Effect Of Ribosomes On Structural Stability Of MRNA In Saccharomyces Cerevisiae

Ribosomes and mRNAs are the most important components of the translation system,in which the mRNA carries the translated template information and the ribosome binds the mRNA from the 5' end to the 3' end during the translation.In addition to the function of encoding amino acids,mRNA can play a key role in the regulation of translation rate and protein co-translational folding and the subcellular localization of mRNA by folding into a complex mRNA structure.During the process of translation,the ribosomes need to melt the mRNA structure in order to maintain the translation,thus creating a complex interaction between the ribosome and the mRNA structure.In recent years,large-scale detection of mRNA structure in vivo has been conducted by using chemical methods and high-throughput sequencing technologies.It has been found that the amount of mRNA in vivo is greatly reduced compared to mRNA that can be freely folded in vitro.However,there is still a portion of mRNA structure that can be stabilized in vivo.Then,in the course of the continuous melting of ribosomes,what factors influence the stability of the mRNA structure in vivo,and what differences exist between the stable and unstable mRNA structure in vivo,these problems restrict our understanding of the structure of mRNA in the translation process.In this study,the eukaryotic Saccharomyces cerevisiae was used as experimental material.The in vivo and in vitro structures of Saccharomyces cerevisiae were sorted and screened using RNA-seq and DMS-probing data.All structures were divided into two status which disappeared in the body(ie,the unstable structures in vivo)and remain in the body(ie,structures that are more stable in vivo).In order to understand the difference between the disappearance and retention structures of different features,we analyzed a series of characteristics of the disappearance and the retention structure in vivo: sequence characteristics,such as rare codon usage frequency,tRNA Adaptation Index(tAI),Minimum Free Energy(MFE)and the relative positions on the genes;the features of genes,such as RPKM(Reads per kilo base per million mapped reads)and gene translation initiation rate.We found that there are differences in the characteristics of the disappearance and the retention structure under different ribosome densities.The effect of ribosomes on the disappearance structure in vivo is not only reflected the number of ribosomes,but also in different position of ribosomes.Our results show that in regions with high ribosome densities,the disappearance structures in a greater extent and in regions with low ribosome densities,the degree of disappearance structures is small.Most ribosomes cluster in upstream of the structural regions.The ribosomes gradually decreased from upstream to downstream of the structural region.In summary,through a detailed analysis of the various features that influencing the structure of mRNA,shows that the structures that disappear in vivo have similar characteristics,and the stable mRNA structure is more “individualized”,that is to say,the reasons for its stable existence in vivo vary greatly.This study analyzed the effect of ribosomes on the mRNA structure of different features during translation from multiple perspectives,clarifies the contribution of various factors to the stability of mRNA structures in vivo,and provides new insights into mRNA structure design and mRNA structure functional studies in vivo.