Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells.

Erik C Hansen,Janet M Siliciano,Ross A Pollack,Jay R Hesselberth,Monica Ransom,Hao Zhang,Adam A Capoferri,James T Stivers,Robert Siliciano,Michael Bradley Drummond,Nina N Hosmane,Katherine M Bruner

doi:10.7554/elife.18447

Abstract

We report that a major subpopulation of monocyte-derived macrophages (MDMs) contains high levels of dUTP, which is incorporated into HIV-1 DNA during reverse transcription (U/A pairs), resulting in pre-integration restriction and post-integration mutagenesis. After entering the nucleus, uracilated viral DNA products are degraded by the uracil base excision repair (UBER) machinery with less than 1% of the uracilated DNA successfully integrating. Although uracilated proviral DNA showed few mutations, the viral genomic RNA was highly mutated, suggesting that errors occur during transcription. Viral DNA isolated from blood monocytes and alveolar macrophages (but not T cells) of drug-suppressed HIV-infected individuals also contained abundant uracils. The presence of viral uracils in short-lived monocytes suggests their recent infection through contact with virus producing cells in a tissue reservoir. These findings reveal new elements of a viral defense mechanism involving host UBER that may be relevant to the establishment and persistence of HIV-1 infection.

Highlights

The uracil nucleobase plays a central role in adaptive and innate immunity against Human immunodeficiency virus type 1 (HIV-1) when it is found in DNA rather than RNA (Priet et al, 2006; Sire et al, 2008)
Upon entry into the macrophage, reverse transcriptase (RT) encounters a nucleotide pool environment that favors the incorporation of deoxyuridine triphosphate (dUTP) into HIV DNA products predominantly in the form of U/A base pairs
The high ratio of dUTP/TTP is maintained, at least in part, by the low levels of dUTPase expression combined with the high expression levels of SAMHD1 in macrophages

Summary

Introduction

The uracil nucleobase plays a central role in adaptive and innate immunity against HIV-1 when it is found in DNA rather than RNA (Priet et al, 2006; Sire et al, 2008). Work from our lab and others has suggested the presence of another uracil-mediated HIV-1 restriction pathway involving the incorporation of dUTP into viral DNA by reverse transcriptase to produce U/A base pairs (’uracilation’) (Weil et al, 2013). U/A pairs resulting from dUTP incorporation are ’invisible’ to normal DNA sequencing methods and they retain the coding potential of normal T/A base pairs. Despite the similarity of U/A and T/A pairs, the presence of uracil in DNA has the potential to introduce diverse effects on viral infection including transcriptional silencing and engagement of the host

Methods

Results

Conclusion