Local Secondary Structure May Be a Critical Characteristic Influencing Translation of Unicellular Organisms mRNA

Abstract

Detection and study of the factors changing the efficiency of gene expression is essential for both a better understanding of the key stages of translation and design of artificial systems with a prespecified expression level. It is known that recognition of the translation start site (TSS) depends on the contextual features of neighboring RNA regions. Patterns of codon compositions and local secondary structures of the protein coding regions in genes of 74 unicellular organisms, whose complete genomic sequences had been determined, were studied. We divided all the microorganisms into the five major groups that display markedly different patterns in terms of prevalence of selection for codon-frequency bias or selection against local selfcomplementarity. We found the specific secondary structure in the TSS region near AUG codon. We found a significant negative correlation between the predicted secondary structure stability and predicted expression level in the TSS region in some organisms. We assume that stability of the secondary structure in the region of translation start site can be an important factor in TSS recognition.