College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.
Genome Biol Evol. 2013;5(3):484-93. doi: 10.1093/gbe/evt020.
Various regulatory elements in messenger RNAs (mRNAs) carrying the secondary structure play important roles in a wide range of expression processes. Numerous recent works have focused on the discovery of these functional elements that contain the conserved mRNA structures. However, to date, regions with high structural stability have been largely overlooked. In this study, we defined high stability regions (HSRs) in the coding sequences (CDSs) in bacteria based on the normalized folding free energy. We found that CDSs had high number of HSRs, and these HSRs showed high structural context robustness compared with random sequences, indicating a direct selective constraint imposed on HSRs. A reduced ribosome speed was detected near the start position of HSR, implying a possibility that HSR acted as obstacle to drive translational pausing that coordinated protein synthesis. Interestingly, we found that genes with high HSR density were enriched in the processes of translation, protein folding, and cell division. In addition, essential genes exhibited higher HSR density than nonessential genes. Overall, our study presented the previously unappreciated correlation between the number variation of HSRs and cellular processes.
信使 RNA(mRNA)中的各种调节元件在广泛的表达过程中发挥着重要作用。最近的许多研究都集中在发现这些包含保守 mRNA 结构的功能元件上。然而，迄今为止，高结构稳定性区域在很大程度上被忽视了。在这项研究中，我们基于归一化折叠自由能定义了细菌中编码序列(CDS)中的高稳定性区域(HSR)。我们发现 CDS 中有大量的 HSR，与随机序列相比，这些 HSR 表现出高结构上下文稳健性，这表明 HSR 受到直接的选择性约束。在 HSR 的起始位置附近检测到核糖体速度降低，这表明 HSR 可能充当障碍，导致翻译暂停，从而协调蛋白质合成。有趣的是，我们发现高 HSR 密度的基因富集在翻译、蛋白质折叠和细胞分裂等过程中。此外，必需基因的 HSR 密度高于非必需基因。总的来说，我们的研究揭示了 HSR 数量变化与细胞过程之间以前未被认识到的相关性。
