Deficient uracil base excision repair leads to persistent dUMP in HIV proviruses during infection of monocytes and macrophages.

Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

Original Publication: San Francisco, CA : Public Library of Science

DNA Repair*; HIV Infections/*genetics ; Macrophages/*virology ; Monocytes/*virology ; Proviruses/*genetics ; Uracil/*metabolism; DNA, Viral/genetics ; Deoxyuracil Nucleotides/deficiency ; Deoxyuracil Nucleotides/metabolism ; HIV-1/genetics ; Humans ; Uracil-DNA Glycosidase/metabolism

Non-dividing cells of the myeloid lineage such as monocytes and macrophages are target cells of HIV that have low dNTP pool concentrations and elevated levels of dUTP, which leads to frequent incorporation of dUMP opposite to A during reverse transcription ("uracilation"). One factor determining the fate of dUMP in proviral DNA is the host cell uracil base excision repair (UBER) system. Here we explore the relative UBER capacity of monocytes (MC) and monocyte-derived macrophages (MDM) and the fate of integrated uracilated viruses in both cell types to understand the implications of viral dUMP on HIV diversification and infectivity. We find that the kinetics for MC infection is compatible with their lifetime in vivo and their near absence of hUNG2 activity is consistent with the retention of viral dUMP at high levels at least until differentiation into macrophages, where UBER becomes possible. Overexpression of human uracil DNA glycosylase in MDM prior to infection resulted in rapid removal of dUMP from HIV cDNA and near complete depletion of dUMP-containing viral copies. This finding establishes that the low hUNG2 expression level in these cells limits UBER but that hUNG2 is restrictive against uracilated viruses. In contrast, overexpression of hUNG2 after viral integration did not accelerate the excision of uracils, suggesting that they may poorly accessible in the context of chromatin. We found that viral DNA molecules with incorporated dUMP contained unique (+) strand transversion mutations that were not observed when dUMP was absent (G→T, T→A, T→G, A→C). These observations and other considerations suggest that dUMP introduces errors predominantly during (-) strand synthesis when the template is RNA. Overall, the likelihood of producing a functional virus from in vitro infection of MC is about 50-fold and 300-fold reduced as compared to MDM and activated T cells. The results implicate viral dUMP incorporation in MC and MDM as a potential viral diversification and restriction pathway during human HIV infection.
Competing Interests: The authors have declared that no competing interests exist.

J Biol Chem. 2011 Jul 15;286(28):25047-55. (PMID: 21454906)
J Leukoc Biol. 2006 Nov;80(5):1127-35. (PMID: 16923921)
Biochemistry. 2011 Feb 8;50(5):612-7. (PMID: 21190322)
PLoS Pathog. 2010 Dec 16;6(12):e1001228. (PMID: 21187897)
Nucleic Acids Res. 2014 Feb;42(3):1698-710. (PMID: 24178031)
Proc Natl Acad Sci U S A. 2011 May 31;108(22):9244-9. (PMID: 21576478)
Mol Cell. 2005 Feb 18;17(4):479-90. (PMID: 15721252)
J Virol. 1995 May;69(5):2881-8. (PMID: 7707512)
J Virol. 2012 Mar;86(5):2533-44. (PMID: 22171270)
EMBO J. 2017 Mar 1;36(5):604-616. (PMID: 28122869)
Nat Rev Immunol. 2010 Jul;10(7):527-35. (PMID: 20577269)
Acc Chem Res. 2009 Jan 20;42(1):97-106. (PMID: 18837522)
Nucleic Acids Res. 2019 May 7;47(8):4153-4168. (PMID: 30892639)
J Leukoc Biol. 2003 Nov;74(5):635-41. (PMID: 12960232)
J Biol Chem. 2002 Aug 9;277(32):28491-7. (PMID: 12029089)
J Infect. 2001 Nov;43(4):239-45. (PMID: 11869061)
J Biol Chem. 2004 Dec 3;279(49):51545-53. (PMID: 15452123)
J Virol. 1993 May;67(5):2592-600. (PMID: 8386267)
J Virol. 2002 Nov;76(21):10942-50. (PMID: 12368337)
Nat Microbiol. 2018 Feb;3(2):220-233. (PMID: 29158605)
Biochemistry. 2002 Jun 25;41(25):8093-102. (PMID: 12069602)
Nature. 2003 Jul 3;424(6944):94-8. (PMID: 12808465)
J Biol Chem. 2010 Nov 26;285(48):37333-41. (PMID: 20870715)
J Virol. 1994 Jan;68(1):535-40. (PMID: 8254768)
J Virol. 2005 Sep;79(17):10978-87. (PMID: 16103149)
Viruses. 2016 Apr 22;8(4):118. (PMID: 27110814)
Cell Immunol. 2014 Sep-Oct;291(1-2):11-5. (PMID: 25015741)
Curr HIV Res. 2006 Jan;4(1):31-42. (PMID: 16454709)
J Virol. 2000 Aug;74(15):7039-47. (PMID: 10888643)
J Virol. 2009 Oct;83(19):10256-63. (PMID: 19625402)
J Virol. 2008 Mar;82(6):3125-30. (PMID: 18077705)
Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21105-10. (PMID: 22160723)
Biochemistry. 2018 Oct 2;57(39):5666-5671. (PMID: 30185020)
J Immunol. 1997 Apr 1;158(7):3499-510. (PMID: 9120312)
Virology. 2015 May;479-480:131-45. (PMID: 25818029)
Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):E448-57. (PMID: 23341616)
Virology. 1995 Jul 10;210(2):302-13. (PMID: 7542416)
Elife. 2016 Sep 20;5:. (PMID: 27644592)
J Virol. 1996 Feb;70(2):1213-7. (PMID: 8551582)
J Immunol. 1996 Feb 1;156(3):1284-95. (PMID: 8558009)
Virology. 2013 Feb 20;436(2):247-54. (PMID: 23260109)
Mol Biol Int. 2012;2012:625983. (PMID: 22811909)
J Virol. 2010 Oct;84(19):9864-78. (PMID: 20660205)
AIDS. 2001 Jan 5;15(1):17-22. (PMID: 11192864)

P30 AI094189 United States AI NIAID NIH HHS; R01 AI124777 United States AI NIAID NIH HHS; R01 GM056834 United States GM NIGMS NIH HHS

0 (DNA, Viral)
0 (Deoxyuracil Nucleotides)
56HH86ZVCT (Uracil)
964-26-1 (2'-deoxyuridylic acid)
EC 3.2.2.- (Uracil-DNA Glycosidase)

Date Created: 20200715 Date Completed: 20200915 Latest Revision: 20210507

20250114

PMC7360050

10.1371/journal.pone.0235012

32663205