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The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin.

Thyagarajan B, Bloom JD - Elife (2014)

Bottom Line: We used deep mutational scanning to examine the extent to which a high inherent mutational tolerance contributes to this antigenic evolvability.These data enable us to infer the preference for each amino acid at each site in hemagglutinin.These inferences are consistent with existing knowledge about the protein's structure and function, and can be used to create a model that describes hemagglutinin's evolution far better than existing phylogenetic models.

View Article: PubMed Central - PubMed

Affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.

ABSTRACT
Influenza is notable for its evolutionary capacity to escape immunity targeting the viral hemagglutinin. We used deep mutational scanning to examine the extent to which a high inherent mutational tolerance contributes to this antigenic evolvability. We created mutant viruses that incorporate most of the ≈10(4) amino-acid mutations to hemagglutinin from A/WSN/1933 (H1N1) influenza. After passaging these viruses in tissue culture to select for functional variants, we used deep sequencing to quantify mutation frequencies before and after selection. These data enable us to infer the preference for each amino acid at each site in hemagglutinin. These inferences are consistent with existing knowledge about the protein's structure and function, and can be used to create a model that describes hemagglutinin's evolution far better than existing phylogenetic models. We show that hemagglutinin has a high inherent tolerance for mutations at antigenic sites, suggesting that this is one factor contributing to influenza's antigenic evolution.

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The inherent mutational tolerance of NP's CTL epitopes is indistinguishable from that of non-epitope sites in NP.The plot shows the site entropy vs relative solvent accessibility (RSA) of NP residues that participate in multiple CTL epitopes (red triangles) and all other NP residues in the crystal structure (blue circles). Visual inspection suggests that the epitope sites have mutational tolerance comparable to other sites, and this result is supported by the statistical analysis in Table 5. Note that unlike for HA, there is no trend for RSA to correlate with site entropy—this could be because many of NP’s surface-exposed sites are constrained by interactions with viral RNA. The CTL epitopes are those delineated in the first supplementary table of Gong and Bloom (2014). The site entropies are computed from a previously described deep mutational scan of NP, and are the values in the first supplementary file of Bloom (2014); the RSA values are also taken from that reference. The data and code used to generate this plot is available via http://jbloom.github.io/mapmuts/example_WSN_HA_2014Analysis.html; the plot itself is the file NP_CTL_entropy_rsa_correlation.pdf described therein.DOI:http://dx.doi.org/10.7554/eLife.03300.023
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fig11: The inherent mutational tolerance of NP's CTL epitopes is indistinguishable from that of non-epitope sites in NP.The plot shows the site entropy vs relative solvent accessibility (RSA) of NP residues that participate in multiple CTL epitopes (red triangles) and all other NP residues in the crystal structure (blue circles). Visual inspection suggests that the epitope sites have mutational tolerance comparable to other sites, and this result is supported by the statistical analysis in Table 5. Note that unlike for HA, there is no trend for RSA to correlate with site entropy—this could be because many of NP’s surface-exposed sites are constrained by interactions with viral RNA. The CTL epitopes are those delineated in the first supplementary table of Gong and Bloom (2014). The site entropies are computed from a previously described deep mutational scan of NP, and are the values in the first supplementary file of Bloom (2014); the RSA values are also taken from that reference. The data and code used to generate this plot is available via http://jbloom.github.io/mapmuts/example_WSN_HA_2014Analysis.html; the plot itself is the file NP_CTL_entropy_rsa_correlation.pdf described therein.DOI:http://dx.doi.org/10.7554/eLife.03300.023

Mentions: To test this hypothesis, we used a previously described delineation of epitopes in NP from the human H3N2 strain A/Aichi/2/1968 with experimentally validated human CTL responses (Gong and Bloom, 2014). In this delineation, less than a quarter of NP’s sites participate in multiple CTL epitopes. We used the results of our previous deep mutational scanning of NP to compare the inherent mutational tolerance of sites that participate in multiple CTL epitopes to all other sites in NP. As shown in Figure 11 and Table 5, the NP sites involved in multiple CTL epitopes have an inherent mutational tolerance that is indistinguishable from other sites in the protein. Therefore, NP does not possess any special inherent mutational tolerance in its CTL epitopes. This finding implies that a high level of antigenic evolvability is not a general feature of all viral proteins, but is instead at least somewhat unique to HA.10.7554/eLife.03300.023Figure 11.The inherent mutational tolerance of NP's CTL epitopes is indistinguishable from that of non-epitope sites in NP.


The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin.

Thyagarajan B, Bloom JD - Elife (2014)

The inherent mutational tolerance of NP's CTL epitopes is indistinguishable from that of non-epitope sites in NP.The plot shows the site entropy vs relative solvent accessibility (RSA) of NP residues that participate in multiple CTL epitopes (red triangles) and all other NP residues in the crystal structure (blue circles). Visual inspection suggests that the epitope sites have mutational tolerance comparable to other sites, and this result is supported by the statistical analysis in Table 5. Note that unlike for HA, there is no trend for RSA to correlate with site entropy—this could be because many of NP’s surface-exposed sites are constrained by interactions with viral RNA. The CTL epitopes are those delineated in the first supplementary table of Gong and Bloom (2014). The site entropies are computed from a previously described deep mutational scan of NP, and are the values in the first supplementary file of Bloom (2014); the RSA values are also taken from that reference. The data and code used to generate this plot is available via http://jbloom.github.io/mapmuts/example_WSN_HA_2014Analysis.html; the plot itself is the file NP_CTL_entropy_rsa_correlation.pdf described therein.DOI:http://dx.doi.org/10.7554/eLife.03300.023
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109307&req=5

fig11: The inherent mutational tolerance of NP's CTL epitopes is indistinguishable from that of non-epitope sites in NP.The plot shows the site entropy vs relative solvent accessibility (RSA) of NP residues that participate in multiple CTL epitopes (red triangles) and all other NP residues in the crystal structure (blue circles). Visual inspection suggests that the epitope sites have mutational tolerance comparable to other sites, and this result is supported by the statistical analysis in Table 5. Note that unlike for HA, there is no trend for RSA to correlate with site entropy—this could be because many of NP’s surface-exposed sites are constrained by interactions with viral RNA. The CTL epitopes are those delineated in the first supplementary table of Gong and Bloom (2014). The site entropies are computed from a previously described deep mutational scan of NP, and are the values in the first supplementary file of Bloom (2014); the RSA values are also taken from that reference. The data and code used to generate this plot is available via http://jbloom.github.io/mapmuts/example_WSN_HA_2014Analysis.html; the plot itself is the file NP_CTL_entropy_rsa_correlation.pdf described therein.DOI:http://dx.doi.org/10.7554/eLife.03300.023
Mentions: To test this hypothesis, we used a previously described delineation of epitopes in NP from the human H3N2 strain A/Aichi/2/1968 with experimentally validated human CTL responses (Gong and Bloom, 2014). In this delineation, less than a quarter of NP’s sites participate in multiple CTL epitopes. We used the results of our previous deep mutational scanning of NP to compare the inherent mutational tolerance of sites that participate in multiple CTL epitopes to all other sites in NP. As shown in Figure 11 and Table 5, the NP sites involved in multiple CTL epitopes have an inherent mutational tolerance that is indistinguishable from other sites in the protein. Therefore, NP does not possess any special inherent mutational tolerance in its CTL epitopes. This finding implies that a high level of antigenic evolvability is not a general feature of all viral proteins, but is instead at least somewhat unique to HA.10.7554/eLife.03300.023Figure 11.The inherent mutational tolerance of NP's CTL epitopes is indistinguishable from that of non-epitope sites in NP.

Bottom Line: We used deep mutational scanning to examine the extent to which a high inherent mutational tolerance contributes to this antigenic evolvability.These data enable us to infer the preference for each amino acid at each site in hemagglutinin.These inferences are consistent with existing knowledge about the protein's structure and function, and can be used to create a model that describes hemagglutinin's evolution far better than existing phylogenetic models.

View Article: PubMed Central - PubMed

Affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.

ABSTRACT
Influenza is notable for its evolutionary capacity to escape immunity targeting the viral hemagglutinin. We used deep mutational scanning to examine the extent to which a high inherent mutational tolerance contributes to this antigenic evolvability. We created mutant viruses that incorporate most of the ≈10(4) amino-acid mutations to hemagglutinin from A/WSN/1933 (H1N1) influenza. After passaging these viruses in tissue culture to select for functional variants, we used deep sequencing to quantify mutation frequencies before and after selection. These data enable us to infer the preference for each amino acid at each site in hemagglutinin. These inferences are consistent with existing knowledge about the protein's structure and function, and can be used to create a model that describes hemagglutinin's evolution far better than existing phylogenetic models. We show that hemagglutinin has a high inherent tolerance for mutations at antigenic sites, suggesting that this is one factor contributing to influenza's antigenic evolution.

Show MeSH
Related in: MedlinePlus