Number Variation of High Stability Regions Is Correlated with Gene Functions

Abstract

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.

Genome-Wide Analysis of Selective Constraints on High Stability Regions of mRNA Reveals Multiple Compensatory Mutations in Escherichia coli

“…We calculated the ratio paired/unpaired and surprisingly found that the ratio is lower than the expected value in the two species ( t -test, all p- values <10 −7 , Table 3), which is different from the pattern inferred from the conserved secondary structure (the ratio is higher than the expected value) [27]. This result is consistent with the idea that structural stability instead of structural conformation in HSR is conserved during evolution [16], [35].…”

“…We thus identified HSRs on mRNAs only based on the minimum folding free energy (MFE) of local regions. The method was described previously [16]. The main steps are as follows.…”

“…Z-score was calculated by equation (1):where is the MFE of native sequence, and are the mean and standard deviation of MFE of 100 random sequences, respectively. Second, we used the following criteria to define HSR: 1) if a region contains more than two continuous sliding windows, in which the z-scores were all below the threshold of -0.65 [16], the region was defined as HSR. 2) If the percentage of the overlapping sites of two adjacent HSRs was higher than 50%, the two HSRs were combined.…”

“…In our previous study, we found that most of these structures exhibit high structural stability, while their structural conformations are non-conserved across different species [16]. We therefore identified the regions with high structural stability in Escherichia coli (HSR, high structural stability regions) using a loose threshold (Figure 1, Table S1-S2) [16], and revealed that number variation of HSR is correlated with gene functions, probably involving the regulations on the rhythm of translation elongation. However, the evolutionary pattern of HSR is still undetermined in that study.…”

Biological Significance of Nascent Polypeptides That Stall the Ribosome

“…The nonuniformity in the elongation step of translation could influence the fate of the newly synthesized polypeptide, including its subcellular localization, folding, modification, and stability (Zhang and Ignatova 2011;Pechmann and Frydman 2013;Kramer et al 2009;Zhou et al 2013). The rhythm in translation (Rosenblum et al 2013) is determined in part by features of mRNA, such as biased codon usage (Sorensen et al 1989;Plotkin and Kudla 2011), local secondary structure (Tholstrup et al 2012;Mao et al 2013), and complementary interactions with the RNA component of the ribosome (Li et al 2012). Can such mRNAinstructed translation modulation respond to environmental changes?…”