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Gain-of-sensitivity mutations in a Trim5-resistant primary isolate of pathogenic SIV identify two independent conserved determinants of Trim5α specificity.

McCarthy KR, Schmidt AG, Kirmaier A, Wyand AL, Newman RM, Johnson WE - PLoS Pathog. (2013)

Bottom Line: Despite the high degree of amino acid identity between Trim5α(Q) and Trim5α(TFP) alleles, the Q/TFP polymorphism results in the differential restriction of some primate lentiviruses, suggesting these alleles differ in how they engage these capsids.We believe targeting this site is an evolutionary innovation driven specifically by the emergence of primate lentiviruses in Africa during the last 12 million years.This modularity in targeting may be a general feature of Trim5 evolution, permitting different regions of the PRYSPRY domain to evolve independent interactions with capsid.

View Article: PubMed Central - PubMed

Affiliation: Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America.

ABSTRACT
Retroviral capsid recognition by Trim5 blocks productive infection. Rhesus macaques harbor three functionally distinct Trim5 alleles: Trim5α(Q) , Trim5α(TFP) and Trim5(CypA) . Despite the high degree of amino acid identity between Trim5α(Q) and Trim5α(TFP) alleles, the Q/TFP polymorphism results in the differential restriction of some primate lentiviruses, suggesting these alleles differ in how they engage these capsids. Simian immunodeficiency virus of rhesus macaques (SIVmac) evolved to resist all three alleles. Thus, SIVmac provides a unique opportunity to study a virus in the context of the Trim5 repertoire that drove its evolution in vivo. We exploited the evolved rhesus Trim5α resistance of this capsid to identify gain-of-sensitivity mutations that distinguish targets between the Trim5α(Q) and Trim5α(TFP) alleles. While both alleles recognize the capsid surface, Trim5α(Q) and Trim5α(TFP) alleles differed in their ability to restrict a panel of capsid chimeras and single amino acid substitutions. When mapped onto the structure of the SIVmac239 capsid N-terminal domain, single amino acid substitutions affecting both alleles mapped to the β-hairpin. Given that none of the substitutions affected Trim5α(Q) alone, and the fact that the β-hairpin is conserved among retroviral capsids, we propose that the β-hairpin is a molecular pattern widely exploited by Trim5α proteins. Mutations specifically affecting rhesus Trim5α(TFP) (without affecting Trim5α(Q) ) surround a site of conservation unique to primate lentiviruses, overlapping the CPSF6 binding site. We believe targeting this site is an evolutionary innovation driven specifically by the emergence of primate lentiviruses in Africa during the last 12 million years. This modularity in targeting may be a general feature of Trim5 evolution, permitting different regions of the PRYSPRY domain to evolve independent interactions with capsid.

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Structure of the SIVmac239 Capsid N-terminal domain.(A) Structure of the SIVmac239 CA N-terminal domain at 2.9 Å resolution. There was no clear density for Pro88, and thus, it was omitted from the structure. A dashed line is used to indicate its place. (B) Comparison of the SIVmac239 β-hairpin and 4–5 loop to all other wild type HIV-1 and HIV-2 X-ray structures deposited in the PDB. HIV-1 structures are colored dark gray, except PDB: 2X2D, which is colored red (and used in all subsequent comparisons). HIV-2 structures are colored light gray, and the SIVmac239 N-terminal domain is colored blue. (C and D) Locations of amino acids mutations associated with rhesus Trim5αQ (C) and rhesus Trim5αTFP (D) restriction from Table 1. Blue spheres indicate amino acid differences that do not impact Trim5α restriction. Orange spheres show the location of mutations associated with 2.5–5 fold gains in sensitivity to rhesus Trim5α relative to SIVmac239. Red spheres indicate positions associated with >5 fold gains in sensitivity to rhesus Trim5α. Images created in PyMol.
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ppat-1003352-g004: Structure of the SIVmac239 Capsid N-terminal domain.(A) Structure of the SIVmac239 CA N-terminal domain at 2.9 Å resolution. There was no clear density for Pro88, and thus, it was omitted from the structure. A dashed line is used to indicate its place. (B) Comparison of the SIVmac239 β-hairpin and 4–5 loop to all other wild type HIV-1 and HIV-2 X-ray structures deposited in the PDB. HIV-1 structures are colored dark gray, except PDB: 2X2D, which is colored red (and used in all subsequent comparisons). HIV-2 structures are colored light gray, and the SIVmac239 N-terminal domain is colored blue. (C and D) Locations of amino acids mutations associated with rhesus Trim5αQ (C) and rhesus Trim5αTFP (D) restriction from Table 1. Blue spheres indicate amino acid differences that do not impact Trim5α restriction. Orange spheres show the location of mutations associated with 2.5–5 fold gains in sensitivity to rhesus Trim5α relative to SIVmac239. Red spheres indicate positions associated with >5 fold gains in sensitivity to rhesus Trim5α. Images created in PyMol.

Mentions: To provide a relevant structural context for evaluating the mutagenesis results, we determined the structure of the SIVmac239 CA N-terminal domain (Figures 4A, S4, S5 and Table S1). The SIVmac239 CA N-terminal domain was very similar to reported structures of HIV-1 (PDB: 2X2D) (RMSD at Cα positions: 2.29 Å) and HIV-2 (PDB: 2WLV) (RMSD at Cα positions: 1.42 Å) (calculations used SuperPose [76]). In particular, the five α-helices of the SIVmac239 N-terminal domain core did not deviate from those of HIV-1 or HIV-2, consistent with the observation that the SIV-HIVinterior chimera remained largely resistant to restriction (Figure 3C).


Gain-of-sensitivity mutations in a Trim5-resistant primary isolate of pathogenic SIV identify two independent conserved determinants of Trim5α specificity.

McCarthy KR, Schmidt AG, Kirmaier A, Wyand AL, Newman RM, Johnson WE - PLoS Pathog. (2013)

Structure of the SIVmac239 Capsid N-terminal domain.(A) Structure of the SIVmac239 CA N-terminal domain at 2.9 Å resolution. There was no clear density for Pro88, and thus, it was omitted from the structure. A dashed line is used to indicate its place. (B) Comparison of the SIVmac239 β-hairpin and 4–5 loop to all other wild type HIV-1 and HIV-2 X-ray structures deposited in the PDB. HIV-1 structures are colored dark gray, except PDB: 2X2D, which is colored red (and used in all subsequent comparisons). HIV-2 structures are colored light gray, and the SIVmac239 N-terminal domain is colored blue. (C and D) Locations of amino acids mutations associated with rhesus Trim5αQ (C) and rhesus Trim5αTFP (D) restriction from Table 1. Blue spheres indicate amino acid differences that do not impact Trim5α restriction. Orange spheres show the location of mutations associated with 2.5–5 fold gains in sensitivity to rhesus Trim5α relative to SIVmac239. Red spheres indicate positions associated with >5 fold gains in sensitivity to rhesus Trim5α. Images created in PyMol.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3649984&req=5

ppat-1003352-g004: Structure of the SIVmac239 Capsid N-terminal domain.(A) Structure of the SIVmac239 CA N-terminal domain at 2.9 Å resolution. There was no clear density for Pro88, and thus, it was omitted from the structure. A dashed line is used to indicate its place. (B) Comparison of the SIVmac239 β-hairpin and 4–5 loop to all other wild type HIV-1 and HIV-2 X-ray structures deposited in the PDB. HIV-1 structures are colored dark gray, except PDB: 2X2D, which is colored red (and used in all subsequent comparisons). HIV-2 structures are colored light gray, and the SIVmac239 N-terminal domain is colored blue. (C and D) Locations of amino acids mutations associated with rhesus Trim5αQ (C) and rhesus Trim5αTFP (D) restriction from Table 1. Blue spheres indicate amino acid differences that do not impact Trim5α restriction. Orange spheres show the location of mutations associated with 2.5–5 fold gains in sensitivity to rhesus Trim5α relative to SIVmac239. Red spheres indicate positions associated with >5 fold gains in sensitivity to rhesus Trim5α. Images created in PyMol.
Mentions: To provide a relevant structural context for evaluating the mutagenesis results, we determined the structure of the SIVmac239 CA N-terminal domain (Figures 4A, S4, S5 and Table S1). The SIVmac239 CA N-terminal domain was very similar to reported structures of HIV-1 (PDB: 2X2D) (RMSD at Cα positions: 2.29 Å) and HIV-2 (PDB: 2WLV) (RMSD at Cα positions: 1.42 Å) (calculations used SuperPose [76]). In particular, the five α-helices of the SIVmac239 N-terminal domain core did not deviate from those of HIV-1 or HIV-2, consistent with the observation that the SIV-HIVinterior chimera remained largely resistant to restriction (Figure 3C).

Bottom Line: Despite the high degree of amino acid identity between Trim5α(Q) and Trim5α(TFP) alleles, the Q/TFP polymorphism results in the differential restriction of some primate lentiviruses, suggesting these alleles differ in how they engage these capsids.We believe targeting this site is an evolutionary innovation driven specifically by the emergence of primate lentiviruses in Africa during the last 12 million years.This modularity in targeting may be a general feature of Trim5 evolution, permitting different regions of the PRYSPRY domain to evolve independent interactions with capsid.

View Article: PubMed Central - PubMed

Affiliation: Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America.

ABSTRACT
Retroviral capsid recognition by Trim5 blocks productive infection. Rhesus macaques harbor three functionally distinct Trim5 alleles: Trim5α(Q) , Trim5α(TFP) and Trim5(CypA) . Despite the high degree of amino acid identity between Trim5α(Q) and Trim5α(TFP) alleles, the Q/TFP polymorphism results in the differential restriction of some primate lentiviruses, suggesting these alleles differ in how they engage these capsids. Simian immunodeficiency virus of rhesus macaques (SIVmac) evolved to resist all three alleles. Thus, SIVmac provides a unique opportunity to study a virus in the context of the Trim5 repertoire that drove its evolution in vivo. We exploited the evolved rhesus Trim5α resistance of this capsid to identify gain-of-sensitivity mutations that distinguish targets between the Trim5α(Q) and Trim5α(TFP) alleles. While both alleles recognize the capsid surface, Trim5α(Q) and Trim5α(TFP) alleles differed in their ability to restrict a panel of capsid chimeras and single amino acid substitutions. When mapped onto the structure of the SIVmac239 capsid N-terminal domain, single amino acid substitutions affecting both alleles mapped to the β-hairpin. Given that none of the substitutions affected Trim5α(Q) alone, and the fact that the β-hairpin is conserved among retroviral capsids, we propose that the β-hairpin is a molecular pattern widely exploited by Trim5α proteins. Mutations specifically affecting rhesus Trim5α(TFP) (without affecting Trim5α(Q) ) surround a site of conservation unique to primate lentiviruses, overlapping the CPSF6 binding site. We believe targeting this site is an evolutionary innovation driven specifically by the emergence of primate lentiviruses in Africa during the last 12 million years. This modularity in targeting may be a general feature of Trim5 evolution, permitting different regions of the PRYSPRY domain to evolve independent interactions with capsid.

Show MeSH
Related in: MedlinePlus