Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses

Tong Zhou is with the Section of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Institute for Personalized Respiratory Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA – Claus O. Wilke is with the Center for Computational Biology and Bioinformatics, Institute for Cell and Molecular Biology, and Section of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USABackground: 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. Results: Here, 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. Conclusions: We 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.Center for Computational Biology and BioinformaticsInstitute for Cellular and Molecular BiologyIntegrative Biologywilke@austin.utexas.ed