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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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Mutations modulating rhesus Trim5αTFP restriction ring a conserved surface patch.(A) Top row: Orientations of the SIVmac239 capsid used for Figure 5A. Middle row: Surface representation of the SIVmac239 capsid N-terminal domain colored to reflect amino acid conservation across divergent primate lentiviruses. The number of unique amino acids found at each position in an amino acid alignment of eleven divergent primate lentiviruses (Figure S7) was scored and colored according to the legend: Orange ≥4 unique amino acids at the specified position, yellow 3 unique amino acids at the specified position, light gray 2 unique residues at the specified position and dark gray 1 amino acid (100% conservation) at the specified position. The location of the conserved surface patch is indicated by dashed lines. Bottom panel: Locations of mutations that are associated with a >2.5 fold gain in sensitivity to rhTrim5αTFP are shown in dark red. (B) Atomic view of the conserved surface patch. For reference the SIVmac239 and HIV-1 (2X2D) ribbon diagrams are shown in light blue and pink, respectively. The amino acids that make up the conserved surface patch are shown in sticks that are colored according to the capsid ribbon diagram, SIVmac239 in light blue and HIV-1 in light red. Variable positions shown to modulate rhesus Trim5αTFP sensitivity are colored in dark blue (SIVmac239) and dark red sticks (HIV-1) for emphasis. Images created in PyMol.
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ppat-1003352-g005: Mutations modulating rhesus Trim5αTFP restriction ring a conserved surface patch.(A) Top row: Orientations of the SIVmac239 capsid used for Figure 5A. Middle row: Surface representation of the SIVmac239 capsid N-terminal domain colored to reflect amino acid conservation across divergent primate lentiviruses. The number of unique amino acids found at each position in an amino acid alignment of eleven divergent primate lentiviruses (Figure S7) was scored and colored according to the legend: Orange ≥4 unique amino acids at the specified position, yellow 3 unique amino acids at the specified position, light gray 2 unique residues at the specified position and dark gray 1 amino acid (100% conservation) at the specified position. The location of the conserved surface patch is indicated by dashed lines. Bottom panel: Locations of mutations that are associated with a >2.5 fold gain in sensitivity to rhTrim5αTFP are shown in dark red. (B) Atomic view of the conserved surface patch. For reference the SIVmac239 and HIV-1 (2X2D) ribbon diagrams are shown in light blue and pink, respectively. The amino acids that make up the conserved surface patch are shown in sticks that are colored according to the capsid ribbon diagram, SIVmac239 in light blue and HIV-1 in light red. Variable positions shown to modulate rhesus Trim5αTFP sensitivity are colored in dark blue (SIVmac239) and dark red sticks (HIV-1) for emphasis. Images created in PyMol.

Mentions: In contrast to rhTrim5αQ, we found that rhTrim5αTFP restricts at least three phylogenetically distinct primate lentiviruses: HIV-1, SIVagmTan, and SIVsm (Figure 1). While single amino acid substitutions affecting rhTrim5αQ were confined to the β-hairpin, substitutions that increased sensitivity to rhTrim5αTFP were spread across the N-terminal domain surface (Figures 4C and 4D). Based on these two observations, we hypothesized that rhTrim5αTFP may have evolved to target a conserved element(s) unique to the primate lentivirus CA N-terminal domain. To identify uncharacterized sites of primate lentivirus conservation, we generated an alignment of CA N-terminal domains using one representative virus from eleven different primate lentivirus lineages (Figure S7). We then scored the number of unique amino acids found at each position, and mapped the results onto the SIVmac239 structure (Figure 5A).


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)

Mutations modulating rhesus Trim5αTFP restriction ring a conserved surface patch.(A) Top row: Orientations of the SIVmac239 capsid used for Figure 5A. Middle row: Surface representation of the SIVmac239 capsid N-terminal domain colored to reflect amino acid conservation across divergent primate lentiviruses. The number of unique amino acids found at each position in an amino acid alignment of eleven divergent primate lentiviruses (Figure S7) was scored and colored according to the legend: Orange ≥4 unique amino acids at the specified position, yellow 3 unique amino acids at the specified position, light gray 2 unique residues at the specified position and dark gray 1 amino acid (100% conservation) at the specified position. The location of the conserved surface patch is indicated by dashed lines. Bottom panel: Locations of mutations that are associated with a >2.5 fold gain in sensitivity to rhTrim5αTFP are shown in dark red. (B) Atomic view of the conserved surface patch. For reference the SIVmac239 and HIV-1 (2X2D) ribbon diagrams are shown in light blue and pink, respectively. The amino acids that make up the conserved surface patch are shown in sticks that are colored according to the capsid ribbon diagram, SIVmac239 in light blue and HIV-1 in light red. Variable positions shown to modulate rhesus Trim5αTFP sensitivity are colored in dark blue (SIVmac239) and dark red sticks (HIV-1) for emphasis. Images created in PyMol.
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Related In: Results  -  Collection

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ppat-1003352-g005: Mutations modulating rhesus Trim5αTFP restriction ring a conserved surface patch.(A) Top row: Orientations of the SIVmac239 capsid used for Figure 5A. Middle row: Surface representation of the SIVmac239 capsid N-terminal domain colored to reflect amino acid conservation across divergent primate lentiviruses. The number of unique amino acids found at each position in an amino acid alignment of eleven divergent primate lentiviruses (Figure S7) was scored and colored according to the legend: Orange ≥4 unique amino acids at the specified position, yellow 3 unique amino acids at the specified position, light gray 2 unique residues at the specified position and dark gray 1 amino acid (100% conservation) at the specified position. The location of the conserved surface patch is indicated by dashed lines. Bottom panel: Locations of mutations that are associated with a >2.5 fold gain in sensitivity to rhTrim5αTFP are shown in dark red. (B) Atomic view of the conserved surface patch. For reference the SIVmac239 and HIV-1 (2X2D) ribbon diagrams are shown in light blue and pink, respectively. The amino acids that make up the conserved surface patch are shown in sticks that are colored according to the capsid ribbon diagram, SIVmac239 in light blue and HIV-1 in light red. Variable positions shown to modulate rhesus Trim5αTFP sensitivity are colored in dark blue (SIVmac239) and dark red sticks (HIV-1) for emphasis. Images created in PyMol.
Mentions: In contrast to rhTrim5αQ, we found that rhTrim5αTFP restricts at least three phylogenetically distinct primate lentiviruses: HIV-1, SIVagmTan, and SIVsm (Figure 1). While single amino acid substitutions affecting rhTrim5αQ were confined to the β-hairpin, substitutions that increased sensitivity to rhTrim5αTFP were spread across the N-terminal domain surface (Figures 4C and 4D). Based on these two observations, we hypothesized that rhTrim5αTFP may have evolved to target a conserved element(s) unique to the primate lentivirus CA N-terminal domain. To identify uncharacterized sites of primate lentivirus conservation, we generated an alignment of CA N-terminal domains using one representative virus from eleven different primate lentivirus lineages (Figure S7). We then scored the number of unique amino acids found at each position, and mapped the results onto the SIVmac239 structure (Figure 5A).

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