Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.
Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States.
Elife. 2020 Feb 17;9:e55002. doi: 10.7554/eLife.55002.
Shine-Dalgarno (SD) motifs are thought to play an important role in translational initiation in bacteria. Paradoxically, ribosome profiling studies in show no correlation between the strength of an mRNA's SD motif and how efficiently it is translated. Performing profiling on ribosomes with altered anti-Shine-Dalgarno sequences, we reveal a genome-wide correlation between SD strength and ribosome occupancy that was previously masked by other contributing factors. Using the antibiotic retapamulin to trap initiation complexes at start codons, we find that the mutant ribosomes select start sites correctly, arguing that start sites are hard-wired for initiation through the action of other mRNA features. We show that A-rich sequences upstream of start codons promote initiation. Taken together, our genome-wide study reveals that SD motifs are not necessary for ribosomes to determine where initiation occurs, though they do affect how efficiently initiation occurs.
Shine-Dalgarno (SD) 基序被认为在细菌中的翻译起始中发挥重要作用。矛盾的是，在 的核糖体图谱研究中，mRNA 的 SD 基序的强度与翻译效率之间没有相关性。通过对改变了反 Shine-Dalgarno 序列的核糖体进行分析，我们揭示了 SD 强度与核糖体占据之间的全基因组相关性，而这一相关性以前被其他因素所掩盖。我们使用抗生素瑞他帕林将起始复合物固定在起始密码子上，发现突变核糖体能够正确选择起始位点，这表明起始位点是通过其他 mRNA 特征的作用而被硬连线用于起始的。我们发现起始密码子上游富含 A 的序列可以促进起始。总之，我们的全基因组研究表明，SD 基序对于核糖体确定起始发生的位置并不是必需的，尽管它们确实会影响起始的效率。
