Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.
Nat Commun. 2022 Nov 11;13(1):6829. doi: 10.1038/s41467-022-34664-0.
Stability of eukaryotic mRNAs is associated with their codon, amino acid, and GC content. Yet, coding sequence motifs that predictably alter mRNA stability in human cells remain poorly defined. Here, we develop a massively parallel assay to measure mRNA effects of thousands of synthetic and endogenous coding sequence motifs in human cells. We identify several families of simple dipeptide repeats whose translation triggers mRNA destabilization. Rather than individual amino acids, specific combinations of bulky and positively charged amino acids are critical for the destabilizing effects of dipeptide repeats. Remarkably, dipeptide sequences that form extended β strands in silico and in vitro slowdown ribosomes and reduce mRNA levels in vivo. The resulting nascent peptide code underlies the mRNA effects of hundreds of endogenous peptide sequences in the human proteome. Our work suggests an intrinsic role for the ribosome as a selectivity filter against the synthesis of bulky and aggregation-prone peptides.
真核生物 mRNA 的稳定性与其密码子、氨基酸和 GC 含量有关。然而，能够有预测性地改变人类细胞中 mRNA 稳定性的编码序列基序仍未被很好地定义。在这里，我们开发了一种大规模平行测定法来测量数千种合成和内源性编码序列基序在人类细胞中的 mRNA 效应。我们鉴定出了几种简单二肽重复家族，其翻译会触发 mRNA 不稳定性。对于二肽重复的不稳定性效应，关键是大体积和带正电荷的氨基酸的特定组合，而不是单个氨基酸。值得注意的是，在计算机模拟和体外实验中形成扩展β链的二肽序列会使核糖体减速，并降低体内的 mRNA 水平。这种新生肽密码子是人类蛋白质组中数百种内源性肽序列的 mRNA 效应的基础。我们的工作表明，核糖体在作为一种选择性过滤器方面具有内在作用，可以防止大体积和易于聚集的肽的合成。
