Letter | Published:

cGAS senses long and HMGB/TFAM-bound U-turn DNA by forming protein–DNA ladders

Nature volume 549, pages 394398 (21 September 2017) | Download Citation

Abstract

Cytosolic DNA arising from intracellular pathogens triggers a powerful innate immune response1,2. It is sensed by cyclic GMP–AMP synthase (cGAS), which elicits the production of type I interferons by generating the second messenger 2′3′-cyclic-GMP–AMP (cGAMP)3,4,5. Endogenous nuclear or mitochondrial DNA can also be sensed by cGAS under certain conditions, resulting in sterile inflammation. The cGAS dimer binds two DNA ligands shorter than 20 base pairs side-by-side6,7,8,9, but 20-base-pair DNA fails to activate cGAS in vivo and is a poor activator in vitro. Here we show that cGAS is activated in a strongly DNA length-dependent manner both in vitro and in human cells. We also show that cGAS dimers form ladder-like networks with DNA, leading to cooperative sensing of DNA length: assembly of the pioneering cGAS dimer between two DNA molecules is ineffective; but, once formed, it prearranges the flanking DNA to promote binding of subsequent cGAS dimers. Remarkably, bacterial and mitochondrial nucleoid proteins HU and mitochondrial transcription factor A (TFAM), as well as high-mobility group box 1 protein (HMGB1), can strongly stimulate long DNA sensing by cGAS. U-turns and bends in DNA induced by these proteins pre-structure DNA to nucleate cGAS dimers. Our results suggest a nucleation-cooperativity-based mechanism for sensitive detection of mitochondrial DNA10 and pathogen genomes11, and identify HMGB/TFAM proteins as DNA-structuring host factors. They provide an explanation for the peculiar cGAS dimer structure and suggest that cGAS preferentially binds incomplete nucleoid-like structures or bent DNA.

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References

  1. 1.

    & Type I interferon-mediated monogenic autoinflammation: the type I interferonopathies, a conceptual overview. J. Exp. Med. 213, 2527–2538 (2016)

  2. 2.

    STING: infection, inflammation and cancer. Nat. Rev. Immunol. 15, 760–770 (2015)

  3. 3.

    , , , & Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science 339, 786–791 (2013)

  4. 4.

    et al. Cyclic GMP-AMP containing mixed phosphodiester linkages is an endogenous high-affinity ligand for STING. Mol. Cell 51, 226–235 (2013)

  5. 5.

    , & Regulation and function of the cGAS–STING pathway of cytosolic DNA sensing. Nat. Immunol. 17, 1142–1149 (2016)

  6. 6.

    et al. Cyclic [G(2′,5′)pA(3′,5′)p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase. Cell 153, 1094–1107 (2013)

  7. 7.

    et al. Structural mechanism of cytosolic DNA sensing by cGAS. Nature 498, 332–337 (2013)

  8. 8.

    et al. Cyclic GMP-AMP synthase is activated by double-stranded DNA-induced oligomerization. Immunity 39, 1019–1031 (2013)

  9. 9.

    et al. The cytosolic DNA sensor cGAS forms an oligomeric complex with DNA and undergoes switch-like conformational changes in the activation loop. Cell Reports 6, 421–430 (2014)

  10. 10.

    et al. Mitochondrial DNA stress primes the antiviral innate immune response. Nature 520, 553–557 (2015)

  11. 11.

    et al. Listeria monocytogenes induces IFNβ expression through an IFI16-, cGAS- and STING-dependent pathway. EMBO J. 33, 1654–1666 (2014)

  12. 12.

    et al. Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses. Science 341, 903–906 (2013)

  13. 13.

    et al. Sensing of HSV-1 by the cGAS–STING pathway in microglia orchestrates antiviral defence in the CNS. Nat. Commun. 7, 13348 (2016)

  14. 14.

    et al. Cyclic GMP-AMP synthase is an innate immune DNA sensor for Mycobacterium tuberculosis. Cell Host Microbe 17, 820–828 (2015)

  15. 15.

    et al. Mycobacterium tuberculosis differentially activates cGAS- and inflammasome-dependent intracellular immune responses through ESX-1. Cell Host Microbe 17, 799–810 (2015)

  16. 16.

    et al. The cytosolic sensor cGAS detects Mycobacterium tuberculosis DNA to induce type I interferons and activate autophagy. Cell Host Microbe 17, 811–819 (2015)

  17. 17.

    et al. Sequence-specific activation of the DNA sensor cGAS by Y-form DNA structures as found in primary HIV-1 cDNA. Nat. Immunol. 16, 1025–1033 (2015)

  18. 18.

    et al. Virus-cell fusion as a trigger of innate immunity dependent on the adaptor STING. Nat. Immunol. 13, 737–743 (2012)

  19. 19.

    The Hill equation revisited: uses and misuses. FASEB J. 11, 835–841 (1997)

  20. 20.

    , & The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA. Nat. Struct. Mol. Biol. 18, 1290–1296 (2011)

  21. 21.

    et al. Human mitochondrial transcription factor A induces a U-turn structure in the light strand promoter. Nat. Struct. Mol. Biol. 18, 1281–1289 (2011)

  22. 22.

    et al. HMGB proteins function as universal sentinels for nucleic-acid-mediated innate immune responses. Nature 462, 99–103 (2009)

  23. 23.

    et al. Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding. EMBO J. 18, 2563–2579 (1999)

  24. 24.

    , , & Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation. Nat. Commun. 5, 3077 (2014)

  25. 25.

    et al. Apoptotic caspases prevent the induction of type I interferons by mitochondrial DNA. Cell 159, 1563–1577 (2014)

  26. 26.

    et al. Apoptotic caspases suppress mtDNA-induced STING-mediated type I IFN production. Cell 159, 1549–1562 (2014)

  27. 27.

    et al. Monocytic cells hyperacetylate chromatin protein HMGB1 to redirect it towards secretion. EMBO J. 22, 5551–5560 (2003)

  28. 28.

    et al. PQBP1 is a proximal sensor of the cGAS-dependent innate response to HIV-1. Cell 161, 1293–1305 (2015)

  29. 29.

    et al. IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP. Nat. Commun. 8, 14391 (2017)

  30. 30.

    & Filament assemblies in foreign nucleic acid sensors. Curr. Opin. Struct. Biol. 37, 134–144 (2016)

  31. 31.

    et al. Cell intrinsic immunity spreads to bystander cells via the intercellular transfer of cGAMP. Nature 503, 530–534 (2013)

  32. 32.

    et al. C/EBPα induces highly efficient macrophage transdifferentiation of B lymphoma and leukemia cell lines and impairs their tumorigenicity. Cell Reports 3, 1153–1163 (2013)

  33. 33.

    , & Synthesis of an arrayed sgRNA library targeting the human genome. Sci. Rep. 5, 14987 (2015)

  34. 34.

    et al. OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines. Genome Res. 24, 1719–1723 (2014)

  35. 35.

    et al. Human monocytes engage an alternative inflammasome pathway. Immunity 44, 833–846 (2016)

  36. 36.

    Acta Crystallogr. D 66, 125–132 (2010)

  37. 37.

    et al. STARANISO (Global Phasing, 2016)

  38. 38.

    Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  39. 39.

    Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr. D 57, 1373–1382 (2001)

  40. 40.

    & MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry. J. Comput. Aided Mol. Des. 9, 251–268 (1995)

  41. 41.

    et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355–367 (2011)

  42. 42.

    et al. Autocrine amplification of type I interferon gene expression mediated by interferon stimulated gene factor 3 (ISGF3). J. Biochem. 120, 160–169 (1996)

  43. 43.

    et al. ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA. eLife 4, e10859 (2015)

  44. 44.

    Schrödinger. The PyMOL molecular graphics system, version 1.8 (2010)

  45. 45.

    et al. Jalview version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009)

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Acknowledgements

We thank E. Kremmer for the generation of antibodies, A. Butryn for help with structure determination, K. Lammens and G. Witte for help with crystallization, S. Somarokov for help with protein co-localization studies, S. Bauernfried for help with cell studies, C. Isakaj and O. Fettscher for technical assistance, H. Harz and F. Schüder for advice on staining, F. Civril for cGAS constructs, T. Graf for BLaER1 cells, T. Cremer for fibroblasts, and T. Fujita for the p-125luc reporter plasmid. We thank the Swiss Light Source (Villigen), the European Synchrotron Radiation Facility (Grenoble), and the DESY Petra III (Hamburg) for technical assistance. This work was funded by German Research Foundation grant HO2489/8-1 to K.-P.H., and the Center for Integrated Protein Sciences to K.-P.H., H.L., and V.H. L.A. acknowledges the International Max Planck Research School for Molecular Life Sciences. C.L. and K.-P.H. acknowledge support from BioSysNet (Bavarian Ministry of Education). D.J.D. and C.C.O.M. acknowledge German Research Foundation RTG1721.

Author information

Author notes

    • Carina C. de Oliveira Mann

    Present address: Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115-5418, USA.

Affiliations

  1. Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany

    • Liudmila Andreeva
    • , Björn Hiller
    • , Dirk Kostrewa
    • , Charlotte Lässig
    • , Carina C. de Oliveira Mann
    • , David Jan Drexler
    • , Moritz Gaidt
    • , Veit Hornung
    •  & Karl-Peter Hopfner
  2. Gene Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany

    • Liudmila Andreeva
    • , Björn Hiller
    • , Dirk Kostrewa
    • , Charlotte Lässig
    • , Carina C. de Oliveira Mann
    • , David Jan Drexler
    • , Moritz Gaidt
    • , Veit Hornung
    •  & Karl-Peter Hopfner
  3. Department of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany

    • Andreas Maiser
    •  & Heinrich Leonhardt
  4. Center for Integrated Protein Science Munich, 81377 Munich, Germany

    • Heinrich Leonhardt
    • , Veit Hornung
    •  & Karl-Peter Hopfner

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Contributions

L.A. performed crystallographic and biochemical studies. B.H. performed enzyme-linked immunosorbent assay (ELISA) assays and IFN-β mRNA expression analysis. D.K. built and refined the structure. C.L. performed co-immunopurification studies. C.C.O.M. established staining protocols for three-dimensional structured illumination microscopy (3D SIM). D.J.D. performed luciferase reporter assays and analysed cGAS products. A.M. performed microscopy. M.G. generated cGAS-deficient BLaER1 cells. H.L., C.C.O.M., C.L., and L.A. designed and interpreted microscopy experiments. V.H., B.H., and C.L. designed and interpreted cell-based experiments. K.-P.H. designed the study, derived the mathematical model, and analysed data. K.-P.H. and L.A. wrote the paper with contributions from all other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Karl-Peter Hopfner.

Reviewer Information Nature thanks O. Nureki and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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  1. 1.

    Supplementary Information

    This file contains Supplementary Methods and Supplementary Tables 1-3. The Supplementary Methods contain a detailed explanation of the DPL model and the derivation of equations for its mathematical description. They also contain a description of the global fitting of the experimental data with DPL and generic Hill equations.

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https://doi.org/10.1038/nature23890

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