Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster.
Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster.
复制标题
核糖体分析揭示了果蝇果蝇中普遍存在的终止密码子读取。
DOI：
10.7554/elife.01179
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发表时间：
2013-12-03
期刊：
影响因子：
7.7
通讯作者：
Weissman JS
中科院分区：
文献类型：
--
作者：
Dunn JG;Foo CK;Belletier NG;Gavis ER;Weissman JS
核糖体可以以受调控的方式读取终止密码子，延长而不是终止新生肽。终止密码子通读对于不同的病毒是必不可少的，并且在遗传学上预测在果蝇的几百个基因中发生，但是在真核生物中调节通读的重要性仍然在很大程度上未被探索。在这里，我们提出了一个核糖体分析法（核糖体保护的mRNA片段的深度测序）的果蝇，并提供了第一个全基因组的实验分析通读。通读比预期的要普遍得多：绝大多数通读事件都是在D.黑腹的，并没有预测的遗传学。由此产生的C-末端蛋白质延伸显示出选择的证据，包含功能性亚细胞定位信号，并且它们的通读受到调节，从而证明了它们的重要性。我们进一步证明，通读发生在酵母和人类。通读因此提供了一般机制，既调节基因表达和功能，并增加可塑性的蛋白质组在进化过程中。DOI：http://dx.doi.org/10.7554/eLife.01179.001对于一个产生蛋白质的基因，它的DNA首先被用作模板来产生信使RNA分子。信使RNA中的每一组三个核苷酸编码一个氨基酸，称为核糖体的结构通过将氨基酸以正确的顺序连接在一起来组装蛋白质。核苷酸三联体被称为密码子，有些被称为终止密码子，因为它们通常指示核糖体停止添加氨基酸。有时核糖体将终止密码子解释为氨基酸插入信号，产生具有修饰的结构或功能的延伸蛋白质。这种现象被称为终止密码子通读，并且是许多病毒完成其繁殖周期所必需的。然而，在其他生物体中对终止密码子通读的了解要少得多。现在，Dunn等人使用一种称为核糖体分析的技术来分析果蝇整个基因组的终止密码子通读。用一种酶将信使RNA片段化，然后对那些与核糖体特异性结合的片段进行测序，这些片段可能编码蛋白质。终止密码子通读发生的频率远远高于先前研究的预期。事实上，计算分析强烈表明，进化有利于某些果蝇基因的这一过程。此外，在酵母和人类细胞中也观察到了终止密码子通读，这表明它在许多生物中都很重要，而不仅仅是果蝇。因此，终止密码子通读为生物体提供了一种新的方式来调节其基因的表达水平和功能，无论是在个体的一生中，还是在物种的进化中。DOI：http://dx.doi.org/10.7554/eLife.01179.002网站
Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough is far more pervasive than expected: the vast majority of readthrough events evolved within D. melanogaster and were not predicted phylogenetically. The resulting C-terminal protein extensions show evidence of selection, contain functional subcellular localization signals, and their readthrough is regulated, arguing for their importance. We further demonstrate that readthrough occurs in yeast and humans. Readthrough thus provides general mechanisms both to regulate gene expression and function, and to add plasticity to the proteome during evolution. DOI: http://dx.doi.org/10.7554/eLife.01179.001 For a gene to give rise to a protein, its DNA is first used as a template to produce a messenger RNA molecule. Each group of three nucleotides within the messenger RNA encodes an amino acid, and structures called ribosomes assemble the protein by joining together amino acids in the correct order. The nucleotide triplets are called codons, and some are known as stop codons because they typically instruct the ribosome to stop adding amino acids. Sometimes ribosomes interpret stop codons as amino acid insertion signals, giving rise to an extended protein with a modified structure or function. This phenomenon is known as stop codon readthrough, and is required for many viruses to complete their reproductive cycles. However, much less is known about stop codon readthrough in other organisms. Now, Dunn et al. have used a technique called ribosome profiling to analyze stop codon readthrough across the entire genome of the fruit fly Drosophila melanogaster. An enzyme was used to fragment messenger RNA, and those fragments that were specifically engaged by ribosomes—and thus likely to encode protein—were sequenced. Stop codon readthrough occurred much more often than had been expected based on previous studies. Indeed, computational analysis strongly suggests that evolution has favored this process for certain fruit fly genes. Moreover, stop codon readthrough was also observed in yeast and human cells, suggesting that it is important in many organisms, not just the fruit fly. Stop codon readthrough thus provides a novel way for organisms to tune the expression levels and functions of their genes, both throughout the lifetime of an individual, and the evolution of a species. DOI: http://dx.doi.org/10.7554/eLife.01179.002