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.

Figure 1.

A schematic illustration of the interaction between mRNA secondary structure and translating ribosomes. (A) The distance between adjacent secondary structures within mRNA. mRNA secondary structures in yeast were obtained from the work of Kertesz et al. (27). (B) Structural dynamics when a ribosome moves along mRNA. pre-mF refers to the folding of mRNA without ribosome binding (see text).

Figure 2.

The model. In our model, ribosomes arrive at translation start site with rate , and release proteins with rate . During elongation, translating ribosomes wait for their cognate tRNAs at position i and simultaneously unwind the base pairings located at position i + L/2 (L = 42 nt). (A) shows the structure that the first ribosome encounters (the first ribosome is blue). (B) shows the structure that the third ribosome encounters. mRNA secondary structure is weakened due to the constraints of ribosomes. In our model, we assume that different ribosomes might encounter the structure with different folding strength at the same site because the pattern of mRNA folding might be changed when ribosomes have bound to mRNA (see text for details).

Figure 3.

Variation of mF strength against ribosomal distance. All mRNAs were divided into five groups (G1–G5) based on their pre-mF strength from high to low. (A) There is no significant difference in (see ‘Materials and Methods’ section for the calculation of ) among the five groups when ribosomal distance is longer than 5 nt. (B) When the distance is shorter than 5 nt, there is no structure between adjacent ribosomes, is determined by pre-mF strength.

Figure 4.

mRNA secondary structure shortens ribosomal distance. (A) Correlation between the number of ribosomes and pre-mF strength. (B) Correlation between ribosomal distance and pre-mF strength. (C) Mean dwell time at each codon. R1 and R3 indicate the mean dwell time (averaging the values of all mRNAs) of the first and third ribosomes at each codon, respectively. R3 shows translation pattern of the ribosomes when translation does not reach steady state. R_mean indicates the mean dwell time at each codon during steady state. (D) Ribosomal distance decreases over time. (E) The variation of the percentage of mRNAs with ribosomal collisions against elongation time during steady state.

Figure 5.

Effect of mRNA secondary structure at different positions. (A) The sliding structural region on an artificial sequence. The paired sites are indicated by gray lattices (each lattice represents a site). The PP of paired site was set to 0.5. (B) The variation of ribosomal distance during steady state when mRNA secondary structure is located in different regions. The distance without considering the effect of secondary structure is indicated by dashes. (C) Comparison of normalized PARS scores at the end of CDSs between the two groups with ribosomal densities at the top and bottom 30%. PARS score at each site was normalized by the mean score of CDS. RD, ribosomal density.

Figure 6.

Effect of codon usage. (A) The variation of the mean value of flag against ribosomal distance. The mean value of flag increases sharply with the decrease in ribosomal distance when the distance is <30 nt. If the value is <1.5 (below the red dashes), mRNA secondary structure determines elongation rate. If the value is >1.5, indicating that most of mRNA secondary structures disappear, codon usage determines elongation rate. (B) All mRNAs were classified into five groups (G1–G5) based on their pre-mF strength from high to low. For each group, mRNAs were classified into five subgroups (T1–T5) based on their tAI from low to high (see text).

Figure 7.

Correlation between pre-mF strength and translation time. (A) A schematic illustration of the effect of mRNA secondary structure on translation efficiency. We propose that high pre-mF strength leads to a short ribosomal distance, which in turn eliminates the effect of mRNA secondary structure during translation (see descriptions in the ‘Results’ and ‘Discussion’ sections). (B) Mean ribosomal distance at different initiation rates. (C) Correlation between pre-mF strength and the mean value of flag (averaging the value of flag at all sites of mRNA). A positive correlation is observed when ribosomes are close (corresponding initiation rate = 2, 3, 4 or 5 s), suggesting that high pre-mF strength leads to a less use of mRNA secondary structure during elongation. (D) Correlation between pre-mF strength and translation time/sequence length. A negative correlation indicates that high pre-mF strength leads to high translation efficiency.