Key Role of the Influenza A Virus PA Gene Segment in the Emergence of Pandemic Viruses

Abstract

Influenza A viruses (IAVs) are a significant human pathogen that cause seasonal epidemics and occasional pandemics. Avian waterfowl are the natural reservoir of IAVs, but a wide range of species can serve as hosts. Most IAV strains are adapted to one host species and avian strains of IAV replicate poorly in most mammalian hosts. Importantly, IAV polymerases from avian strains function poorly in mammalian cells but host adaptive mutations can restore activity. The 2009 pandemic H1N1 (H1N1pdm09) virus acquired multiple mutations in the PA gene that activated polymerase activity in mammalian cells, even in the absence of previously identified host adaptive mutations in other polymerase genes. These mutations in PA localize within different regions of the protein suggesting multiple mechanisms exist to activate polymerase activity. Additionally, an immunomodulatory protein, PA-X, is expressed from the PA gene segment. PA-X expression is conserved amongst many IAV strains but activity varies between viruses specific for different hosts, suggesting that PA-X also plays a role in host adaptation. Here, we review the role of PA in the emergence of currently circulating H1N1pdm09 viruses and the most recent studies of host adaptive mutations in the PA gene that modulate polymerase activity and PA-X function.

Keywords: PA; PA-X; RNA-dependent RNA polymerase; host adaptation; influenza A virus.

Figure 1

Structure of the Influenza A virus (IAV) polymerase and host adaptive mutations in PA. (A) Human H3N2 polymerase structure (PDB:6RR7) [6]. The PA subunit is colored gray, PB2 subunit is colored teal, and PB1 subunit is colored blue. Viral genome (vRNA) bound to the PB1 and PA subunits is colored red and a 5′ 7-methylguanosine (m7G)-capped substrate bound to PB2 is colored yellow. (B) Detailed view of the PA endonuclease domain with host adaptive mutations is indicated in green and residues involved in endonuclease activity are indicated in blue. (C) Detailed view of the PA C-terminal domain with host adaptive mutations indicated in green, residues involved in binding to RNA Pol II C-terminal domain peptides in pink, and residues involved in dimerization in orange.

Figure 2

Structure of the IAV PA-X protein. (A) Schematic diagram of PA-X showing functional domains. Residues within the shared N-terminal domain known to affect PA-X shutoff activity are shown in red. Blue stars indicate the location of residues involved in endonuclease activity as previously shown in Figure 1. (B) Crystal structure of H3N2 PA N-terminal domain (PDB: 2W69) showing the location of key residues highlighted in (A) and the beginning of the X open reading frame (X-ORF) at Phe 191 [27].