Dispersed sites of HIV Vif-dependent polyubiquitination in the DNA deaminase APOBEC3F

John S. Albin, John S. Anderson, Jeffrey R. Johnson, Elena Harjes, Hiroshi Matsuo, Nevan J. Krogan, Reuben S. Harris

Research output: Contribution to journalArticlepeer-review

19 Scopus citations

Abstract

APOBEC3F (A3F) and APOBEC3G (A3G) are DNA cytosine deaminases that potently restrict human immunodeficiency virus type 1 replication when the virus is deprived of its accessory protein Vif (virion infectivity factor). Vif counteracts these restriction factors by recruiting A3F and A3G to an E3 ubiquitin (Ub) ligase complex that mediates their polyubiquitination (polyUb) and proteasomal degradation. While previous efforts have identified single amino acid residues in APOBEC3 proteins required for Vif recognition, less is known about the downstream Ub acceptor sites that are targeted. One prior report identified a cluster of polyubiquitinated residues in A3G and proposed an antiparallel model of A3G interaction with the Vif-E3 Ub ligase complex wherein Vif binding at one terminus of A3G orients the opposite terminus for polyUb [Iwatani et al. (2009). Proc. Natl. Acad. Sci. USA, 106, 19539-19544]. To test the generalizability of this model, we carried out a complete mutagenesis of the lysine residues in A3F and used a complementary, unbiased proteomic approach to identify Ub acceptor sites targeted by Vif. Our data indicate that internal lysines are the dominant Ub acceptor sites in both A3F and A3G. In contrast with the proposed antiparallel model, however, we find that the Vif-dependent polyUb of A3F and A3G can occur at multiple acceptor sites dispersed along predicted lysine-enriched surfaces of both the N- and C-terminal deaminase domains. These data suggest an alternative model for binding of APOBEC3 proteins to the Vif-E3 Ub ligase complex and diminish enthusiasm for the amenability of APOBEC3 Ub acceptor sites to therapeutic intervention.

Original languageEnglish (US)
Pages (from-to)1172-1182
Number of pages11
JournalJournal of Molecular Biology
Volume425
Issue number7
DOIs
StatePublished - Apr 12 2013

Bibliographical note

Funding Information:
We thank A. K. Bielinsky, K. Walters, and the University of Minnesota Statistical Consulting Service for helpful discussion, and Y.-H. Zheng and the AIDS Research and Reference Reagent Program for materials. This research was funded by the National Institute of Allergy and Infectious Diseases ( R01 AI064046 to R.S.H. and P01 AI090935 to N.J.K.) and the National Institute of General Medical Sciences ( P01 GM091743 to R.S.H. and P50 GM082250 and P50 GM081879 to N.J.K.). J.S.A. was supported in part by the National Institute on Drug Abuse ( F30 DA026310 ) and by the University of Minnesota Medical Scientist Training Program ( T32 GM008244 ). N.J.K. is a Searle Fellow and Keck Young Investigator.

Keywords

  • APOBEC3F
  • APOBEC3G
  • HIV
  • Vif
  • ubiquitin

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