title: Influenza A virus utilizes a suboptimal Kozak sequence to fine-tune virus replication and host response.
abstract: The segment-specific non-coding regions (NCRs) of influenza A virus RNA genome play important roles in controlling viral RNA transcription, replication and genome packaging. In this report, we present, for the first time to our knowledge, a full view of the segment-specific NCRs of all influenza A viruses by bioinformatics analysis. Our systematic functional analysis revealed that the eight segment-specific NCRs identified could differentially regulate viral RNA synthesis and protein expression at both transcription and translation levels. Interestingly, a highly conserved suboptimal nucleotide at -3 position of the Kozak sequence, which downregulated protein expression at the translation level, was only present in the segment-specific NCR of PB1. By reverse genetics, we demonstrate that recombinant viruses with an optimized Kozak sequence at the -3 position in PB1 resulted in a significant multiple-cycle replication reduction that was independent of PB1-F2 expression. Our detailed dynamic analysis of virus infection revealed that the mutant virus displays slightly altered dynamics from the wild-type virus on both viral RNA synthesis and protein production. Furthermore, we demonstrated that the level of PB1 expression is involved in regulating type I IFN production. Together, these data reveal a novel strategy exploited by influenza A virus to fine-tune virus replication dynamics and host antiviral response through regulating PB1 protein expression.
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China.
authors.forename: Jingfeng
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Information Science and Engineering, Hunan University, Changsha 410082, PR China.
authors.forename: Yousong
authors.initials: Y
authors.lastname: Peng
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China.
authors.forename: Lili
authors.initials: L
authors.lastname: Zhao
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China.
authors.forename: Mengmeng
authors.initials: M
authors.lastname: Cao
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China.
authors.forename: Tao
authors.initials: T
authors.lastname: Hung
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China.
authors.forename: Tao
authors.initials: T
authors.lastname: Deng
mesh_terms: D000818:Animals; D002460:Cell Line; D045744:Cell Line, Tumor; D002522:Chlorocebus aethiops; D019295:Computational Biology / Q000379:methods; D004285:Dogs; D015536:Down-Regulation / Q000235:genetics; D015967:Gene Expression Regulation, Viral / Q000235:genetics; D057809:HEK293 Cells; D006801:Humans; D009980:Influenza A virus / Q000235:genetics / Q000502:physiology*; D007251:Influenza, Human / Q000821:virology*; D061985:Madin Darby Canine Kidney Cells; D009976:Orthomyxoviridae Infections / Q000821:virology*; D014176:Protein Biosynthesis; D012367:RNA, Viral / Q000235:genetics; D014158:Transcription, Genetic; D014709:Vero Cells; D014764:Viral Proteins / Q000235:genetics; D014779:Virus Replication / Q000235:genetics / Q000502:physiology*
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins; C077346:influenza virus polymerase basic protein 1