Department of Biochemistry, University College Cork, Cork, Ireland.
Bioinformatics. 2013 Jun 15;29(12):1488-91. doi: 10.1093/bioinformatics/btt184. Epub 2013 Apr 19.
Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine-Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints.
Here, we provide evidence that in addition to pausing effect, internal SD sequences induce a caterpillar-like movement of mRNA through the ribosome cavity. Once an SD site binds to the ribosome, it remains attached to it while the ribosome decodes a few subsequent codons. This leads to asymmetric progressive elongation of ribosome footprints at the 3'-end. It is likely that internal SD sequences induce a pause not on a single, but on several adjacent codons. This finding is important for our understanding of mRNA movement through the ribosome and also should facilitate interpretation of ribosome profiling data.
核糖体谱是一种新技术，可在整个转录组水平上监测 mRNA 上翻译核糖体的位置。最近的核糖体谱研究表明，内部 Shine-Dalgarno（SD）序列对细菌中的翻译速率有重大的全局影响：核糖体在 mRNA 的 SD 位点暂停。因此，了解 SD 位点如何影响 mRNA 通过核糖体的运动以及核糖体足迹的产生非常重要。
在这里，我们提供的证据表明，除了暂停效应外，内部 SD 序列还诱导 mRNA 通过核糖体腔进行毛毛虫样运动。一旦 SD 位点与核糖体结合，它就会附着在核糖体上，而核糖体解码随后的几个密码子。这导致核糖体足迹在 3' 端的不对称渐进伸长。内部 SD 序列可能不是在单个密码子上，而是在几个相邻的密码子上诱导暂停。这一发现对于我们理解 mRNA 通过核糖体的运动很重要，也应该有助于解释核糖体谱数据。
