Phospho-dependent Regulation of SAMHD1 Oligomerisation Couples Catalysis and Restriction

English version České info

SAMHD1 is a restriction factor that blocks infection of certain immune cells by HIV-1. It was discovered to be an enzyme that catalyses the breakdown of dNTPs, suggesting that it inhibits HIV-1 replication by reducing cellular dNTP pools to such low levels that reverse transcriptase cannot function. However, recently, alternative mechanisms have been proposed. SAMHD1 is also regulated by phosphorylation, although the effects of phosphorylation on protein function are unclear. In order to address these issues, we carried out combined structural and virological studies and have demonstrated that in addition to allosteric activation and triphosphohydrolase activity, restriction correlates with the capacity of SAMHD1 to form “long-lived” enzymatically competent tetramers. Disrupting the tetramer in various ways always abolished restriction but had differing effects on enzyme activity in vitro. SAMHD1 phosphorylation also prevented restriction and tetramer formation but without affecting enzyme catalysis under steady-state dNTP conditions. However phosphorylated SAMHD1 was unable to catalyse dNTP turnover at very low nucleotide levels that more accurately represent conditions in the cells in which restriction takes place. Based on our findings we propose a model for phosphorylation-dependent regulation of SAMHD1 activity and substantiate that degradation of dNTPs by SAMHD1 is sufficient to restrict HIV-1.

Vyšlo v časopise: Phospho-dependent Regulation of SAMHD1 Oligomerisation Couples Catalysis and Restriction. PLoS Pathog 11(10): e32767. doi:10.1371/journal.ppat.1005194
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1005194

Souhrn

Zdroje

1. Sonza S, Maerz A, Deacon N, Meanger J, Mills J, Crowe S. Human immunodeficiency virus type 1 replication is blocked prior to reverse transcription and integration in freshly isolated peripheral blood monocytes. Journal of virology. 1996;70(6):3863–9. Epub 1996/06/01.8648722; PubMed Central PMCID: PMC190263.

2. Kaushik R, Zhu X, Stranska R, Wu Y, Stevenson M. A cellular restriction dictates the permissivity of nondividing monocytes/macrophages to lentivirus and gammaretrovirus infection. Cell host & microbe. 2009;6(1):68–80. Epub 2009/07/21. doi: S1931-3128(09)00221-2 [pii] doi: 10.1016/j.chom.2009.05.022 19616766; PubMed Central PMCID: PMC2777639.

3. Sharkey M. Restriction of retroviral infection of macrophages. Current topics in microbiology and immunology. 2013;371:105–22. Epub 2013/05/21. doi: 10.1007/978-3-642-37765-5_4 23686233.

4. Hrecka K, Hao C, Gierszewska M, Swanson SK, Kesik-Brodacka M, Srivastava S, et al. Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature. 2011;474(7353):658–61. Epub 2011/07/02. doi: 10.1038/nature10195 21720370; PubMed Central PMCID: PMC3179858.

5. Laguette N, Sobhian B, Casartelli N, Ringeard M, Chable-Bessia C, Segeral E, et al. SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx. Nature. 2011;474(7353):654–7. Epub 2011/05/27. doi: nature10117 [pii] doi: 10.1038/nature10117 21613998.

6. Baldauf HM, Pan X, Erikson E, Schmidt S, Daddacha W, Burggraf M, et al. SAMHD1 restricts HIV-1 infection in resting CD4(+) T cells. Nature medicine. 2012;18(11):1682–7. Epub 2012/09/14. doi: 10.1038/nm.2964 22972397.

7. Goldstone DC, Ennis-Adeniran V, Hedden JJ, Groom HC, Rice GI, Christodoulou E, et al. HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Nature. 2011;480(7377):379–82. Epub 2011/11/08. doi: 10.1038/nature10623 22056990.

8. Rice GI, Bond J, Asipu A, Brunette RL, Manfield IW, Carr IM, et al. Mutations involved in Aicardi-Goutieres syndrome implicate SAMHD1 as regulator of the innate immune response. Nat Genet. 2009;41(7):829–32. Epub 2009/06/16. doi: ng.373 [pii] doi: 10.1038/ng.373 19525956.

9. Brandariz-Nunez A, Valle-Casuso JC, White TE, Laguette N, Benkirane M, Brojatsch J, et al. Role of SAMHD1 nuclear localization in restriction of HIV-1 and SIVmac. Retrovirology. 2012;9:49. Epub 2012/06/14. doi: 10.1186/1742-4690-9-49 22691373; PubMed Central PMCID: PMC3410799.

10. Ahn J, Hao C, Yan J, DeLucia M, Mehrens J, Wang C, et al. HIV/simian immunodeficiency virus (SIV) accessory virulence factor Vpx loads the host cell restriction factor SAMHD1 onto the E3 ubiquitin ligase complex CRL4DCAF1. The Journal of biological chemistry. 2012;287(15):12550–8. Epub 2012/03/01. doi: 10.1074/jbc.M112.340711 22362772; PubMed Central PMCID: PMC3321004.

11. Schwefel D, Groom HC, Boucherit VC, Christodoulou E, Walker PA, Stoye JP, et al. Structural basis of lentiviral subversion of a cellular protein degradation pathway. Nature. 2014;505(7482):234–8. Epub 2013/12/18. doi: 10.1038/nature12815 24336198; PubMed Central PMCID: PMC3886899.

12. Kim CA, Bowie JU. SAM domains: uniform structure, diversity of function. Trends Biochem Sci. 2003;28(12):625–8. Epub 2003/12/09. doi: S0968000403002779 [pii].14659692.

13. Ji X, Wu Y, Yan J, Mehrens J, Yang H, DeLucia M, et al. Mechanism of allosteric activation of SAMHD1 by dGTP. Nature structural & molecular biology. 2013;20(11):1304–9. Epub 2013/10/22. doi: 10.1038/nsmb.2692 24141705; PubMed Central PMCID: PMC3833828.

14. Zhu C, Gao W, Zhao K, Qin X, Zhang Y, Peng X, et al. Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase. Nat Commun. 2013;4:2722. Epub 2013/11/13. doi: 10.1038/ncomms3722 24217394.

15. Lahouassa H, Daddacha W, Hofmann H, Ayinde D, Logue EC, Dragin L, et al. SAMHD1 restricts the replication of human immunodeficiency virus type 1 by depleting the intracellular pool of deoxynucleoside triphosphates. Nature immunology. 2012;13(3):223–8. Epub 2012/02/14. doi: 10.1038/ni.2236 22327569.

16. Kim B, Nguyen LA, Daddacha W, Hollenbaugh JA. Tight interplay among SAMHD1 protein level, cellular dNTP levels, and HIV-1 proviral DNA synthesis kinetics in human primary monocyte-derived macrophages. The Journal of biological chemistry. 2012;287(26):21570–4. Epub 2012/05/17. doi: 10.1074/jbc.C112.374843 22589553; PubMed Central PMCID: PMC3381122.

17. St Gelais C, de Silva S, Amie SM, Coleman CM, Hoy H, Hollenbaugh JA, et al. SAMHD1 restricts HIV-1 infection in dendritic cells (DCs) by dNTP depletion, but its expression in DCs and primary CD4+ T-lymphocytes cannot be upregulated by interferons. Retrovirology. 2012;9:105. Epub 2012/12/13. doi: 10.1186/1742-4690-9-105 23231760; PubMed Central PMCID: PMC3527137.

18. White TE, Brandariz-Nunez A, Valle-Casuso JC, Amie S, Nguyen L, Kim B, et al. Contribution of SAM and HD domains to retroviral restriction mediated by human SAMHD1. Virology. 2013;436(1):81–90. Epub 2012/11/20. doi: 10.1016/j.virol.2012.10.029 23158101.

19. Cribier A, Descours B, Valadao AL, Laguette N, Benkirane M. Phosphorylation of SAMHD1 by cyclin A2/CDK1 regulates its restriction activity toward HIV-1. Cell Rep. 2013;3(4):1036–43. Epub 2013/04/23. doi: 10.1016/j.celrep.2013.03.017 23602554.

20. Beloglazova N, Flick R, Tchigvintsev A, Brown G, Popovic A, Nocek B, et al. Nuclease activity of the human SAMHD1 protein implicated in the Aicardi-Goutieres syndrome and HIV-1 restriction. The Journal of biological chemistry. 2013;288(12):8101–10. Epub 2013/02/01. doi: 10.1074/jbc.M112.431148 23364794; PubMed Central PMCID: PMC3605629.

21. Yan J, Kaur S, DeLucia M, Hao C, Mehrens J, Wang C, et al. Tetramerization of SAMHD1 is required for biological activity and inhibition of HIV infection. The Journal of biological chemistry. 2013;288(15):10406–17. Epub 2013/02/22. doi: 10.1074/jbc.M112.443796 23426366; PubMed Central PMCID: PMC3624423.

22. Welbourn S, Dutta SM, Semmes OJ, Strebel K. Restriction of virus infection but not catalytic dNTPase activity is regulated by phosphorylation of SAMHD1. Journal of virology. 2013;87(21):11516–24. Epub 2013/08/24. doi: 10.1128/JVI.01642-13 23966382; PubMed Central PMCID: PMC3807338.

23. Ryoo J, Choi J, Oh C, Kim S, Seo M, Kim SY, et al. The ribonuclease activity of SAMHD1 is required for HIV-1 restriction. Nature medicine. 2014;20(8):936–41. Epub 2014/07/21. doi: 10.1038/nm.3626 25038827.

24. Goncalves A, Karayel E, Rice GI, Bennett KL, Crow YJ, Superti-Furga G, et al. SAMHD1 is a nucleic-acid binding protein that is mislocalized due to aicardi-goutieres syndrome-associated mutations. Human mutation. 2012;33(7):1116–22. Epub 2012/03/31. doi: 10.1002/humu.22087 22461318.

25. Tungler V, Staroske W, Kind B, Dobrick M, Kretschmer S, Schmidt F, et al. Single-stranded nucleic acids promote SAMHD1 complex formation. J Mol Med (Berl). 2013;91(6):759–70. Epub 2013/02/02. doi: 10.1007/s00109-013-0995-3 23371319.

26. White TE, Brandariz-Nunez A, Valle-Casuso JC, Amie S, Nguyen LA, Kim B, et al. The retroviral restriction ability of SAMHD1, but not its deoxynucleotide triphosphohydrolase activity, is regulated by phosphorylation. Cell host & microbe. 2013;13(4):441–51. Epub 2013/04/23. doi: 10.1016/j.chom.2013.03.005 23601106.

27. Van Cor-Hosmer SK, Daddacha W, Kelly Z, Tsurumi A, Kennedy EM, Kim B. The impact of molecular manipulation in residue 114 of human immunodeficiency virus type-1 reverse transcriptase on dNTP substrate binding and viral replication. Virology. 2012;422(2):393–401. Epub 2011/12/14. doi: 10.1016/j.virol.2011.11.004 22153297; PubMed Central PMCID: PMC3804253.

28. Xu HT, Oliveira M, Quashie PK, McCallum M, Han Y, Quan Y, et al. Subunit-selective mutational analysis and tissue culture evaluations of the interactions of the E138K and M184I mutations in HIV-1 reverse transcriptase. Journal of virology. 2012;86(16):8422–31. Epub 2012/05/25. doi: 10.1128/JVI.00271-12 22623801; PubMed Central PMCID: PMC3421741.

29. Weiss KK, Chen R, Skasko M, Reynolds HM, Lee K, Bambara RA, et al. A role for dNTP binding of human immunodeficiency virus type 1 reverse transcriptase in viral mutagenesis. Biochemistry. 2004;43(15):4490–500. Epub 2004/04/14. doi: 10.1021/bi035258r 15078095.

30. Ji X, Tang C, Zhao Q, Wang W, Xiong Y. Structural basis of cellular dNTP regulation by SAMHD1. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(41):E4305–14. Epub 2014/10/01. doi: 10.1073/pnas.1412289111 25267621; PubMed Central PMCID: PMC4205617.

31. Hansen EC, Seamon KJ, Cravens SL, Stivers JT. GTP activator and dNTP substrates of HIV-1 restriction factor SAMHD1 generate a long-lived activated state. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(18):E1843–51. Epub 2014/04/23. doi: 10.1073/pnas.1401706111 24753578; PubMed Central PMCID: PMC4020072.

32. Arnold LH, Kunzelmann S, Webb MR, Taylor IA. A continuous enzyme-coupled assay for triphosphohydrolase activity of HIV-1 restriction factor SAMHD1. Antimicrobial agents and chemotherapy. 2015;59(1):186–92. Epub 2014/10/22. doi: 10.1128/AAC.03903-14 25331707; PubMed Central PMCID: PMC4291348.

33. Diamond TL, Roshal M, Jamburuthugoda VK, Reynolds HM, Merriam AR, Lee KY, et al. Macrophage tropism of HIV-1 depends on efficient cellular dNTP utilization by reverse transcriptase. J Biol Chem. 2004;279(49):51545–53. Epub 2004/09/29. doi: 10.1074/jbc.M408573200 M408573200 [pii].15452123; PubMed Central PMCID: PMC1351161.

34. Franzolin E, Pontarin G, Rampazzo C, Miazzi C, Ferraro P, Palumbo E, et al. The deoxynucleotide triphosphohydrolase SAMHD1 is a major regulator of DNA precursor pools in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(35):14272–7. Epub 2013/07/17. doi: 10.1073/pnas.1312033110 23858451; PubMed Central PMCID: PMC3761606.

35. Gallois-Montbrun S, Kramer B, Swanson CM, Byers H, Lynham S, Ward M, et al. Antiviral protein APOBEC3G localizes to ribonucleoprotein complexes found in P bodies and stress granules. Journal of virology. 2007;81(5):2165–78. Epub 2006/12/15. doi: 10.1128/JVI.02287-06 17166910; PubMed Central PMCID: PMC1865933.

36. Naldini L, Blomer U, Gallay P, Ory D, Mulligan R, Gage FH, et al. In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. Science. 1996;272(5259):263–7. Epub 1996/04/12.8602510.

37. Wight DJ, Boucherit VC, Nader M, Allen DJ, Taylor IA, Bishop KN. The gammaretroviral p12 protein has multiple domains that function during the early stages of replication. Retrovirology. 2012;9(1):83. Epub 2012/10/06. doi: 10.1186/1742-4690-9-83 23035841; PubMed Central PMCID: PMC3492146.

38. Bainbridge JW, Stephens C, Parsley K, Demaison C, Halfyard A, Thrasher AJ, et al. In vivo gene transfer to the mouse eye using an HIV-based lentiviral vector; efficient long-term transduction of corneal endothelium and retinal pigment epithelium. Gene therapy. 2001;8(21):1665–8. Epub 2002/03/16. doi: 10.1038/sj.gt.3301574 11895005.

39. Bock M, Bishop KN, Towers G, Stoye JP. Use of a transient assay for studying the genetic determinants of Fv1 restriction. J Virol. 2000;74(16):7422–30.10906195.

40. del Val IJ, Kyriakopoulos S, Polizzi KM, Kontoravdi C. An optimized method for extraction and quantification of nucleotides and nucleotide sugars from mammalian cells. Analytical biochemistry. 2013;443(2):172–80. Epub 2013/09/17. doi: 10.1016/j.ab.2013.09.005 24036437.

41. Sherman PA, Fyfe JA. Enzymatic assay for deoxyribonucleoside triphosphates using synthetic oligonucleotides as template primers. Analytical biochemistry. 1989;180(2):222–6. Epub 1989/08/01.2554751.

42. Ferraro P, Franzolin E, Pontarin G, Reichard P, Bianchi V. Quantitation of cellular deoxynucleoside triphosphates. Nucleic acids research. 2010;38(6):e85. Epub 2009/12/17. doi: 10.1093/nar/gkp1141 20008099; PubMed Central PMCID: PMC2847218.

43. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997;276:307–26.

44. Kabsch W. Xds. Acta crystallographica Section D, Biological crystallography. 2010;66(Pt 2):125–32. Epub 2010/02/04. doi: 10.1107/S0907444909047337 20124692; PubMed Central PMCID: PMC2815665.

45. Kabsch W. Integration, scaling, space-group assignment and post-refinement. Acta crystallographica Section D, Biological crystallography. 2010;66(Pt 2):133–44. Epub 2010/02/04. doi: 10.1107/S0907444909047374 20124693; PubMed Central PMCID: PMC2815666.

46. Vagin A, Teplyakov A. Molecular replacement with MOLREP. Acta Crystallographica Section D. 2010;66(1):22–5. doi: 10.1107/S0907444909042589

47. Potterton E, Briggs P, Turkenburg M, Dodson E. A graphical user interface to the CCP4 program suite. Acta crystallographica Section D, Biological crystallography. 2003;59(Pt 7):1131–7. Epub 2003/07/02.12832755.

48. Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta crystallographica Section D, Biological crystallography. 2010;66(Pt 4):486–501. Epub 2010/04/13. doi: 10.1107/S0907444910007493 20383002; PubMed Central PMCID: PMC2852313.

49. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta crystallographica Section D, Biological crystallography. 2010;66(Pt 2):213–21. Epub 2010/02/04. doi: 10.1107/S0907444909052925 20124702; PubMed Central PMCID: PMC2815670.

50. Krissinel E, Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr. 2004;60(Pt 12 Pt 1):2256–68.15572779.

51. Kleywegt GJ, Jones TA. Detecting folding motifs and similarities in protein structures. Methods Enzymol. 1997;277:525–45.18488323.

52. Schrodinger, LLC. The PyMOL Molecular Graphics System, Version 1.3r1. 2010.

53. Brune M, Hunter JL, Howell SA, Martin SR, Hazlett TL, Corrie JE, et al. Mechanism of inorganic phosphate interaction with phosphate binding protein from Escherichia coli. Biochemistry. 1998;37(29):10370–80. Epub 1998/07/22. doi: 10.1021/bi9804277 9671505.

54. Brune M, Hunter JL, Corrie JE, Webb MR. Direct, real-time measurement of rapid inorganic phosphate release using a novel fluorescent probe and its application to actomyosin subfragment 1 ATPase. Biochemistry. 1994;33(27):8262–71. Epub 1994/07/12.8031761.

55. Brown NR, Noble ME, Endicott JA, Johnson LN. The structural basis for specificity of substrate and recruitment peptides for cyclin-dependent kinases. Nature cell biology. 1999;1(7):438–43. Epub 1999/11/24. doi: 10.1038/15674 10559988.

56. Kinoshita E, Kinoshita-Kikuta E, Takiyama K, Koike T. Phosphate-binding tag, a new tool to visualize phosphorylated proteins. Molecular & cellular proteomics: MCP. 2006;5(4):749–57. Epub 2005/12/13. doi: 10.1074/mcp.T500024-MCP200 16340016.