Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Bioinformatics Knowledge Center, Howest University of Applied Sciences, Bruges, Belgium.
BMC Mol Cell Biol. 2021 May 16;22(1):29. doi: 10.1186/s12860-021-00363-9.
A large fraction of genes contains upstream ORFs (uORFs) in the 5' untranslated region (5'UTR). The translation of uORFs can inhibit the translation of the main coding sequence, for example by causing premature dissociation of the two ribosomal units or ribosome stalling. However, it is currently unknown if most uORFs are inhibitory or if this activity is restricted to specific cases. Here we interrogate ribosome profiling data from three different stress experiments in yeast to gain novel insights into this question.
By comparing ribosome occupancies in different conditions and experiments we obtain strong evidence that, in comparison to primary coding sequences (CDS), which undergo translational arrest during stress, the translation of uORFs is mostly unaffected by changes in the environment. As a result, the relative abundance of uORF-encoded peptides increases during stress. In general, the changes in the translational efficiency of regions containing uORFs do not seem to affect downstream translation. The exception are uORFs found in a subset of genes that are significantly up-regulated at the level of translation during stress; these uORFs tend to be translated at lower levels in stress conditions than in optimal growth conditions, facilitating the translation of the CDS during stress. We find new examples of uORF-mediated regulation of translation, including the Gcn4 functional homologue fil1 and ubi4 genes in S. pombe.
We find evidence that the relative amount of uORF-encoded peptides increases during stress. The increased translation of uORFs is however uncoupled from the general CDS translational repression observed during stress. In a subset of genes that encode proteins that need to be rapidly synthesized upon stress uORFs act as translational switches.
大量基因的 5'非翻译区（5'UTR）中含有上游开放阅读框（uORFs）。uORFs 的翻译可以抑制主要编码序列的翻译，例如通过导致两个核糖体单元过早解离或核糖体停滞。然而，目前尚不清楚大多数 uORFs 是否具有抑制作用，或者这种活性是否仅限于特定情况。在这里，我们通过分析酵母中三种不同应激实验的核糖体图谱数据，来深入探讨这个问题。
通过比较不同条件和实验中的核糖体占有率，我们获得了强有力的证据表明，与在应激过程中经历翻译暂停的主要编码序列（CDS）相比，uORFs 的翻译受环境变化的影响不大。因此，在应激期间，uORF 编码肽的相对丰度增加。一般来说，含有 uORF 的区域翻译效率的变化似乎不会影响下游翻译。例外的是在应激期间翻译水平显著上调的一组基因中发现的 uORFs；这些 uORFs 在应激条件下的翻译水平低于最佳生长条件下的翻译水平，从而促进了 CDS 在应激期间的翻译。我们发现了新的 uORF 介导的翻译调控的例子，包括 S. pombe 中的 Gcn4 功能同源物 fil1 和 ubi4 基因。
我们有证据表明，在应激期间，uORF 编码肽的相对含量增加。然而，uORFs 的翻译增加与应激过程中观察到的一般 CDS 翻译抑制无关。在一组编码应激时需要快速合成的蛋白质的基因中，uORFs 作为翻译开关。
