Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5a Specificity

Retroviral capsid recognition by Trim5 blocks productive infection. Rhesus macaques harbor three functionally distinct Trim5 alleles: Trim5a, Trim5a and Trim5. Despite the high degree of amino acid identity between Trim5a and Trim5a 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 Trim5a resistance of this capsid to identify gain-ofsensitivity mutations that distinguish targets between the Trim5a and Trim5a alleles. While both alleles recognize the capsid surface, Trim5a and Trim5a 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 b-hairpin. Given that none of the substitutions affected Trim5a alone, and the fact that the b-hairpin is conserved among retroviral capsids, we propose that the b-hairpin is a molecular pattern widely exploited by Trim5a proteins. Mutations specifically affecting rhesus Trim5a (without affecting Trim5a) 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. Citation: McCarthy KR, Schmidt AG, Kirmaier A, Wyand AL, Newman RM, et al. (2013) Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5a Specificity. PLoS Pathog 9(5): e1003352. doi:10.1371/journal.ppat.1003352 Editor: Michael Emerman, Fred Hutchinson Cancer Research Center, United States of America Received November 25, 2012; Accepted March 25, 2013; Published May 9, 2013 Copyright: 2013 McCarthy et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by NIH grants AI095092 and AI083118 to WEJ (http://www.nih.gov/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected]