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. 2009 Nov 3;106(44):18786-91.
doi: 10.1073/pnas.0905859106. Epub 2009 Oct 20.

Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection

Boris Kantor  1 , Hong Ma, Jennifer Webster-Cyriaque, Paul E Monahan, Tal Kafri
Affiliations

Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection

Boris Kantor et al. Proc Natl Acad Sci U S A. .

Abstract

Integration of HIV-1 linear DNA into the host chromatin is an essential step in the viral life cycle. However, the majority of reverse-transcribed, nuclear-imported viral genomes remain episomal, either as linear or circular DNA. To date, these nonintegrated viral genomes are largely considered "dead-end products" of reverse transcription. Indeed, limited gene expression from nonintegrated HIV-1 has been reported, although the mechanism that renders nonintegrating HIV-1 genomes incapable of supporting efficient viral replication has not been fully elucidated. Here, we demonstrate that nonintegrating HIV-1 and HIV-1-based vector genomes are organized into chromatin structures and enriched with histone modifications typical of transcriptionally silenced chromatin. Gene expression and replication of nonintegrating HIV-1 was notably increased in vitro upon exposure to histone deacetylase inhibitors (HDACi) in the form of various short-chain fatty acids (SCFAs) known to be endogenously produced by normal microbial-gut flora. Furthermore, we demonstrated genetic and functional crosstalk between episomal and integrated vector/viral genomes, resulting in recombination between integrated and nonintegrated HIV-1, as well as mobilization of episomal vector genomes by productive viral particles encoded by integrated viral genomes. Finally, we propose a mechanism describing the role of episomal HIV-1 forms in the viral life cycle in a SCFA-rich gut environment.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Episomal HIV vector genomes are organized into chromatin structures associated with histone modifications typical of silenced chromatin. ChIP assays were carried out on HEF cells using integrating and nonintegrating vectors (m.o.i. of 2.5 was used), with or without SB treatment, at days 3 (A) and 14 (B) pt and employing antibodies to dimethylated H3-K4 (i), acetylated H3 and H4 (ii), and trimethylated H3-K9 (iii). The GAPDH and β-globin genes were used as references to active and silent chromatin, respectively. (C) Luciferase assay carried out on HEFs at days 3 and 14 pt (panels 1 and 2, respectively).
Fig. 2.
Fig. 2.
Enhanced SCFA-mediated expression following a single round of infection with nonintegrating HIV-1 in SupT1 cells. (A) (i) Luciferase assay carried out on SupT1 cells following infection with integrase-proficient (IN-WT) and integrase-deficient (IN-Mut) HIV-1 at m.o.i. of 0.2. (ii) p24gag ELISA of viral particles released from SupT1-infected cells. The results are presented as PP/mg total protein/copy number/cell. (B) ChIP assay carried out on infected SupT1 cells at day 3 pi employing antibodies directed to H3 (i), dimethylated H3-K4 (ii), acetylated H3 and H4 (iii), and trimethylated H3-K9 (iv) antibodies. LTR, GAPDH, and β-globin regions were analyzed. (C) Luciferase assay (i) and p24gag ELISA (ii) carried out on SupT1 infected with integrase-deficient HIV-1 in the presence of SCFAs-, P. gingivalis (PG4)-, F. nucleatum (FN)-, or S. mutans bacteria (S1)-derived spent media treatments.
Fig. 3.
Fig. 3.
Effects of SCFAs on integrase-deficient HIV-1 replication in MDMs. (A) MDMs infected by integrase-deficient HIV-1 (IN-Mut) at m.o.i. of 0.5, in the presence of 1 mM propionic (PROP), valproic (VPA), and heptanoic (HEPT) acids for 0 to 20 days, were subjected to p24gag ELISA. (B) p24gag ELISA carried out on MDMs infected by wild-type HIV-1, incubated with raltegravir (35 nM), and treated with or without SCFAs. The results are presented as ng p24/mL.
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