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Crystal structure of the Varkud satellite ribozyme

Nature Chemical Biology volume 11, pages 840–846 (2015)Cite this article

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Abstract

The Varkud satellite (VS) ribozyme mediates rolling-circle replication of a plasmid found in the Neurospora mitochondrion. We report crystal structures of this ribozyme from Neurospora intermedia at 3.1 Å resolution, which revealed an intertwined dimer formed by an exchange of substrate helices. In each protomer, an arrangement of three-way helical junctions organizes seven helices into a global fold that creates a docking site for the substrate helix of the other protomer, resulting in the formation of two active sites in trans. This mode of RNA−RNA association resembles the process of domain swapping in proteins and has implications for RNA regulation and evolution. Within each active site, adenine and guanine nucleobases abut the scissile phosphate, poised to serve direct roles in catalysis. Similarities to the active sites of the hairpin and hammerhead ribozymes highlight the functional importance of active-site features, underscore the ability of RNA to access functional architectures from distant regions of sequence space, and suggest convergent evolution.

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Figure 1: Global architecture of the crystallized dimeric VS ribozyme.
Figure 2: Trans form of the VS ribozyme including docked substrate.
Figure 3: Three-way junctions in the VS ribozyme monomer.
Figure 4: Local environment of the VS ribozyme active site.
Figure 5: Active site similarities in the VS, hairpin and hammerhead ribozymes.

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Acknowledgements

We thank J. Kieft for the gift of iridium hexamine; X. Yang, S. Montaño, K. Perry, B. Dhakshnamoorthy and K. Dolan for advice with crystallographic data processing; R. Hulse, I. Dementieva, A. Mateja, F. Qufei, D. Urusova and G. Dobosz for recommendations on growing crystals; and J. Olvera for expression and purification of T7 RNA polymerase. We thank staff of the Advanced Photon Source at Argonne National Laboratory for providing technical advice on X-ray data collection: K. Perry, C. Ogata, N. Venugopalan, B. Nocek and S. Banerjee; and the staff of SIBYLS beam line at Lawrence Berkeley National Laboratory for SAXS data collection. We thank S. Koide, T. Sosnick and S. Crosson for their feedback and discussion on the project, A. Kossiakoff and K. Moffat for use of their data-processing stations, F.-C. Chao and R. Das for their aid with ERRASER software, S. Shelke for help with figures, Y. Shao for help with Amigos II, and N. Tuttle, Q. Dai, N.-S. Li, K. Ceslinski, S. Fica, R. Sengupta, T. Wilson, T. Cech and A. Pyle for discussion and comments on the manuscript. This work was supported by grants from the US National Institutes of Health (R01AI081987 and R01GM102489) to J.A.P. This work is based on research conducted at the Advanced Photon Source on the Northeastern Collaborative Access Team beamline which are supported by a grant from the National Institute of General Medical Sciences (P41 GM103403) from the National Institutes of Health and Advanced Light Source beamline SIBYLS, all supported by US Department of Energy (DOE). This research used resources of the Advanced Photon Source, a US DOE Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract DE-AC02-06CH11357 and Advanced Light Source, a US DOE Office of Science User Facility operated for the DOE Office of Science by Lawrence Berkeley National Laboratory under Integrated Diffraction Analysis (IDAT) grant contract DE-AC02-05CH11231.

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  1. Nikolai B Suslov

    Present address: Present address: Antibody and Protein Engineering Group, Takeda California, San Diego, California, USA.,

  2. Nikolai B Suslov and Saurja DasGupta: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA

    Nikolai B Suslov, James R Fuller, Phoebe A Rice & Joseph A Piccirilli

  2. Department of Chemistry, The University of Chicago, Chicago, Illinois, USA

    Saurja DasGupta, Hao Huang & Joseph A Piccirilli

  3. Cancer Research UK Nucleic Acid Structure Research Group, University of Dundee, Dundee,, UK

    David M J Lilley

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Contributions

N.B.S., S.D. and J.A.P. designed the study; N.B.S., S.D. and H.H. set up high-throughput crystallization experiments; N.B.S. and S.D. screened crystals and optimized crystallization conditions; N.B.S., S.D. and P.A.R. collected the data; N.B.S. and S.D. phased and solved the structures; N.B.S. collected SAXS data,, J.R.F., S.D. and J.A.P. analyzed the SAXS data. N.B.S., S.D., D.M.J.L., P.A.R. and J.A.P. analyzed the overall data and wrote the manuscript.

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Correspondence to Joseph A Piccirilli.

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Suslov, N., DasGupta, S., Huang, H. et al. Crystal structure of the Varkud satellite ribozyme. Nat Chem Biol 11, 840–846 (2015). https://doi.org/10.1038/nchembio.1929

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