Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation
Kunlakanya Jitobaom,
Supinya Phakaratsakul,
Thanyaporn Sirihongthong,
Sasithorn Chotewutmontri,
Prapat Suriyaphol,
Ornpreya Suptawiwat,
Prasert Auewarakul
Affiliations
Kunlakanya Jitobaom
Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
Supinya Phakaratsakul
Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
Thanyaporn Sirihongthong
Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
Sasithorn Chotewutmontri
Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
Prapat Suriyaphol
Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand; Center of Excellence in Bioinformatics and Clinical Data Management, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
Ornpreya Suptawiwat
Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
Prasert Auewarakul
Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand; Corresponding author.
The codon usage pattern is a specific characteristic of each species; however, the codon usage of all of the genes in a genome is not uniform. Intriguingly, most viruses have codon usage patterns that are vastly different from the optimal codon usage of their hosts. How viral genes with different codon usage patterns are efficiently expressed during a viral infection is unclear. An analysis of the similarity between viral codon usage and the codon usage of the individual genes of a host genome has never been performed. In this study, we demonstrated that the codon usage of human RNA viruses is similar to that of some human genes, especially those involved in the cell cycle. This finding was substantiated by its concordance with previous reports of an upregulation at the protein level of some of these biological processes. It therefore suggests that some suboptimal viral codon usage patterns may actually be compatible with cellular translational machineries in infected conditions.
