在核糖体中,蛋白质合成虽然发生在一个线性底物上,却以着不均匀的速率进行。核糖体的短暂停留能够影响许多联合的翻译过程,包括蛋白定位及折叠,这种短暂停留被mRNA的序列所影响。而且,遗传密码的冗余使得相同的蛋白以不同的效率被翻译。
然而在体内,翻译暂停的机制以及定位有关的的知识还很有限。这里,美国加利福尼亚大学Jonathan S. Weissman等人利用细菌核糖体保护的mRNA片段深度测序及核糖体图谱,做了一个翻译暂停有关的全基因组分析。
当大多数转录物处于平静的内源性表达水平时,这种方法能够高分辨率测量核糖体的密度图。出乎预料的是,他们发现在营养丰富的环境下,由稀有tRNA解码的密码子不会减缓翻译过程。
相反的,编码序列的SD序列样(SD-like)的特征会引起了普遍的翻译暂停。使用一个改变了的抗SD序列表明,暂停是由于翻译中的核糖体出现mRNA与16S rRNA杂化。
在蛋白编码序列,内部的SD序列被疏远,导致了使用的偏差,避免了相似于典型的SD位点的密码子和密码子的配对。
这项研究表明,SD样的序列对细菌基因组编码的翻译率及推动力来说,是一个主要的决定因素。相关论文在线发表于3月28日的Nature。(生物谷Deepblue编译)
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.