School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.
Nucleic Acids Res. 2009 Nov;37(21):7302-11. doi: 10.1093/nar/gkp796.
In +1 programmed ribosomal frameshifting (PRF), ribosomes skip one nucleotide toward the 3'-end during translation. Most of the genes known to demonstrate +1 PRF have been discovered by chance or by searching homologous genes. Here, a bioinformatic framework called FSscan is developed to perform a systematic search for potential +1 frameshift sites in the Escherichia coli genome. Based on a current state of the art understanding of the mechanism of +1 PRF, FSscan calculates scores for a 16-nt window along a gene sequence according to different effects of the stimulatory signals, and ribosome E-, P- and A-site interactions. FSscan successfully identified the +1 PRF site in prfB and predicted yehP, pepP, nuoE and cheA as +1 frameshift candidates in the E. coli genome. Empirical results demonstrated that potential +1 frameshift sequences identified promoted significant levels of +1 frameshifting in vivo. Mass spectrometry analysis confirmed the presence of the frameshifted proteins expressed from a yehP-egfp fusion construct. FSscan allows a genome-wide and systematic search for +1 frameshift sites in E. coli. The results have implications for bioinformatic identification of novel frameshift proteins, ribosomal frameshifting, coding sequence detection and the application of mass spectrometry on studying frameshift proteins.
在+1 程序性核糖体移码（PRF）中，核糖体在翻译过程中向 3' 端跳过一个核苷酸。大多数已知表现出+1 PRF 的基因是偶然发现的，或者是通过搜索同源基因发现的。在这里，开发了一种称为 FSscan 的生物信息学框架，用于在大肠杆菌基因组中进行系统搜索潜在的+1 移码位点。基于对+1 PRF 机制的当前最新理解，FScan 根据刺激信号的不同影响以及核糖体 E、P 和 A 位相互作用，根据基因序列中的 16 个核苷酸窗口计算分数。FScan 成功地在 prfB 中识别出+1 PRF 位点，并预测 yehP、pepP、nuoE 和 cheA 是大肠杆菌基因组中的+1 移码候选者。实验结果表明，鉴定出的潜在+1 移码序列在体内促进了显著水平的+1 移码。质谱分析证实了从 yehP-egfp 融合构建体表达的移码蛋白的存在。FScan 允许在大肠杆菌中进行全基因组和系统搜索+1 移码位点。这些结果对于生物信息学识别新型移码蛋白、核糖体移码、编码序列检测以及将质谱技术应用于研究移码蛋白具有重要意义。
