Abstract
Animal and bacterial cells use nucleotidyltransferase (NTase) enzymes to respond to viral infection and control major forms of immune signalling including cGAS-STING innate immunity and CBASS anti-phage defence1, 2, 3–4. Here we discover a family of bacterial defence systems, which we name Hailong, that use NTase enzymes to constitutively synthesize DNA signals and guard against phage infection. Hailong protein B (HalB) is an NTase that converts deoxy-ATP into single-stranded DNA oligomers. A series of X-ray crystal structures define a stepwise mechanism of HalB DNA synthesis initiated by a C-terminal tyrosine residue that enables de novo enzymatic priming. We show that HalB DNA signals bind to and repress activation of a partnering Hailong protein A (HalA) effector complex. A 2.0-Å cryo-electron microscopy structure of the HalA–DNA complex reveals a membrane protein with a conserved ion channel domain and a unique crown domain that binds the DNA signal and gates activation. Analysing Hailong defence in vivo, we demonstrate that viral DNA exonucleases required for phage replication trigger release of the primed HalA complex and induce protective host cell growth arrest. Our results explain how inhibitory nucleotide immune signals can serve as molecular guards against phage infection and expand the mechanisms NTase enzymes use to control antiviral immunity.
| Original language | English |
|---|---|
| Journal | Nature |
| DOIs | |
| Publication status | Published Online - 30 Apr 2025 |
Funding
We thank members of the Kranzusch and Sorek laboratories for helpful comments and discussion. We thank D. Wassarman and S. Yamaguchi from the Kranzusch laboratory for assistance with LC–MS analysis, and M. Gilman from the Kruse laboratory for assistance with cryo-EM data collection and processing. Mass spectrometry was performed at the Harvard Taplin Mass Spectrometry Facility with assistance from R. Tomaino. The work was funded by grants to P.J.K. from the Pew Biomedical Scholars programme, the Burroughs Wellcome Fund PATH programme, the G. Harold and Leila Y. Mathers Charitable Foundation, the Mark Foundation for Cancer Research, the Cancer Research Institute, the Parker Institute for Cancer Immunotherapy and the National Institutes of Health (grant no. 1DP2GM146250-01); grants to R.S. from the European Research Council (grant no. ERC-AdG GA 101018520), the Israel Science Foundation (MAPATS grant no. 2720/22), the Ernest and Bonnie Beutler Research Program of Excellence in Genomic Medicine, the Deutsche Forschungsgemeinschaft (SPP 2330, grant no. 464312965), a research grant from the Estate of Marjorie Plesset and the Knell Family Center for Microbiology; a grant to A.C.K. from the National Institutes of Health (grant no. U19AI158028); grants to M.J. from the National Institutes of Health (grant no. 1DP2GM154152) and the G. Harold and Leila Y. Mathers Charitable Foundation; and a grant to J.d.M. from National Institutes of Health (grant no. 5R00DC019401) and the Howard Hughes Medical Institute. J.M.J.T. is supported by a Servier PhD Fellowship. S.J.H. is supported through a Cancer Research Institute Irvington Postdoctoral Fellowship (grant no. CRI3996), and J.C.C. is supported by a Helen Hay Whitney postdoctoral fellowship. X-ray data were collected through support from an agreement between the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357, and the Diamond Light Source, the UK’s national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire. X-ray data were additionally collected at the Center for Bio-Molecular Structure (CBMS) which is primarily supported by the NIH-NIGMS through a Center Core P30 Grant (no. P30GM133893), and by the DOE Office of Biological and Environmental Research (grant no. KP1607011). NSLS2 is a US DOE Office of Science User Facility operated under Contract No. DE-SC0012704. This publication resulted from the data collected using the beamtime obtained through NECAT BAG proposal no. 311950. Cryo-EM data were collected at the Harvard Cryo-EM Center for Structural Biology at Harvard Medical School. Imaging experiments were supported by the Microscopy Resources on the North Quad (MicRoN) core at Harvard Medical School.
All Science Journal Classification (ASJC) codes
- General