Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5α Specificity

Kevin R Mccarthy,Aaron G Schmidt,Welkin E Johnson,Ruchi M Newman,Andrea Kirmaier,Allison L Wyand,Michael Emerman

doi:10.1371/journal.ppat.1003352

Kevin R Mccarthy, Aaron G Schmidt + Show 5 more

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https://doi.org/10.1371/journal.ppat.1003352

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Abstract

Retroviral capsid recognition by Trim5 blocks productive infection. Rhesus macaques harbor three functionally distinct Trim5 alleles: Trim5αQ, Trim5αTFP and Trim5CypA. Despite the high degree of amino acid identity between Trim5αQ and Trim5αTFP 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 Trim5αQ and Trim5αTFP alleles. While both alleles recognize the capsid surface, Trim5αQ and Trim5αTFP 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 Trim5αQ 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 Trim5αTFP (without affecting Trim5αQ) 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.

Highlights

The anti-retroviral activity of Trim5a was discovered in a screen to identify rhesus macaque cDNAs conferring resistance to HIV-1 replication [1]
SIVmac239, a simian immunodeficiency virus that causes AIDS in rhesus macaques, is resistant to all three, whereas its relative, the human AIDS virus HIV-1, is inhibited by rhTrim5aTFP and rhTrim5aQ alleles. We exploited this difference between these two retroviruses to figure out how Trim5a proteins recognize viral capsids
We found evidence suggesting that rhTrim5aTFP evolved to recognize an additional target that is conserved among primate immunodeficiency viruses

Summary

Introduction

The anti-retroviral activity of Trim5a was discovered in a screen to identify rhesus macaque cDNAs conferring resistance to HIV-1 replication [1]. Trim5a is composed of four domains: the RING, the B-Box and the Coiled-coil domains, which make up the tripartite RBCC of TRIM proteins, and a C-terminal PRYSPRY domain [8,9]. The PRYSPRY domain is thought to recognize the viral capsid [1,10,11]. An HIV-1 CA monomer has two a-helical domains connected by a flexible linker [14]. The N-terminal domain makes up the outer surface of the capsid and mediates interactions with cellular cofactors [15,16,17,18,19,20,21]

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