Limits...
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.

Show MeSH

Related in: MedlinePlus

The frequencies of amino acids among the naturally occurring HA sequences in Figure 8 vs the amino-acid preferences inferred from the combined replicates (Figure 5).Note that a natural frequency close to one or zero could indicate absolute selection for or against a specific amino acid, but could also simply result from the fact that natural evolution has not completely sampled all possible mutations compatible with HA structure and function. The Pearson correlation coefficient (R) and associated p-value are shown on the plot. This plot is the file natural_frequency_vs_preference.pdf described at http://jbloom.github.io/phyloExpCM/example_2014Analysis_Influenza_H1_HA.html.DOI:http://dx.doi.org/10.7554/eLife.03300.018
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4109307&req=5

fig9: The frequencies of amino acids among the naturally occurring HA sequences in Figure 8 vs the amino-acid preferences inferred from the combined replicates (Figure 5).Note that a natural frequency close to one or zero could indicate absolute selection for or against a specific amino acid, but could also simply result from the fact that natural evolution has not completely sampled all possible mutations compatible with HA structure and function. The Pearson correlation coefficient (R) and associated p-value are shown on the plot. This plot is the file natural_frequency_vs_preference.pdf described at http://jbloom.github.io/phyloExpCM/example_2014Analysis_Influenza_H1_HA.html.DOI:http://dx.doi.org/10.7554/eLife.03300.018

Mentions: The crudest comparison is simply to correlate amino-acid frequencies in the natural sequences to the experimentally inferred amino-acid preferences. Figure 9 shows that the inferred preferences are substantially although imperfectly correlated with the natural amino-acid frequencies. However, this comparison is problematic because it fails to account for the contingent and limited sampling of mutations by natural evolution. While the deep mutational scanning is designed to sample all possible mutations, only a fraction of theoretically tolerable mutations have fixed in natural H1 HAs due to the finite timespan during which evolution has been exploring possible sequences (in other words, evolution is not at equilibrium; see Povolotskaya and Kondrashov, 2010). Therefore, an amino-acid frequency of close to one among the natural HA sequences in Figure 8 might imply an absolute functional requirement for that amino acid—or it might simply mean that natural evolution has not yet happened to fix a mutation to another tolerable amino acid at that site.10.7554/eLife.03300.018Figure 9.The frequencies of amino acids among the naturally occurring HA sequences in Figure 8 vs the amino-acid preferences inferred from the combined replicates (Figure 5).


The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin.

Thyagarajan B, Bloom JD - Elife (2014)

The frequencies of amino acids among the naturally occurring HA sequences in Figure 8 vs the amino-acid preferences inferred from the combined replicates (Figure 5).Note that a natural frequency close to one or zero could indicate absolute selection for or against a specific amino acid, but could also simply result from the fact that natural evolution has not completely sampled all possible mutations compatible with HA structure and function. The Pearson correlation coefficient (R) and associated p-value are shown on the plot. This plot is the file natural_frequency_vs_preference.pdf described at http://jbloom.github.io/phyloExpCM/example_2014Analysis_Influenza_H1_HA.html.DOI:http://dx.doi.org/10.7554/eLife.03300.018
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig9: The frequencies of amino acids among the naturally occurring HA sequences in Figure 8 vs the amino-acid preferences inferred from the combined replicates (Figure 5).Note that a natural frequency close to one or zero could indicate absolute selection for or against a specific amino acid, but could also simply result from the fact that natural evolution has not completely sampled all possible mutations compatible with HA structure and function. The Pearson correlation coefficient (R) and associated p-value are shown on the plot. This plot is the file natural_frequency_vs_preference.pdf described at http://jbloom.github.io/phyloExpCM/example_2014Analysis_Influenza_H1_HA.html.DOI:http://dx.doi.org/10.7554/eLife.03300.018
Mentions: The crudest comparison is simply to correlate amino-acid frequencies in the natural sequences to the experimentally inferred amino-acid preferences. Figure 9 shows that the inferred preferences are substantially although imperfectly correlated with the natural amino-acid frequencies. However, this comparison is problematic because it fails to account for the contingent and limited sampling of mutations by natural evolution. While the deep mutational scanning is designed to sample all possible mutations, only a fraction of theoretically tolerable mutations have fixed in natural H1 HAs due to the finite timespan during which evolution has been exploring possible sequences (in other words, evolution is not at equilibrium; see Povolotskaya and Kondrashov, 2010). Therefore, an amino-acid frequency of close to one among the natural HA sequences in Figure 8 might imply an absolute functional requirement for that amino acid—or it might simply mean that natural evolution has not yet happened to fix a mutation to another tolerable amino acid at that site.10.7554/eLife.03300.018Figure 9.The frequencies of amino acids among the naturally occurring HA sequences in Figure 8 vs the amino-acid preferences inferred from the combined replicates (Figure 5).

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