Structural insight into cap-snatching and RNA synthesis by influenza polymerase

• Published in: Nature (London) 2014-12, Vol.516 (7531), p.361-366
• Main Authors: Reich, Stefan, Guilligay, Delphine, Pflug, Alexander, Malet, Hélène, Berger, Imre, Crépin, Thibaut, Hart, Darren, Lunardi, Thomas, Nanao, Max, Ruigrok, Rob W. H., Cusack, Stephen
• Format: Article
• Language: English
• Subjects: 631/326/596/1578; Analysis; Binding sites; Biochemistry, Molecular Biology; Catalytic Domain; Crystal structure; Crystallization; Crystals; DNA-Directed RNA Polymerases; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - metabolism; Gene Expression Regulation, Viral; Health aspects; Humanities and Social Sciences; Influenza; Influenza A virus; Influenza A virus - chemistry; Influenza A virus - enzymology; Influenza B virus; Influenza B virus - chemistry; Influenza B virus - enzymology; Influenza viruses; Life Sciences; Models, Molecular; multidisciplinary; Promoter Regions, Genetic; Protein Binding; Protein Structure, Tertiary; Ribonucleic acid; RNA; RNA Caps; RNA Caps - chemistry; RNA Caps - metabolism; RNA polymerases; RNA, Viral; RNA, Viral - biosynthesis; RNA, Viral - chemistry; Science; Structural Biology; Structure; Synthesis; Virus Replication
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature14009

Influenza virus polymerase uses a capped primer, derived by ‘cap-snatching’ from host pre-messenger RNA, to transcribe its RNA genome into mRNA and a stuttering mechanism to generate the poly(A) tail. By contrast, genome replication is unprimed and generates exact full-length copies of the template. Here we use crystal structures of bat influenza A and human influenza B polymerases (FluA and FluB), bound to the viral RNA promoter, to give mechanistic insight into these distinct processes. In the FluA structure, a loop analogous to the priming loop of flavivirus polymerases suggests that influenza could initiate unprimed template replication by a similar mechanism. Comparing the FluA and FluB structures suggests that cap-snatching involves in situ rotation of the PB2 cap-binding domain to direct the capped primer first towards the endonuclease and then into the polymerase active site. The polymerase probably undergoes considerable conformational changes to convert the observed pre-initiation state into the active initiation and elongation states. Atomic resolution crystal structures of influenza A and B polymerases are presented; comparison of these structures provides mechanistic insight into influenza polymerase functions, explaining the processes of cap-snatching and cap-dependent priming, which are unique to segmented negative-strand RNA viruses. Complete structure of influenza polymerase A Stephen Cusack and colleagues have solved the crystal structure of the complete influenza polymerase, comprising subunits PA, PB1 and PB2, bound to its viral RNA promoter. In the first of two papers they present the structure of the polymerase from a bat-specific influenza A virus, which is evolutionarily close to human/avian influenza A strains. The second paper presents the structure of the polymerase from a human isolate of influenza B. Together, the structures provide a wealth of information about how the influenza polymerase functions and how the different subunits interact with each other.