Minimal Secondary Structure Formation on mRNAs with a Shine-Dalgarno Sequence for Chromosomal Genes in &amp;lt;i&amp;gt;Rhodobacter sphaeroides&amp;lt;/i&amp;gt;

Damilola Omotajo,Hyuk Cho,Madhusudan Choudhary

doi:10.4236/aim.2021.1110039

Abstract

The Shine-Dalgarno (SD) sequence, when present, is known to promote translation initiation in a bacterial cell. However, the thermodynamic stability of the messenger RNA (mRNA) through its secondary structures has an inhibitory effect on the efficiency of translation. This poses the question of whether bacterial mRNAs with SD have low secondary structure formation or not. About 3500 protein-coding genes in Rhodobacter sphaeroides were analyzed and a sliding window analysis of the last 100 nucleotides of the 5’ UTR and the first 100 nucleotides of ORFs was performed using RNAfold, a software for RNA secondary structure analysis. It was shown that mRNAs with SD are less stable than those without SD for genes located on the primary chromosome, but not for the plasmid encoded genes. Furthermore, mRNA stability is similar for genes within each chromosome except those encoded by the accessory chromosome (second chromosome). Results highlight the possible contribution of other factors like replicon-specific nucleotide composition (GC content), codon bias, and protein stability in determining the efficiency of translation initiation in both SD-dependent and SD-independent translation systems.

Highlights

Translation initiation, a rate-limiting step in protein biosynthesis, involves the recognition, attachment, and adaptation of the messenger RNA (mRNA) to the 30S subunit of the ribosome [1]
This suggests that mRNAs with SD form less stable secondary structures in comparison to those without SD for genes located in chromosomes 1 and 2
The Role of SD Is Independent of mRNA Secondary Structure in Plasmid-Encoded Genes

Summary

Introduction

Translation initiation, a rate-limiting step in protein biosynthesis, involves the recognition, attachment, and adaptation of the mRNA to the 30S subunit of the ribosome [1]. Messenger RNA recognition is facilitated by the non-random distribution of purines about 5 - 10 nucleotides upstream the start codon [2] [3]. This purine-rich sequence (typically 3 - 6 nucleotides long), known as the Shine-Dalgarno (SD) sequence, is complementary to a conserved region at the 3’ end of the 16S rRNA located in the platform of the 30S subunit [4] [5]. In some of the cases where there is no complementarity between 16S rRNA and the sequence upstream of the mRNA start site, it has been shown that ribosomal protein S1 interacts with AU-rich regions to facilitate translation initiation [3]

Methods

Results

Conclusion