Abstract
BackgroundRecent studies have demonstrated a selection pressure for reduced mRNA secondary-structure stability near the start codon of coding sequences. This selection pressure can be observed in bacteria, archaea, and eukaryotes, and is likely caused by the requirement of efficient translation initiation in cellular organism.ResultsHere, we surveyed the complete genomes of 650 dsDNA virus strains for signals of reduced stability of mRNA secondary structure near the start codon. Our analysis included viruses infecting eukaryotic, prokaryotic, and archaeic hosts. We found that many viruses showed evidence for reduced mRNA secondary-structure stability near the start codon. The effect was most pronounced in viruses infecting prokaryotes, but was also observed in viruses infecting eukaryotes and archaea. The reduction in stability generally increased with increasing genomic GC content. For bacteriophage, the reduction was correlated with a corresponding reduction of stability in the phage hosts.ConclusionsWe conclude that reduced stability of the mRNA secondary structure near the start codon is a common feature for dsDNA viruses, likely driven by the same selective pressures that cause it in cellular organisms.
Highlights
Recent studies have demonstrated a selection pressure for reduced mRNA secondary-structure stability near the start codon of coding sequences
We addressed the following questions: (i) Is there a selection pressure on synonymous sites to reduce the stability of local mRNA secondary structure at the translation-initiation region in dsDNA viruses? (ii) Are overlapping open reading frames confounding the results? (iii) Does 5’ mRNA stability correlate with GC composition? (iv) Does the selection pressure depend on the kingdom of the host organism? (v) Does the selection pressure correlate with other host properties, such as the host’s GC content?
These results mirror the results of Gu et al [15], who found that Z G was generally positive near the start codon and negative further downstream
Summary
Recent studies have demonstrated a selection pressure for reduced mRNA secondary-structure stability near the start codon of coding sequences. This selection pressure can be observed in bacteria, archaea, and eukaryotes, and is likely caused by the requirement of efficient translation initiation in cellular organism. Downstream of the start codon, various sequence features promote translation initiation. Translation initiation is enhanced if the mRNA downstream of the start codon is AT-rich and does not form a stable secondary structure [9,10,11,12,13].
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