untranslated region (UTR) of an mRNA. However, some genes lack SD sequences (non-SD genes), and the fraction of non-SD genes in a genome varies depending on the prokaryotic species. To elucidate non-SD translation initiation mechanisms in prokaryotes from an evolutionary perspective, we statistically examined the nucleotide frequencies around the initiation codons in non-SD genes from 260 prokaryotes (235 bacteria and 25 archaea). We identified distinct nucleotide frequency biases upstream of the initiation codon in bacteria and archaea, likely because of the presence of leaderless mRNAs lacking a 5΄ UTR. Moreover, we observed overall similarities in the nucleotide patterns between upstream and downstream regions of the initiation codon in all examined phyla. Symmetric nucleotide frequency biases might facilitate translation initiation by preventing the formation of secondary structures around the initiation codon. These features are more prominent in species’ genomes that harbor large fractions of non-SD sequences, suggesting that a reduced stability around the initiation codon is important for efficient translation initiation in prokaryotes.
影响因子：
14.9
作者：
Hasan, Samiul;Schreiber, Mark
通讯作者：
Schreiber, Mark