APOBEC3G-Induced Hypermutation of Human Immunodeficiency Virus Type-1 Is Typically a Discrete “All or Nothing” Phenomenon

Abstract

The rapid evolution of Human Immunodeficiency Virus (HIV-1) allows studies of ongoing host–pathogen interactions. One key selective host factor is APOBEC3G (hA3G) that can cause extensive and inactivating Guanosine-to-Adenosine (G-to-A) mutation on HIV plus-strand DNA (termed hypermutation). HIV can inhibit this innate anti-viral defense through binding of the viral protein Vif to hA3G, but binding efficiency varies and hypermutation frequencies fluctuate in patients. A pivotal question is whether hA3G-induced G-to-A mutation is always lethal to the virus or if it may occur at sub-lethal frequencies that could increase viral diversification. We show in vitro that limiting-levels of hA3G-activity (i.e. when only a single hA3G-unit is likely to act on HIV) produce hypermutation frequencies similar to those in patients and demonstrate in silico that potentially non-lethal G-to-A mutation rates are ∼10-fold lower than the lowest observed hypermutation levels in vitro and in vivo . Our results suggest that even a single incorporated hA3G-unit is likely to cause extensive and inactivating levels of HIV hypermutation and that hypermutation therefore is typically a discrete “all or nothing” phenomenon. Thus, therapeutic measures that inhibit the interaction between Vif and hA3G will likely not increase virus diversification but expand the fraction of hypermutated proviruses within the infected host.

Possible Footprints of APOBEC3F and/or Other APOBEC3 Deaminases, but Not APOBEC3G, on HIV-1 from Patients with Acute/Early and Chronic Infections

“…Specifically, we observed that G-to-A mutations occurred more frequently in APOBEC3G-disfavored contexts than in APOBEC3G-favored contexts, strongly suggesting that APOBEC3G activity does not contribute to beneficial HIV-1 diversification in vivo. This result is consistent with our previous in vitro and in silico analyses of APOBEC3G, which indicated that the activity of even a single APOBEC3G unit is highly likely to be lethal for HIV-1 (21).…”

“…induced mutagenesis (12,21), the limitation that we are not able to compare the mutational context in the same gene is unlikely to affect the results.…”

“…Whereas the lowest observed levels of APOBEC3G-induced hypermutation in vitro are highly likely to introduce multiple lethal stop codons within HIV-1 (21), it is unclear whether some or all of the APOBEC3 proteins induce mutations at sublethal levels that increase viral diversification in vivo. Such increased diversification may facilitate viral adaptation to selective pressures in the host and thereby enhance HIV-1 propagation.…”

Comparative analysis of the gene-inactivating potential of retroviral restriction factors APOBEC3F and APOBEC3G

“…With a lower gene inactivation potential and a high rate of NS substitution generation, our results support that A3F is much more effective than A3G at promoting viral sequence evolution. This is also consistent with previous findings that employed other analysis methods and systems (Ara et al, 2014;Armitage et al, 2012Armitage et al, , 2014Kim et al, 2014;Sato et al, 2014;Wood et al, 2009).…”

“…This thereby provided us with the ability to directly compare how DNA target specificity impacts gene inactivation and retroviral sequence evolution. This is an issue of particular importance as A3F, more than A3G, has been shown to promote HIV-1 diversification and evolution in vivo (Ara et al, 2014;Armitage et al, 2012Armitage et al, , 2014Kim et al, 2014;Sato et al, 2014;Wood et al, 2009). However, the extent to which this diversification correlates with alterations in gene function had not been assessed until now.…”