Abstract
Key points
- Interspecies transmission of influenza A viruses is the result of many factors. One of the key factors involved is a shift in the receptor-binding specificity of the virus, which is mostly determined by mutations in viral haemagglutinin (HA).
- Recent structural studies have provided molecular insights into the HA–host receptor interactions that have enabled several influenza A virus subtypes to jump from avian to human hosts.
- The combination of distinct amino acids at positions 225 and 190 of HA is important for determining the receptor-binding specificity of the H1 subtype.
- The Q226L and G228S substitutions in the HA glycoproteins of the H2 and H3 subtypes are sufficient to change the binding preference from the avian receptor to the human receptor.
- In an experimentally adapted H5 subtype, the Q226L substitution and loss of a glycosylation site near the receptor-binding site contribute to the shift in binding preference from the avian receptor to the human receptor.
- In the H7 subtype, amino acid substitutions at positions 186 and 226 of HA increase the preference for binding to the human receptor.
Introduction
Figure 1: Structure and life cycle of influenza A viruses.
a | Influenza A viruses are enveloped, single-stranded, negative-sense RNA viruses that contain eight gene segments that encode 16 proteins (although not all influenza viruses express all 16 proteins). The non-structural segment encodes the nuclear export protein NS2 and the host antiviral response antagonist NS1; the matrix segment encodes the matrix protein M1, the ion channel protein M2 and the M2-related protein M42 (which can functionally replace M2); the haemagglutinin (HA) segment encodes the receptor-binding glycoprotein HA; and the neuraminidase (NA) segment encodes NA (which cleaves sialic acid from cell surfaces). In addition, nucleoprotein (NP) and the components of the RNA-dependent RNA polymerase complex (PB1, PB2 and PA) are expressed from their respective genome segments. The two newly identified proteins N40 (the function of which is unknown93) and PA-X94, which represses cellular gene expression, are encoded by the PB1 and PA segments, respectively. Another two forms of PA (with amino-terminal truncations) have been found recently, named PA-N155 and PA-N182, which are likely to have important functions in the replication cycle of influenza A viruses5. In addition, some viruses express the pro-apoptotic protein PB1-F2, which is encoded by a second ORF in the PB1 segment. b | Virus infection is initiated by binding of the virus to sialylated host cell-surface receptors, and entry is mediated by endocytosis. In the host cell, fusion of viral and endosomal membranes occurs at low pH, which enables the release of the segmented viral genome into the cytoplasm. The viral genome is subsequently translocated to the nucleus, where it is transcribed and replicated. Following synthesis in the cytoplasm, viral proteins are assembled into viral ribonucleoproteins (vRNPs) in the nucleus. Export of vRNPs to the cytoplasm is mediated by M1 and NS2. Virus particles are assembled at the cell membrane, and the newly generated progeny virus buds into extracellular fluid.
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Figure 2: The haemagglutinin binding site and host receptors.
a | The crystal structure of the ectodomain of haemagglutinin (HA) reveals two distinct domains: the globular domain and the stem domain. The receptor-binding site is located on the membrane-distal globular domain and forms a shallow pocket comprising three secondary elements: the 130-loop, 190-helix and 220-loop (the numbers correspond to the amino acids in the H3 subtype; see inset). Four highly conserved residues (Y98, W153, H183 and Y195) form the base element of the receptor-binding site (indicated in orange). The fusion peptide, which inserts into the host membrane during membrane fusion, is indicated. The structural figures were created using Protein Data Bank (PDB) accession 4JUG. b,c | The HA receptor analogues can be categorized into two types: the avian receptor analogue (α2,3-linked sialylated glycan receptor) (part b) and the human receptor analogue (α2,6-linked sialylated glycan receptor) (part c). Sialylated glycans of the host receptors that influenza viruses bind to contain the three terminal saccharides: the terminal sialic acid SA1, the galactose ring Gal2 (at position two relative to SA) and N-acetylglucosamine GlcNAc3 (at position three relative to SA). When bound by HA, the α2,3-linked SA receptor adopts a trans conformation and the hydrophilic glycosidic oxygen atom faces the 220-loop in the receptor-binding site (part b), whereas the α2,6-linked SA receptor adopts a cis conformation and the hydrophobic C6 atom points towards the 220-loop (part c). The structural figures are created using the PDB accessions 4JUH and 4JUJ.
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Figure 3: Haemagglutinin proteins from the H1, H2 and H3 subtypes in complex with the avian and human receptor analogues.
Crystal structures of H1, H2 and H3 haemagglutinin (HA)–receptor complexes have revealed the structural basis for the switch in binding specificity. a | H1 HA from the avian subtype contains the residues E190 and G225 in the receptor-binding site, and can bind to both α2,3-linked (avian; shown in cyan) and α2,6-linked (human; shown in magenta) sialic acid (SA) receptors. The structural figures were created using Protein Data Bank (PDB) accessions 1RVX and 1RVZ. b | H1 HA proteins from two human isolates from the 1918 and 2009 pandemics contain the residues D190 and D225 and specifically bind to the human receptor. The crystal structure revealed that D190 interacts with N-acetylgalactosamine GlcNAc3, whereas D225 contacts the galactose ring Gal2.These interactions are absent in the avian HA–receptor complex owing to the different configurations of the human receptor (folded) compared with the avian receptor (extended)29, 30. The structural figure was created using the PDB accession 4JTV. c | H1 HA mutants from later isolates from the 1918 and 2009 pandemics contain the residues D190 and G225 and can bind to both avian and human receptors. It is likely that G225 increases the flexibility of the 220-loop, which provides a suitable microenvironment to accommodate the extended configuration of the avian α2,3-linked SA receptor. The structural figures were created using PDB accessions 4JUH and 4JUJ. d | Avian HA proteins from the H2 and H3 subtypes contain the residues Q226 and G228, and can bind to both avian and human receptors. The structural figures were created using PDB accessions 2WR3 and 2WR4. e | HA proteins from human-adapted H2 and H3 subtypes contain the residues L226 and S228, and preferentially bind to the human receptor. L226 creates a hydrophobic environment that is favourable for the orientation of the hydrophobic C6 atom of the α2,6-linked SA receptor but is incompatible with the orientation of the hydrophilic glycosidic oxygen of the α2,3-linked SA receptor. The residue S228 forms a hydrogen bond with SA1, which increases the binding affinity of HA for the human receptor. Moreover, the avian H2 HA binds more efficiently to the human receptor than the avian H3 HA owing to hydrogen-bond interactions between N186 in H2 HA and Gal2, which are absent in H3 HA owing to the short side chain of S186. The structural figure was created using PDB accession 2WR7.
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Figure 4: Haemagglutinin proteins from the H5 and H7 subtypes in complex with the avian and human receptor analogues.
Crystal structures of H5 and H7 haemagglutinin (HA) proteins in complex with avian and human receptor analogues. a | Wild-type H5 HA contains the residue Q226 and is glycosylated at residue N158. It has the capacity to bind preferentially to the avian receptor (α2,3-linked sialic acid (SA) receptor; shown in cyan) in a favourable trans conformation, but it binds weakly to the human receptor (α2,6-linked SA receptor; shown in magenta) in an unfavourable trans conformation. The hydrophilic residue Q226 provides a hydrophilic environment, which is compatible with the hydrophilic glycosidic oxygen atom of the avian receptor and incompatible with the hydrophobic C6 atom of the human receptor. Thus, the H5 HA preferentially binds the avian receptor. The structural figures were created using the Protein Data Bank (PDB) accessions 4K63 and 4K64. b | The ferret-transmissible mutant H5 HA (H5mut) has the residue L226 and residue 158 is deglycosylated. It binds preferentially to human receptor in a favourable cis conformation, whereas it binds weakly to the avian receptor in an unfavourable cis conformation. The hydrophobic residue L226 creates a hydrophobic environment, which is compatible with the hydrophobic C6 atom and incompatible with the hydrophilic glycosidic oxygen atom. Thus, H5mut preferentially binds to the human receptor. The structural figures were created using PDB accessions 4K66 and 4K67. c,d | The crystal structures of Anhui-H7N9 HA (AHH7, carrying the four amino acid substitutions S138A, G186V, T221P and Q226L) and an Anhui-H7N9 HA mutant (AHH7mut), in which L226 has been mutated to Q226, in complex with the avian or human receptor analogues provide insights into the structural basis of the shift in receptor binding. AHH7 and AHH7mut bind to both avian and human receptor analogues. The avian receptor analogues bind in different conformations to AHH7 (cis) and the AHH7mut carrying Q226 (trans), whereas the human receptor analogue binds to both proteins in a cis conformation. The four amino acid substitutions in AHH7 create a more hydrophobic environment that is favourable for binding to the human receptor. Furthermore, mutagenesis assays showed that the amino acid substitution Q226L is not solely responsible for the shift in receptor-binding preference of AHH7, and other substitutions also have a role. The structural figures were created using the PDB accessions 4KOM, 4KON, 4LKJ and 4LKK.
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