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The ribonuclease activity of SAMHD1 is required for HIV-1 restriction

Nature Medicine volume 20, pages 936–941 (2014)Cite this article

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Abstract

The HIV-1 restriction factor SAM domain– and HD domain–containing protein 1 (SAMHD1)1,2 is proposed to inhibit HIV-1 replication by depleting the intracellular dNTP pool3,4,5. However, phosphorylation of SAMHD1 regulates its ability to restrict HIV-1 without decreasing cellular dNTP levels6,7,8, which is not consistent with a role for SAMHD1 dNTPase activity in HIV-1 restriction. Here, we show that SAMHD1 possesses RNase activity and that the RNase but not the dNTPase function is essential for HIV-1 restriction. By enzymatically characterizing Aicardi-Goutières syndrome (AGS)-associated SAMHD1 mutations and mutations in the allosteric dGTP-binding site of SAMHD1 for defects in RNase or dNTPase activity, we identify SAMHD1 point mutants that cause loss of one or both functions. The RNase-positive and dNTPase-negative SAMHD1D137N mutant is able to restrict HIV-1 infection, whereas the RNase-negative and dNTPase-positive SAMHD1Q548A mutant is defective for HIV-1 restriction. SAMHD1 associates with HIV-1 RNA and degrades it during the early phases of cell infection. SAMHD1 silencing in macrophages and CD4+ T cells from healthy donors increases HIV-1 RNA stability, rendering the cells permissive for HIV-1 infection. Furthermore, phosphorylation of SAMHD1 at T592 negatively regulates its RNase activity in cells and impedes HIV-1 restriction. Our results reveal that the RNase activity of SAMHD1 is responsible for preventing HIV-1 infection by directly degrading the HIV-1 RNA.

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Figure 1: The RNase but not the dNTPase function of SAMHD1 is required for HIV-1 restriction.
Figure 2: SAMHD1 directly degrades HIV-1 RNA in human monocytic cells.
Figure 3: SAMHD1 degrades HIV-1 RNA in primary human MDMs and CD4+ T cells.
Figure 4: Phosphorylation of SAMHD1 regulates RNase activity.

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Acknowledgements

We are grateful to the members of our laboratory for discussion and technical help. We thank D. Littman (New York University School of Medicine) for HIV-1-GFP and HCMV-VSV-G, N. Manel (Institut Curie) for pLaiΔenvGFP3 and A. Cimarelli (University of Lyon) for pSIV3+ and pSIV3+ΔVpx. This work was supported by the US National Institutes of Health (R01 A1087390 and R21 AI102824 to F.D.-G. and GM104198 and AI049781 to B.K.), the Korean Institute for Basic Science (EM1402 to D.B.), the Korean Basic Science Research Program (2011-0014523 to D.B.), the Korean Creative Research Initiative Program (Research Center for Antigen Presentation, 2006-0050689 to K.A.) and BK21 plus fellowship to J.C., S.-Y.K. and M.S. from a National Research Foundation grant funded by the Ministry of Education, Science, and Technology of Korea.

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Authors and Affiliations

  1. Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul, Republic of Korea

    Jeongmin Ryoo, Jongsu Choi, Changhoon Oh, Sungchul Kim, Minji Seo, Seok-Young Kim & Kwangseog Ahn

  2. Department of the Interdisciplinary Program in Genetic Engineering, Seoul National University, Seoul, Republic of Korea

    Jeongmin Ryoo & Changhoon Oh

  3. Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea

    Jongsu Choi, Sungchul Kim, Minji Seo, Seok-Young Kim, Daekwan Seo, Jongkyu Kim, Daehyun Baek & Kwangseog Ahn

  4. Center for RNA Research, Institute for Basic Science, Seoul

    Jongkyu Kim & Daehyun Baek

  5. Republic of Korea,

    Jongkyu Kim & Daehyun Baek

  6. Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA

    Tommy E White, Alberto Brandariz-Nuñez & Felipe Diaz-Griffero

  7. Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea

    Cheol-Heui Yun

  8. Department of Pediatrics, Center for Drug Discovery, Emory School of Medicine, Atlanta, Georgia, USA

    Joseph A Hollenbaugh & Baek Kim

  9. School of Pharmacy, Kyung Hee University, Seoul, Republic of Korea

    Baek Kim

  10. Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea

    Daehyun Baek

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  1. Jeongmin Ryoo
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Contributions

J.R., C.O., S.K. and K.A. designed the study and wrote the manuscript. J.R., C.O., J.C., S.K., S.-Y.K., M.S. and J.A.H. performed the experiments and analyses. J.K., D.S., B.K., D.B. and C.-H.Y. analyzed the data. T.E.W., A.B.-N. and F.D.-G. provided materials. All authors discussed the data.

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Correspondence to Kwangseog Ahn.

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Ryoo, J., Choi, J., Oh, C. et al. The ribonuclease activity of SAMHD1 is required for HIV-1 restriction. Nat Med 20, 936–941 (2014). https://doi.org/10.1038/nm.3626

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