Gong Sha, Wang Yujie, Wang Zhen, Wang Yanli, Zhang Wenbing
Department of Physics, Wuhan University , Wuhan, Hubei 430072, P. R. China.
College of Mathematics and Physics, Huanggang Normal University , Huanggang, Hubei 438000, P. R. China.
J Phys Chem B. 2016 Dec 8;120(48):12305-12311. doi: 10.1021/acs.jpcb.6b09698. Epub 2016 Nov 22.
Riboswitches are self-regulatory elements located at the 5' untranslated region of certain mRNAs. The Enterococcus faecalis SAM-III (S) riboswitch regulates downstream gene expression through conformational change by sensing S-adenosylmethionine (SAM) at the translation level. Using the recently developed systematic helix-based computational method, we studied the co-transcriptional folding behavior of the S riboswitch and its shortened construct lacking the first six nucleotides. We find that there are no obvious misfolded structures formed during the transcription and refolding processes for this riboswitch. The full-length riboswitch quickly folds into the ON-state in the absence of SAM, and the coupling between transcription and translation is not required for the riboswitch to function. The potential to form helix P0 is necessary for the riboswitch to function as a switch. For this thermodynamically controlled reversible riboswitch, the fast helix-exchanging transition pathway between the two functional structures guaranteed that this riboswitch can act as a reversible riboswitch.
核糖开关是位于某些mRNA 5'非翻译区的自我调节元件。粪肠球菌SAM-III（S）核糖开关通过在翻译水平上感知S-腺苷甲硫氨酸（SAM），通过构象变化调节下游基因表达。利用最近开发的基于系统螺旋的计算方法，我们研究了S核糖开关及其缺失前六个核苷酸的缩短构建体的共转录折叠行为。我们发现，该核糖开关在转录和重折叠过程中没有形成明显的错误折叠结构。在没有SAM的情况下，全长核糖开关迅速折叠成ON状态，核糖开关发挥功能不需要转录和翻译之间的偶联。形成螺旋P0的潜力是核糖开关作为开关发挥功能所必需的。对于这种热力学控制的可逆核糖开关，两种功能结构之间快速的螺旋交换转变途径保证了该核糖开关可以作为可逆核糖开关发挥作用。
