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Minimal Secondary Structure Formation on mRNAs with a shine-dalgarno sequence for Chromosomal Genes in <i>Rhodobacter sphaeroides</i>

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Advances in Microbiology 2021年第10期11卷 529-540页

作者： Damilola Omotajo Hyuk Cho Madhusudan Choudhary Department of Biological Sciences Sam Houston State University Huntsville Texas USA Cumming School of Medicine University of Calgary Calgary Alberta Canada Department of Computer Science Sam Houston State University Huntsville Texas USA

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.

关键词： shine-dalgarno sequence Secondary Structure Messenger RNA Translation Initiation

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