High-precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP.
High-precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP.
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DOI：
10.1016/j.celrep.2015.03.014
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发表时间：
2015-04-07
期刊：
影响因子：
8.8
通讯作者：
Buskirk AR
中科院分区：
文献类型：
--
作者：
Woolstenhulme CJ;Guydosh NR;Green R;Buskirk AR
核糖体谱分析是一种全面评估细胞中核糖体活性的有力方法。尽管它在许多生物体中得到了应用，但在细菌中的核糖体分析研究一直难以获得精确定义翻译停顿所需的分辨率。在这里，我们报告了在大肠杆菌分析数据中产生更高分辨率的改进，使我们能够更准确地评估核糖体暂停，并完善早期关于聚脯氨酸基体对延伸影响的研究。我们全面表征了在缺乏延伸因子EFP的情况下富含脯氨酸的基序处的停顿。我们发现只有一小部分具有强暂停基序的基因降低了下游的核糖体密度，并确定了解释这一现象的特征。这些特征使我们能够预测哪些蛋白质可能减少了efp敲除菌株的输出。
Ribosome profiling is a powerful method for globally assessing the activity of ribosomes in a cell. Despite its application in many organisms, ribosome profiling studies in bacteria have struggled to obtain the resolution necessary to precisely define translational pauses. Here we report improvements that yield much higher resolution in E. coli profiling data, enabling us to more accurately assess ribosome pausing and refine earlier studies of the impact of polyproline motifs on elongation. We comprehensively characterize pausing at proline-rich motifs in the absence of elongation factor EFP. We find that only a small fraction of genes with strong pausing motifs have reduced ribosome density downstream and identify features that explain this phenomenon. These features allow us to predict which proteins likely have reduced output in the efp knockout strain.