A cellular trafficking signal in the SIV envelope protein cytoplasmic domain is strongly selected for in pathogenic infection

Abstract

The HIV/SIV envelope glycoprotein (Env) cytoplasmic domain contains a highly conserved Tyr-based trafficking signal that mediates both clathrin-dependent endocytosis and polarized sorting. Despite extensive analysis, the role of these functions in viral infection and pathogenesis is unclear. An SIV molecular clone (SIVmac239) in which this signal is inactivated by deletion of Gly-720 and Tyr-721 (SIVmac239ΔGY), replicates acutely to high levels in pigtail macaques (PTM) but is rapidly controlled. However, we previously reported that rhesus macaques and PTM can progress to AIDS following SIVmac239ΔGY infection in association with novel amino acid changes in the Env cytoplasmic domain. These included an R722G flanking the ΔGY deletion and a nine nucleotide deletion encoding amino acids 734–736 (ΔQTH) that overlaps the rev and tat open reading frames. We show that molecular clones containing these mutations reconstitute signals for both endocytosis and polarized sorting. In one PTM, a novel genotype was selected that generated a new signal for polarized sorting but not endocytosis. This genotype, together with the ΔGY mutation, was conserved in association with high viral loads for several months when introduced into naïve PTMs. For the first time, our findings reveal strong selection pressure for Env endocytosis and particularly for polarized sorting during pathogenic SIV infection in vivo. Author summary: In the cytoplasmic domain (CD) of their envelope glycoproteins (Env), all human and simian immunodeficiency viruses (HIV and SIV) have a tyrosine-dependent motif that is a potent signal for Env endocytosis and polarized sorting in infected cells. The role and relevance of this trafficking signal in pathogenesis is unknown. For a pathogenic SIV, we have shown that deletion of this tyrosine and a preceding glycine, creating a virus termed ΔGY, results in profoundly altered pathogenesis in pigtail macaques. Viral replication is rapidly suppressed, systemic immune activation fails to occur, and CD4 cells are spared. However, although uncommon, ΔGY-infected macaques can develop high viral loads and disease in association with novel mutations in the Env CD. Here we show that these mutations restore trafficking functions, remarkably, at the expense of tat and rev genes in overlapping reading frames. We quantified the effects of these new signals and demonstrated their ability to confer high viral loads and/or disease to ΔGY-infected animals. These findings demonstrate strong in vivo selection pressures to maintain Env trafficking, in particular, polarized sorting. We present hypotheses for why this long recognized, but poorly understood Env function is conserved and essential for HIV/SIV pathogenesis.

Publication information

Originally published in PLOS Pathogens on 2022-06-17. Original DOI: 10.1371/journal.ppat.1010507.

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