在核糖體中,，蛋白質(zhì)合成雖然發(fā)生在一個線性底物上,，卻以著不均勻的速率進(jìn)行。核糖體的短暫停留能夠影響許多聯(lián)合的翻譯過程,，包括蛋白定位及折疊,，這種短暫停留被mRNA的序列所影響。而且,，遺傳密碼的冗余使得相同的蛋白以不同的效率被翻譯,。
然而在體內(nèi),，翻譯暫停的機(jī)制以及定位有關(guān)的的知識還很有限。這里,，美國加利福尼亞大學(xué)Jonathan S. Weissman等人利用細(xì)菌核糖體保護(hù)的mRNA片段深度測序及核糖體圖譜,，做了一個翻譯暫停有關(guān)的全基因組分析,。
當(dāng)大多數(shù)轉(zhuǎn)錄物處于平靜的內(nèi)源性表達(dá)水平時,，這種方法能夠高分辨率測量核糖體的密度圖。出乎預(yù)料的是,，他們發(fā)現(xiàn)在營養(yǎng)豐富的環(huán)境下,，由稀有tRNA解碼的密碼子不會減緩翻譯過程。
相反的,，編碼序列的SD序列樣（SD-like）的特征會引起了普遍的翻譯暫停,。使用一個改變了的抗SD序列表明，暫停是由于翻譯中的核糖體出現(xiàn)mRNA與16S rRNA雜化,。
在蛋白編碼序列,，內(nèi)部的SD序列被疏遠(yuǎn)，導(dǎo)致了使用的偏差,，避免了相似于典型的SD位點(diǎn)的密碼子和密碼子的配對,。
這項(xiàng)研究表明，SD樣的序列對細(xì)菌基因組編碼的翻譯率及推動力來說,，是一個主要的決定因素,。相關(guān)論文在線發(fā)表于3月28日的Nature。（生物谷Deepblue編譯）
doi: 10.1038/nature10965
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The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria
Gene-Wei Li, Eugene Oh1 & Jonathan S. Weissman.
Protein synthesis by ribosomes takes place on a linear substrate but at non-uniform speeds. Transient pausing of ribosomes can affect a variety of co-translational processes, including protein targeting and folding.These pauses are influenced by the sequence of the messenger RNA. Thus, redundancy in the genetic code allows the same protein to be translated at different rates.However, our knowledge of both the position and the mechanism of translational pausing in vivo is highly limited. Here we present a genome-wide analysis of translational pausing in bacteria by ribosome profiling—deep sequencing of ribosome-protected mRNA fragments.This approach enables the high-resolution measurement of ribosome density profiles along most transcripts at unperturbed, endogenous expression levels.Unexpectedly, we found that codons decoded by rare transfer RNAs do not lead to slow translation under nutrient-rich conditions.Instead, Shine–Dalgarno-(SD)-like features within coding sequences cause pervasive translational pausing. Using an orthogonal ribosome possessing an altered anti-SD sequence, we show that pausing is due to hybridization between the mRNA and 16S ribosomal RNA of the translating ribosome.In protein-coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites.Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes.
