Skip to main content

Advertisement

SpringerLink
Log in

Single-stranded nucleic acids promote SAMHD1 complex formation

  • Original Article
  • Published:
Journal of Molecular Medicine Aims and scope Submit manuscript

Abstract

SAM domain and HD domain-containing protein 1 (SAMHD1) is a dGTP-dependent triphosphohydrolase that degrades deoxyribonucleoside triphosphates (dNTPs) thereby limiting the intracellular dNTP pool. Mutations in SAMHD1 cause Aicardi–Goutières syndrome (AGS), an inflammatory encephalopathy that mimics congenital viral infection and that phenotypically overlaps with the autoimmune disease systemic lupus erythematosus. Both disorders are characterized by activation of the antiviral cytokine interferon-α initiated by immune recognition of self nucleic acids. Here we provide first direct evidence that SAMHD1 associates with endogenous nucleic acids in situ. Using fluorescence cross-correlation spectroscopy, we demonstrate that SAMHD1 specifically interacts with ssRNA and ssDNA and establish that nucleic acid-binding and formation of SAMHD1 complexes are mutually dependent. Interaction with nucleic acids and complex formation do not require the SAM domain, but are dependent on the HD domain and the C-terminal region of SAMHD1. We finally demonstrate that mutations associated with AGS exhibit both impaired nucleic acid-binding and complex formation implicating that interaction with nucleic acids is an integral aspect of SAMHD1 function.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

Notes

  1. While this manuscript was in review, a paper by White et al. reported binding of SAMHD1 to phosphorothioate-modified DNA [38].

References

  1. Goldstone DC, Ennis-Adeniran V, Hedden JJ, Groom HC, Rice GI, Christodoulou E, Walker PA, Kelly G, Haire LF, Yap MW et al (2011) HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Nature 480:379–382

    Article  PubMed  CAS  Google Scholar 

  2. Lahouassa H, Daddacha W, Hofmann H, Ayinde D, Logue EC, Dragin L, Bloch N, Maudet C, Bertrand M, Gramberg T et al (2012) SAMHD1 restricts the replication of human immunodeficiency virus type 1 by depleting the intracellular pool of deoxynucleoside triphosphates. Nat Immunol 13:223–228

    Article  PubMed  CAS  Google Scholar 

  3. Hrecka K, Hao C, Gierszewska M, Swanson SK, Kesik-Brodacka M, Srivastava S, Florens L, Washburn MP, Skowronski J (2011) Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature 474:658–661

    Article  PubMed  CAS  Google Scholar 

  4. Laguette N, Sobhian B, Casartelli N, Ringeard M, Chable-Bessia C, Segeral E, Yatim A, Emiliani S, Schwartz O, Benkirane M (2011) SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx. Nature 474:654–657

    Article  PubMed  CAS  Google Scholar 

  5. Rice GI, Bond J, Asipu A, Brunette RL, Manfield IW, Carr IM, Fuller JC, Jackson RM, Lamb T, Briggs TA et al (2009) Mutations involved in Aicardi–Goutieres syndrome implicate SAMHD1 as regulator of the innate immune response. Nat Genet 41:829–832

    Article  PubMed  CAS  Google Scholar 

  6. Crow YJ, Hayward BE, Parmar R, Robins P, Leitch A, Ali M, Black DN, van Bokhoven H, Brunner HG, Hamel BC et al (2006) Mutations in the gene encoding the 3′–5′ DNA exonuclease TREX1 cause Aicardi–Goutieres syndrome at the AGS1 locus. Nat Genet 38:917–920

    Article  PubMed  CAS  Google Scholar 

  7. Crow YJ, Leitch A, Hayward BE, Garner A, Parmar R, Griffith E, Ali M, Semple C, Aicardi J, Babul-Hirji R et al (2006) Mutations in genes encoding ribonuclease H2 subunits cause Aicardi–Goutieres syndrome and mimic congenital viral brain infection. Nat Genet 38:910–916

    Article  PubMed  CAS  Google Scholar 

  8. Ramantani G, Kohlhase J, Hertzberg C, Innes AM, Engel K, Hunger S, Borozdin W, Mah JK, Ungerath K, Walkenhorst H et al (2010) Expanding the phenotypic spectrum of lupus erythematosus in Aicardi–Goutieres syndrome. Arthritis Rheum 62:1469–1477

    Article  PubMed  CAS  Google Scholar 

  9. Ramantani G, Hausler M, Niggemann P, Wessling B, Guttmann H, Mull M, Tenbrock K, Lee-Kirsch MA (2011) Aicardi–Goutieres syndrome and systemic lupus erythematosus (SLE) in a 12-year-old boy with SAMHD1 mutations. J Child Neurol 26:1425–1428

    Google Scholar 

  10. Ravenscroft JC, Suri M, Rice GI, Szynkiewicz M, Crow YJ (2011) Autosomal dominant inheritance of a heterozygous mutation in SAMHD1 causing familial chilblain lupus. Am J Med Genet A 155A:235–237

    PubMed  Google Scholar 

  11. Rice G, Newman WG, Dean J, Patrick T, Parmar R, Flintoff K, Robins P, Harvey S, Hollis T, O’hara A et al (2007) Heterozygous mutations in trex1 cause familial chilblain lupus and dominant Aicardi–Goutieres syndrome. Am J Hum Genet 80:811–815

    Article  PubMed  CAS  Google Scholar 

  12. Lee-Kirsch MA, Chowdhury D, Harvey S, Gong M, Senenko L, Engel K, Pfeiffer C, Hollis T, Gahr M, Perrino FW et al (2007) A mutation in TREX1 that impairs susceptibility to granzyme A-mediated cell death underlies familial chilblain lupus. J Mol Med 85:531–537

    Article  PubMed  CAS  Google Scholar 

  13. Lee-Kirsch MA, Gong M, Chowdhury D, Senenko L, Engel K, Lee YA, de Silva U, Bailey SL, Witte T, Vyse TJ et al (2007) Mutations in the gene encoding the 3′–5′ DNA exonuclease TREX1 are associated with systemic lupus erythematosus. Nat Genet 39:1065–1067

    Article  PubMed  CAS  Google Scholar 

  14. Lorenz M (2009) Visualizing protein–RNA interactions inside cells by fluorescence resonance energy transfer. RNA 15:97–103

    Article  PubMed  CAS  Google Scholar 

  15. Schwille P, Meyer-Almes FJ, Rigler R (1997) Dual-color fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution. Biophys J 72:1878–1886

    Article  PubMed  CAS  Google Scholar 

  16. Bacia K, Kim SA, Schwille P (2006) Fluorescence cross-correlation spectroscopy in living cells. Nat Methods 3:83–89

    Article  PubMed  CAS  Google Scholar 

  17. Foo YH, Naredi-Rainer N, Lamb DC, Ahmed S, Wohland T (2012) Factors affecting the quantification of biomolecular interactions by fluorescence cross-correlation spectroscopy. Biophys J 102:1174–1183

    Article  PubMed  CAS  Google Scholar 

  18. Padilla-Parra S, Auduge N, Lalucque H, Mevel JC, Coppey-Moisan M, Tramier M (2009) Quantitative comparison of different fluorescent protein couples for fast FRET-FLIM acquisition. Biophys J 97:2368–2376

    Article  PubMed  CAS  Google Scholar 

  19. Powell RD, Holland PJ, Hollis T, Perrino FW (2011) Aicardi–Goutieres syndrome gene and HIV-1 restriction factor SAMHD1 is a dGTP-regulated deoxynucleotide triphosphohydrolase. J Biol Chem 286:43596–43600

    Article  PubMed  CAS  Google Scholar 

  20. Lebon P, Badoual J, Ponsot G, Goutieres F, Hemeury-Cukier F, Aicardi J (1988) Intrathecal synthesis of interferon-alpha in infants with progressive familial encephalopathy. J Neurol Sci 84:201–208

    Article  PubMed  CAS  Google Scholar 

  21. Marshak-Rothstein A (2006) Toll-like receptors in systemic autoimmune disease. Nat Rev Immunol 6:823–835

    Article  PubMed  CAS  Google Scholar 

  22. Goncalves A, Karayel E, Rice GI, Bennett KL, Crow YJ, Superti-Furga G and Burckstummer T (2012) SAMHD1 is a nucleic-acid binding protein that is mislocalized due to Aicardi–Goutieres syndrome-associated mutations. Hum Mutat 33:1116–1122

    Google Scholar 

  23. Ahn J, Hao C, Yan J, Delucia M, Mehrens J, Wang C, Gronenborn AM, Skowronski J (2012) HIV/simian immunodeficiency virus (SIV) accessory virulence factor Vpx loads the host cell restriction factor SAMHD1 onto the E3 ubiquitin ligase complex CRL4DCAF1. J Biol Chem 287:12550–12558

    Article  PubMed  CAS  Google Scholar 

  24. Laguette N, Rahm N, Sobhian B, Chable-Bessia C, Munch J, Snoeck J, Sauter D, Switzer WM, Heneine W, Kirchhoff F et al (2012) Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. Cell Host Microbe 11:205–217

    Article  PubMed  CAS  Google Scholar 

  25. Lim ES, Fregoso OI, McCoy CO, Matsen FA, Malik HS, Emerman M (2012) The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx. Cell Host Microbe 11:194–204

    Article  PubMed  CAS  Google Scholar 

  26. Brandariz-Nunez A, Valle-Casuso JC, White TE, Laguette N, Benkirane M, Brojatsch J, Diaz-Griffero F (2012) Role of SAMHD1 nuclear localization in restriction of HIV-1 and SIVmac. Retrovirology 9:49

    Article  PubMed  CAS  Google Scholar 

  27. Wei W, Guo H, Han X, Liu X, Zhou X, Zhang W and Yu XF (2012) A novel DCAF1-binding motif required for Vpx-mediated degradation of nuclear SAMHD1 and Vpr-induced G2 arrest. Cell Microbiol 14:1745–1756

    Google Scholar 

  28. Zhang X, Mathews CK (1995) Natural DNA precursor pool asymmetry and base sequence context as determinants of replication fidelity. J Biol Chem 270:8401–8404

    Article  PubMed  CAS  Google Scholar 

  29. Martomo SA, Mathews CK (2002) Effects of biological DNA precursor pool asymmetry upon accuracy of DNA replication in vitro. Mutat Res 499:197–211

    Article  PubMed  CAS  Google Scholar 

  30. Bubeck D, Reijns MA, Graham SC, Astell KR, Jones EY, Jackson AP (2011) PCNA directs type 2 RNase H activity on DNA replication and repair substrates. Nucleic Acids Res 39:3652–3666

    Article  PubMed  CAS  Google Scholar 

  31. Nick McElhinny SA, Kumar D, Clark AB, Watt DL, Watts BE, Lundstrom EB, Johansson E, Chabes A, Kunkel TA (2010) Genome instability due to ribonucleotide incorporation into DNA. Nat Chem Biol 6:774–781

    Article  PubMed  CAS  Google Scholar 

  32. Leshinsky-Silver E, Malinger G, Ben-Sira L, Kidron D, Cohen S, Inbar S, Bezaleli T, Levine A, Vinkler C, Lev D et al (2011) A large homozygous deletion in the SAMHD1 gene causes atypical Aicardi–Goutieres syndrome associated with mtDNA deletions. Eur J Hum Genet 19:287–292

    Article  PubMed  Google Scholar 

  33. McLure KG, Lee PW (1998) How p53 binds DNA as a tetramer. EMBO J 17:3342–3350

    Article  PubMed  CAS  Google Scholar 

  34. Mott ML, Erzberger JP, Coons MM, Berger JM (2008) Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators. Cell 135:623–634

    Article  PubMed  CAS  Google Scholar 

  35. Collins BM, Cubeddu L, Naidoo N, Harrop SJ, Kornfeld GD, Dawes IW, Curmi PM, Mabbutt BC (2003) Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA. Crystal structure of an oligomeric complex of yeast SmF. J Biol Chem 278:17291–17298

    Article  PubMed  CAS  Google Scholar 

  36. Stetson DB, Ko JS, Heidmann T, Medzhitov R (2008) Trex1 prevents cell-intrinsic initiation of autoimmunity. Cell 134:587–598

    Article  PubMed  CAS  Google Scholar 

  37. Mathews CK (2006) DNA precursor metabolism and genomic stability. FASEB J 20:1300–1314

    Article  PubMed  CAS  Google Scholar 

  38. White TE, Brandariz-Nuñez A, Carlos Valle-Casuso J, Amie S, Nguyen L, Kim B, Brojatsch J, Diaz-Griffero F (2012) Contribution of SAM and HD domains to retroviral restriction mediated by human SAMHD1. Virology. doi:10.1016/j.virol.2012.10.029

Download references

Acknowledgments

We wish to thank Susan Hunger and Kerstin Engel for excellent technical assistance. We are grateful to Barbara Borgonovo (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden) for assistance with gel filtration chromatography and Zdenek Petrasek (Max Planck Institute of Biochemistry, Martinsried) for help with deriving the brightness correction formula. We thank Roger Y. Tsien (University of California, San Diego) for pRSET-mCherry. This work was supported by the Deutsche Forschungsgemeinschaft (KFO 249; LE 1074/4-1 to M.L.-K., KFO 249; SCHW 716/12-1 to P.S.) and a MeDDrive grant (60.283 to B.K.).

Conflicts of interest

The authors declare no conflicts of interest.

Author information

Authors and Affiliations

  1. Children’s Hospital, Technical University Dresden, 01307, Dresden, Germany

    Victoria Tüngler, Barbara Kind, Manuela Dobrick, Stefanie Kretschmer, Franziska Schmidt, Claudia Krug & Min Ae Lee-Kirsch

  2. Biotechnology Center, Technical University Dresden, 01307, Dresden, Germany

    Wolfgang Staroske & Petra Schwille

  3. Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany

    Mike Lorenz

  4. Center for Information Services and High Performance Computing, Technical University Dresden, 01062, Dresden, Germany

    Osvaldo Chara

  5. Institute of Physics of Liquids and Biological Systems (IFLYSIB), CONICET, National University of La Plata, B1900BTE, La Plata, Argentina

    Osvaldo Chara

  6. Max Planck Institute of Biochemistry, 82152, Martinsried, Germany

    Petra Schwille

Authors
  1. Victoria Tüngler
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wolfgang Staroske
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Barbara Kind
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Manuela Dobrick
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Stefanie Kretschmer
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Franziska Schmidt
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Claudia Krug
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Mike Lorenz
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Osvaldo Chara
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Petra Schwille
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Min Ae Lee-Kirsch
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Min Ae Lee-Kirsch.

Additional information

Victoria Tüngler and Wolfgang Staroske joint first authorship.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 623 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tüngler, V., Staroske, W., Kind, B. et al. Single-stranded nucleic acids promote SAMHD1 complex formation. J Mol Med 91, 759–770 (2013). https://doi.org/10.1007/s00109-013-0995-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00109-013-0995-3

Keywords

Search

Navigation