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Structure and function of virion RNA polymerase of a crAss-like phage - Nature

  • ️Sokolova, Maria L.
  • ️Wed Nov 18 2020

Data availability

The following publicly available datasets were used in the study: GenBank reference genome sequences of phages phi14:2 (NC_021806.1), phicrAss001 (MH675552.1), IAS (KJ003983); phage genomes from the Data S1 dataset found in the supplementary information of ref. 13; and PDB atomic models of proteins with the accession numbers 2J7N, 2O5J, 4C2M and 1Y1W. The genome of C. baltica strain 14 has been deposited to the NCBI BioProject and is accessible through the BioProject ID PRJNA552277. The RNA-seq datasets have been deposited to the NCBI Gene Expression Omnibus and are accessible through the GEO Series GenBank accession number GSE133609. The refined atomic model of phi14:2 gp66 and the X-ray structure factors have been deposited to the PDB under the accession number 6VR4. The uncropped gels used for Figs. 1, 2 and Extended Data Figs. 1, 6 are shown in the Supplementary Information. Source data are provided with this paper.

Code availability

The custom code, information about the software used in this study, and annotations of genomes of crAss-like phages are available from GitHub at https://github.com/matveykolesnik/Drobysheva_et_al_2020.

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Acknowledgements

We thank S. Medvedeva for help with the promoter search. The study was carried out using resources of the Skoltech Genomics Core Facility. The work was supported by the Russian Science Foundation (grant 19-74-00011 to M.L.S.). This research used resources of 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. The use of the LS-CAT Sector 21 was supported by the Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor (grant 085P1000817).

Author information

Author notes

  1. These authors contributed equally: Arina V. Drobysheva, Sofia A. Panafidina

Authors and Affiliations

  1. Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia

    Arina V. Drobysheva, Sofia A. Panafidina, Matvei V. Kolesnik, Evgeny I. Klimuk & Maria L. Sokolova

  2. Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia

    Sofia A. Panafidina, Evgeny I. Klimuk & Konstantin V. Severinov

  3. Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA

    Leonid Minakhin & Konstantin V. Severinov

  4. Peter the Great St Petersburg Polytechnic University, St Petersburg, Russia

    Maria V. Yakunina

  5. Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ, USA

    Sergei Borukhov

  6. Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden

    Emelie Nilsson & Karin Holmfeldt

  7. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

    Natalya Yutin, Kira S. Makarova & Eugene V. Koonin

  8. Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA

    Petr G. Leiman

Authors

  1. Arina V. Drobysheva

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  2. Sofia A. Panafidina

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  3. Matvei V. Kolesnik

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  4. Evgeny I. Klimuk

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  5. Leonid Minakhin

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  6. Maria V. Yakunina

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  7. Sergei Borukhov

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  8. Emelie Nilsson

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  9. Karin Holmfeldt

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  10. Natalya Yutin

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  11. Kira S. Makarova

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  12. Eugene V. Koonin

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  13. Konstantin V. Severinov

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  14. Petr G. Leiman

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  15. Maria L. Sokolova

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Contributions

K.V.S., M.L.S. and E.V.K. conceived the study. K.H. and E.N. provided C. baltica cells, phi14:2 phage, and phi14:2 DNA. A.V.D. cultivated C. baltica and phi14:2, prepared RNA for RNA-seq and primer extension experiments and performed RT–qPCR. S.A.P. purified phi14:2 RNAP and its mutants, performed in vitro transcription assays, and some of the primer extension experiments. M.V.K. processed and analysed RNA-seq data. M.V.K., N.Y. and K.S.M. annotated crAss-like phage genomes. E.I.K. performed mutagenesis of phi14:2 RNAP. L.M. performed primer extension experiments. M.V.Y. purified C. baltica RNAP. M.L.S. performed a search for promoters, prepared crystals and supervised the project. P.G.L. solved the crystal structure, and built and refined the atomic model. M.L.S., P.G.L. and S.B. analysed the structure. S.B. examined the activation of the enzyme by single-stranded DNA oligonucleotides. M.L.S., P.G.L. and K.V.S. wrote the manuscript, which was read, edited and approved by all authors.

Corresponding authors

Correspondence to Konstantin V. Severinov, Petr G. Leiman or Maria L. Sokolova.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature thanks Ryland Young and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data figures and tables

Extended Data Fig. 1 Purification of the phi14:2 RNAP gp66 and analysis of its transcriptional activity on an RNA–DNA scaffold.

a, Wild-type gp66 and three aspartate-to-alanine point mutants in the catalytic DFDID motif are visualized on SDS-PAGE. The panel depicts one of two repeat experiments with similar outcomes. b, Unlike E. coli (Eco) and T7 phage RNAPs, gp66 does not extend an RNA primer of an RNA–DNA scaffold in the presence of rNTPs. The sequences of RNA–DNA scaffolds used are shown below the gels. The RNA was radioactively labelled at the 5′ end. The reaction products were resolved by electrophoresis in 16% (w/v) polyacrylamide gel containing 8 M urea and revealed by autoradiography. The assay was performed twice for each of two biological replicates. The uncropped SDS-PAGE gel and autoradiograms are shown in Supplementary Fig. 1.

Extended Data Fig. 2 General parameters of phi14:2 infection and temporal patterns of transcript accumulation of selected early, middle and late phi14:2 genes visualized by RT–qPCR and RNA-seq.

a, Growth curves of C. baltica infected with phi14:2 at different MOIs (mean ± s.d. of three biological replicates). For each condition, the OD600 was normalized to its value measured immediately after the phage was added to the culture (time point 0). b, Single-step multiplication of phi14:2 in C. baltica at an MOI of 0.001. The number of PFUs (mean ± s.d. of three biological replicates) is given for a standard infection protocol (no rifampicin, black line) and for infection in the presence of rifampicin (red line). The value of PFU was normalized to that measured at time point 0. c, Black and red lines and symbols correspond to the infection of C. baltica under a standard protocol and that in the presence of rifampicin, respectively. RT–qPCR reactions are quantified by a cycle threshold (Ct) parameter at which the RT–qPCR signal exceeds a preset value. The signal is converted to the original transcript abundance by plotting it as \({2}^{-{\rm{Ct}}}\). The transcript abundance is normalized to that of the C. baltica 16S ribosomal RNA (rRNA) as follows: \({2}^{-{{\rm{Ct}}}_{{\rm{gene}}}}/{2}^{-{{\rm{Ct}}}_{{\rm{16S}}{\rm{rRNA}}}}={2}^{-\Delta {\rm{Ct}}}\) where \(\Delta {\rm{Ct}}={{\rm{Ct}}}_{{\rm{gene}}}-{{\rm{Ct}}}_{{\rm{16S}}{\rm{rRNA}}}\). Each RT–qPCR reaction contained three technical replicates resulting in up to nine values of \(\Delta {{\rm{Ct}}}_{ij}={{\rm{Ct}}}_{{\rm{gene}}i}-{{\rm{Ct}}}_{{\rm{16S}}{\rm{rRNA}}j}\) \(i,j=1,\,2,\,3\). The line connects the mean values of the function \({2}^{-\Delta {{\rm{Ct}}}_{ij}}\) for each time point that are labelled with a larger symbol. The corresponding RNA-seq data are shown next to the RT–qPCR plots. The RT–qPCR and RNA-seq analyses were performed on different biological replicates.

Source data

Extended Data Fig. 3 SAD-derived electron density of the catalytic loop and cleft-blocking domain of phi14:2 RNAP gp66.

All panels show the initial experimental electron density map, which was calculated using SeMet SAD phases that were improved by solvent flattening and twofold non-crystallographic averaging, and the final refined model. a, b, Two orthogonal views of the catalytic site region. The Cα atoms of the catalytic loop are coloured yellow. The map is contoured at 2 s.d. above the mean. c, The structure of the cleft-blocking domain. The Cα atoms of the cleft-blocking domain are coloured cyan. The map is contoured at 1 s.d. above the mean. The orientation of the molecule and domain colour code are both similar to those shown in Extended Data Fig. 4.

Extended Data Fig. 4 Domain organization and functional elements of phi14:2 RNAP gp66.

phi14:2 gp66 (middle) can be divided into 12 domains, each containing its own separate hydrophobic core (except the cleft-blocking domain, owing to its small size). To improve clarity, the overall structure is shown with a substantial degree of depth cueing, resulting in some parts of the structure (e.g. domain VII) being almost invisible. All panels that show the structure are to scale. The colour code, domain boundaries and secondary structure are given in the lower panels. Known and putative functional elements are labelled. The functions of the channels that span the molecule were assigned as follows: gp66 was first superimposed onto the T. thermophilus RNAP elongation complex crystal structure (PDB ID: 2O5J15), and the RNA and DNA molecules were then extracted from the latter. Then, while keeping the RNA–DNA duplex part of the complex stationary, both the RNA and DNA tails were adjusted as rigid bodies to minimize clashes with gp66, and their geometries were regularized.

Extended Data Fig. 5 The cleft-blocking domain of the phi14:2 RNAP gp66 and the expander element of Pol I clash with nucleic acids in the RNAP elongation complex.

a, Superposition of the Pol I catalytic site (PDB ID: 4C2M22) onto that of the Pol II elongation complex structure (PDB ID: 1Y1W47). b, Superposition of the gp66 catalytic site onto that of the Pol II elongation complex structure (PDB ID: 1Y1W47). c, Two orthogonal views of the superposition of gp66 and Pol I catalytic sites (PDB ID: 4C2M22).

Extended Data Fig. 6 A model of the gp66 catalytic site in the active conformation.

a, DNA-dependent RNA synthesis activity of wild-type gp66 and its two catalytic loop mutants as measured on denatured phi14:2 DNA. The uncropped autoradiogram is shown in Supplementary Fig. 5. The assay was performed three times for each of two biological replicates. b, The crystal structure of the catalytic site of the T. thermophilus RNAP (the elongation state conformation, PDB ID: 2O5J15). Residues of the β subunit are labelled with a superscript index. c, Possible configuration of the catalytic site of the wild-type gp66 (tan coloured) and its I1364G and I1364W mutants (coloured cyan and magenta, respectively) in the active conformation. The models were obtained by rebuilding and regularizing the geometry of the polypeptide chain to make the side chains of the three catalytic aspartates (D1361, D1363 and D1365) point in the same direction. For each of the aspartates, a rotamer that brings the side chains closer in space was chosen. The magnesium ion was placed to match its dictionary distance value. In b, c, the bottom panels show the Ramachandran angles of the amino acids comprising the catalytic loop (the Ramachandran plots of gp66 and its two mutants are overlaid on top of each other); residues that interact with the catalytic loop are semi-transparent and represent the crystal structure conformation.

Extended Data Table 1 Data collection and refinement statistics

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Extended Data Table 2 Absolutely conserved amino acids of RNAPs of crAss-like phages and their analogues in other RNAPs based on structural alignments

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Supplementary information

Supplementary Information

This file contains a Supplementary Discussion, Supplementary Methods, Supplementary Figures 1-7, Supplementary Tables 1-6, and Supplementary References.

Reporting Summary

Video 1

: Structure of gp66 RNAP with putative locations of DNA and RNA molecules. The domain color code is the same as in the Extended data Fig. 4. The location of the RNA and DNA molecules and that of the RNA-DNA duplex are derived from the superposition of gp66 onto the crystal structure of the T. thermophilus RNAP elongation complex (PDB code 2O5J). To avoid clashes with gp66, the direction of RNA and DNA tails was adjusted, and then their geometries were minimized. Neither the structure nor location of the RNA-DNA duplex was changed in this procedure.

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Drobysheva, A.V., Panafidina, S.A., Kolesnik, M.V. et al. Structure and function of virion RNA polymerase of a crAss-like phage. Nature 589, 306–309 (2021). https://doi.org/10.1038/s41586-020-2921-5

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  • Received: 27 February 2020

  • Accepted: 08 September 2020

  • Published: 18 November 2020

  • Issue Date: 14 January 2021

  • DOI: https://doi.org/10.1038/s41586-020-2921-5