Attenuation of reverse transcriptase facilitates SAMHD1 restriction of HIV-1 in cycling cells

Tsai, Ming-Han C.; Caswell, Sarah J.; Morris, Elizabeth R.; Mann, Melanie C.; Pennell, Simon; Kelly, Geoff; Groom, Harriet C.T.; Taylor, Ian A.; Bishop, Kate N.

Abstract

SAMHD1 is a deoxynucleotide triphosphohydrolase that restricts replication of HIV-1 in differentiated leucocytes. HIV-1 is not restricted in cycling cells and it has been proposed that this is due to phosphorylation of SAMHD1 at T592 in these cells inactivating the enzymatic activity. To distinguish between theories for how SAMHD1 restricts HIV-1 in differentiated but not cycling cells, we analysed the effects of substitutions at T592 on restriction and dNTP levels in both cycling and differentiated cells as well as tetramer stability and enzymatic activity in vitro. Results We first showed that HIV-1 restriction was not due to SAMHD1 nuclease activity. We then characterised a panel of SAMHD1 T592 mutants and divided them into three classes. We found that a subset of mutants lost their ability to restrict HIV-1 in differentiated cells which generally corresponded with a decrease in triphosphohydrolase activity and/or tetramer stability in vitro. Interestingly, no T592 mutants were able to restrict WT HIV-1 in cycling cells, despite not being regulated by phosphorylation and retaining their ability to hydrolyse dNTPs. Lowering dNTP levels by addition of hydroxyurea did not give rise to restriction. Compellingly however, HIV-1 RT mutants with reduced affinity for dNTPs were significantly restricted by wild-type and T592 mutant SAMHD1 in both cycling U937 cells and Jurkat T-cells. Restriction correlated with reverse transcription levels. Conclusions Altogether, we found that the amino acid at residue 592 has a strong effect on tetramer formation and, although this is not a simple “on/off” switch, this does correlate with the ability of SAMHD1 to restrict HIV-1 replication in differentiated cells. However, preventing phosphorylation of SAMHD1 and/or lowering dNTP levels by adding hydroxyurea was not enough to restore restriction in cycling cells. Nonetheless, lowering the affinity of HIV-1 RT for dNTPs, showed that restriction is mediated by dNTP levels and we were able to observe for the first time that SAMHD1 is active and capable of inhibiting HIV-1 replication in cycling cells, if the affinity of RT for dNTPs is reduced. This suggests that the very high affinity of HIV-1 RT for dNTPs prevents HIV-1 restriction by SAMHD1 in cycling cells.

Citation

Tsai, M. C., Caswell, S. J., Morris, E. R., Mann, M. C., Pennell, S., Kelly, G., …Bishop, K. N. (2023). Attenuation of reverse transcriptase facilitates SAMHD1 restriction of HIV-1 in cycling cells. Retrovirology, 20(1), Article 5. https://doi.org/10.1186/s12977-023-00620-z

• Journal Article Type: Article
• Acceptance Date: Apr 6, 2023
• Online Publication Date: May 1, 2023
• Publication Date: 2023
• Deposit Date: Jun 26, 2023
• Publicly Available Date: Jun 26, 2023
• Journal: Retrovirology
• Publisher: BioMed Central
• Peer Reviewed: Peer Reviewed
• Volume: 20
• Issue: 1
• Article Number: 5
• DOI: https://doi.org/10.1186/s12977-023-00620-z