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Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus

Nature Structural & Molecular Biology volume 17, pages 830–836 (2010)Cite this article

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Abstract

Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single-particle cryo–electron microscopy yields icosahedral and asymmetrical structures of infectious P-SSP7 with 4.6-Å and 9-Å resolution, respectively. The asymmetric reconstruction reveals how symmetry mismatches are accommodated among five of the gene products at the portal vertex. Reconstructions of infectious and empty particles show a conformational change of the 'valve' density in the nozzle, an orientation difference in the tail fibers, a disordering of the C terminus of the portal protein and the disappearance of the core proteins. In addition, cryo–electron tomography of P-SSP7 infecting Prochlorococcus showed the same tail-fiber conformation as that in empty particles. Our observations suggest a mechanism whereby, upon binding to the host cell, the tail fibers induce a cascade of structural alterations of the portal vertex complex that triggers DNA release.

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Figure 1: Image and reconstruction of P-SSP7 at 4.6-Å resolution.
Figure 2: Asymmetric reconstructions of P-SSP7.
Figure 3: Symmetry mismatch at the portal vertex.
Figure 4: Cryo-ET of P-SSP7 infecting MED-4 cell.

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Acknowledgements

We thank M. Coleman, S. Rodrigue, R. Malmstrom, J. Waldbauer and S. Kern for assistance in the infection experiments, J. Chang, Q. Zeng, S. Labrie and F. Rixon for discussions and J. Chang, K. Welgehausen and R. Rochat for editorial assistance in preparation of the manuscript. This research was supported in parts by grants from the US National Institutes of Health (P41RR002250, R01GM079429 to W.C.), the US National Science Foundation (IIS-0705644 to W.C. and M.L.B.), the Robert Welch Foundation (Q1242 to W.C.), the US Department of Energy, the US National Science Foundation and the Gordon and Betty Moore Foundation (to S.W.C.).

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  1. Matthew B Sullivan

    Present address: Present address: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA.,

Authors and Affiliations

  1. Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, Texas, USA

    Xiangan Liu, Qinfen Zhang, Kazuyoshi Murata, Matthew L Baker, Caroline Fu, Matthew T Dougherty, Michael F Schmid & Wah Chiu

  2. State Key lab for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China

    Qinfen Zhang

  3. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Matthew B Sullivan, Marcia S Osburne & Sallie W Chisholm

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Contributions

M.B.S., M.S.O. and S.W.C. designed and conducted the phage-host experiments and provided the samples; Q.Z. took single-particle images; Q.Z., C.F. and K.M. took tomographic images; X.L. introduced the methodology for and performed the single-particle symmetric and asymmetric reconstructions; X.L. and W.C. interpreted the maps; M.F.S. analyzed the difference maps; K.M. did tomographic reconstructions and performed analysis with assistance from M.F.S.; M.L.B. and X.L. built Cα backbone models; M.T.D. and W.C. designed the animations; X.L. and W.C. wrote the paper with contributions from all coauthors.

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Correspondence to Wah Chiu.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Methods and Supplementary Figures 1–8 (PDF 3879 kb)

Supplementary Video 1

4.6 Å capsid density and backbone models derived from the map with icosahedral symmetry imposed. (a) density map and segmented 7 asymmetric subunits. (MOV 2232 kb)

Supplementary Video 2

Backbone model for 1 subunit. (MOV 1780 kb)

Supplementary Video 3

Backbone models for the whole capsid. (MOV 2945 kb)

Supplementary Video 4

9 Å density map of P-SSP7 phage with no symmetry imposed.Different components comprising the portal vertex machinery are annotated as nozzle, adaptor, portal, tail fiber, core protein and DNA terminus. (MOV 2336 kb)

Supplementary Video 5

Tomogram of P-SSP7 infecting a Prochlorococcus (MED4 strain) cell is shown along the z-direction. (MOV 2840 kb)

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Liu, X., Zhang, Q., Murata, K. et al. Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat Struct Mol Biol 17, 830–836 (2010). https://doi.org/10.1038/nsmb.1823

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