title: Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae.
abstract: Messenger RNA (mRNA) secondary structure decreases the elongation rate, as ribosomes must unwind every structure they encounter during translation. Therefore, the strength of mRNA secondary structure is assumed to be reduced in highly translated mRNAs. However, previous studies in vitro reported a positive correlation between mRNA folding strength and protein abundance. The counterintuitive finding suggests that mRNA secondary structure affects translation efficiency in an undetermined manner. Here, we analyzed the folding behavior of mRNA during translation and its effect on translation efficiency. We simulated translation process based on a novel computational model, taking into account the interactions among ribosomes, codon usage and mRNA secondary structures. We showed that mRNA secondary structure shortens ribosomal distance through the dynamics of folding strength. Notably, when adjacent ribosomes are close, mRNA secondary structures between them disappear, and codon usage determines the elongation rate. More importantly, our results showed that the combined effect of mRNA secondary structure and codon usage in highly translated mRNAs causes a short ribosomal distance in structural regions, which in turn eliminates the structures during translation, leading to a high elongation rate. Together, these findings reveal how the dynamics of mRNA secondary structure coupling with codon usage affect translation efficiency.
authors.affiliation: College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China, Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China and College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China.
authors.forename: Yuanhui
authors.initials: Y
authors.lastname: Mao
authors.forename: HuiLing
authors.initials: H
authors.lastname: Liu
authors.forename: Yanlin
authors.initials: Y
authors.lastname: Liu
authors.forename: Shiheng
authors.initials: S
authors.lastname: Tao
mesh_terms: D003062:Codon; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D059370:RNA Folding; D012333:RNA, Messenger / Q000737:chemistry*; D012270:Ribosomes / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*
chemical_list: D003062:Codon; D012333:RNA, Messenger