title: Fine-tuning translation kinetics selection as the driving force of codon usage bias in the hepatitis A virus capsid.
abstract: Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.
authors.affiliation: Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain.
authors.forename: Lluís
authors.initials: L
authors.lastname: Aragonès
authors.forename: Susana
authors.initials: S
authors.lastname: Guix
authors.forename: Enric
authors.initials: E
authors.lastname: Ribes
authors.forename: Albert
authors.initials: A
authors.lastname: Bosch
authors.forename: Rosa M
authors.initials: RM
authors.lastname: Pintó
mesh_terms: D000926:Anticodon / Q000235:genetics; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics*; D003062:Codon / Q000235:genetics*; D003609:Dactinomycin / Q000494:pharmacology; D039603:Eukaryotic Initiation Factor-4G / Q000235:genetics; D015967:Gene Expression Regulation, Viral; D018841:HSP90 Heat-Shock Proteins / Q000502:physiology; D030041:Hepatitis A virus / Q000235:genetics* / Q000254:growth & development; D014176:Protein Biosynthesis / Q000235:genetics*; D017510:Protein Folding; D011500:Protein Synthesis Inhibitors / Q000494:pharmacology; D012343:RNA, Transfer / Q000235:genetics*; D014779:Virus Replication / Q000235:genetics
chemical_list: D000926:Anticodon; D036022:Capsid Proteins; D003062:Codon; C113920:EIF4G1 protein, human; D039603:Eukaryotic Initiation Factor-4G; D018841:HSP90 Heat-Shock Proteins; D011500:Protein Synthesis Inhibitors; D003609:Dactinomycin; D012343:RNA, Transfer