Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Structural basis of the arbitrium peptide–AimR communication system in the phage lysis–lysogeny decision

Nature Microbiology volume 3, pages 1266–1273 (2018)Cite this article

Subjects

Abstract

A bacteriophage can replicate and release virions from a host cell in the lytic cycle or switch to a lysogenic process in which the phage integrates itself into the host genome as a prophage. In Bacillus cells, some types of phages employ the arbitrium communication system, which contains an arbitrium hexapeptide, the cellular receptor AimR and the lysogenic negative regulator AimX. This system controls the decision between the lytic and lysogenic cycles. However, both the mechanism of molecular recognition between the arbitrium peptide and AimR and how downstream gene expression is regulated remain unknown. Here, we report crystal structures for AimR from the SPbeta phage in the apo form and the arbitrium peptide-bound form at 2.20 Å and 1.92 Å, respectively. With or without the peptide, AimR dimerizes through the C-terminal capping helix. AimR assembles a superhelical fold and accommodates the peptide encircled by its tetratricopeptide repeats, which is reminiscent of RRNPP family members from the quorum-sensing system. In the absence of the arbitrium peptide, AimR targets the upstream sequence of the aimX gene; its DNA binding activity is prevented following peptide binding. In summary, our findings provide a structural basis for peptide recognition in the phage lysis–lysogeny decision communication system.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Crystal structure of the apo form of AimR.
Fig. 2: Effect of the AimR α20 on dimerization.
Fig. 3: Crystal structure of the arbitrium peptide-bound AimR.
Fig. 4: Recognition of GMPRGA by AimR.
Fig. 5: Effect of the arbitrium peptide on the DNA binding activity of AimR.
Fig. 6: Effect of the arbitrium peptides on the infection dynamics of SPbeta and SPbeta ΔaimR.

Similar content being viewed by others

Data availability

Coordinates for the atomic structures have been deposited in the RCSB Protein Data Bank under PDB codes 5XYB and 5Y24. The data that support the findings of this study are available from the corresponding author on request.

References

  1. Oppenheim, A. B., Kobiler, O., Stavans, J., Court, D. L. & Adhya, S. Switches in bacteriophage λ development. Annu. Rev. Genet. 39, 409–429 (2005).

    Article  CAS  Google Scholar 

  2. Golding, I. Single-cell studies of phage λ: hidden treasures under Occam’s rug. Annu. Rev. Virol. 3, 453–472 (2016).

    Article  CAS  Google Scholar 

  3. Zeng, L. et al. Decision making at a subcellular level determines the outcome of bacteriophage infection. Cell 141, 682–691 (2010).

    Article  CAS  Google Scholar 

  4. Golding, I. Decision making in living cells: lessons from a simple system. Annu. Rev. Biophys. 40, 63–80 (2011).

    Article  CAS  Google Scholar 

  5. Echols, H. & Green, L. Establishment and maintenance of repression by bacteriophage λ: the role of the cI, cII, and c3 proteins. Proc. Natl Acad. Sci. USA 68, 2190–2194 (1971).

    Article  CAS  Google Scholar 

  6. Kobiler, O. et al. Quantitative kinetic analysis of the bacteriophage λ genetic network. Proc. Natl Acad. Sci. USA 102, 4470–4475 (2005).

    Article  CAS  Google Scholar 

  7. Hoyt, M. A., Knight, D. M., Das, A., Miller, H. I. & Echols, H. Control of phage lambda development by stability and synthesis of cII protein: role of the viral cIII and host hflA, himA and himD genes. Cell 31, 565–573 (1982).

    Article  CAS  Google Scholar 

  8. Erez, Z. et al. Communication between viruses guides lysis–lysogeny decisions. Nature 541, 488–493 (2017).

    Article  CAS  Google Scholar 

  9. Davidson, A. R. Virology: phages make a group decision. Nature 541, 466–467 (2017).

    Article  CAS  Google Scholar 

  10. Hynes, A. P. & Moineau, S. Phagebook: the social network. Mol. Cell 65, 963–964 (2017).

  11. Perez-Pascual, D., Monnet, V. & Gardan, R. Bacterial cell-cell communication in the host via RRNPP peptide-binding regulators. Front. Microbiol. 7, 706 (2016).

    Article  Google Scholar 

  12. Do, H. & Kumaraswami, M. Structural mechanisms of peptide recognition and allosteric modulation of gene regulation by the RRNPP family of quorum-sensing regulators. J. Mol. Biol. 428, 2793–2804 (2016).

    Article  CAS  Google Scholar 

  13. Rocha-Estrada, J., Aceves-Diez, A. E., Guarneros, G. & de la Torre, M. The RNPP family of quorum-sensing proteins in Gram-positive bacteria. Appl. Microbiol. Biotechnol. 87, 913–923 (2010).

    Article  CAS  Google Scholar 

  14. Neiditch, M. B., Capodagli, G. C., Prehna, G. & Federle, M. J. Genetic and structural analyses of RRNPP intercellular peptide signaling of Gram-positive bacteria. Annu. Rev. Genet. 51, 311–333 (2017).

    Article  CAS  Google Scholar 

  15. Gallego del Sol, F. & Marina, A. Structural basis of Rap phosphatase inhibition by Phr peptides. PLoS Biol. 11, e1001511 (2013).

    Article  Google Scholar 

  16. Parashar, V., Jeffrey, P. D. & Neiditch, M. B. Conformational change-induced repeat domain expansion regulates Rap phosphatase quorum-sensing signal receptors. PLoS Biol. 11, e1001512 (2013).

    Article  CAS  Google Scholar 

  17. Zouhir, S. et al. Peptide-binding dependent conformational changes regulate the transcriptional activity of the quorum-sensor NprR. Nucleic Acids Res. 41, 7920–7933 (2013).

    Article  CAS  Google Scholar 

  18. Grenha, R. et al. Structural basis for the activation mechanism of the PlcR virulence regulator by the quorum-sensing signal peptide PapR. Proc. Natl Acad. Sci. USA 110, 1047–1052 (2013).

    Article  CAS  Google Scholar 

  19. Parashar, V., Mirouze, N., Dubnau, D. A. & Neiditch, M. B. Structural basis of response regulator dephosphorylation by Rap phosphatases. PLoS Biol. 9, e1000589 (2011).

    Article  CAS  Google Scholar 

  20. Holm, L., Kaariainen, S., Rosenstrom, P. & Schenkel, A. Searching protein structure databases with DaliLite v.3. Bioinformatics 24, 2780–2781 (2008).

    Article  CAS  Google Scholar 

  21. Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).

    Article  CAS  Google Scholar 

  22. Waters, C. M. & Bassler, B. L. Quorum sensing: cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21, 319–346 (2005).

    Article  CAS  Google Scholar 

  23. Bassler, B. L. & Losick, R. Bacterially speaking. Cell 125, 237–246 (2006).

    Article  CAS  Google Scholar 

  24. Perego, M. Forty years in the making: understanding the molecular mechanism of peptide regulation in bacterial development. PLoS Biol. 11, e1001516 (2013).

    Article  CAS  Google Scholar 

  25. Monnet, V. & Gardan, R. Quorum-sensing regulators in Gram-positive bacteria: ‘cherchez le peptide’. Mol. Microbiol. 97, 181–184 (2015).

    Article  CAS  Google Scholar 

  26. Monnet, V., Juillard, V. & Gardan, R. Peptide conversations in Gram-positive bacteria. Crit. Rev. Microbiol. 42, 339–351 (2016).

    CAS  PubMed  Google Scholar 

  27. Core, L. & Perego, M. TPR-mediated interaction of RapC with ComA inhibits response regulator-DNA binding for competence development in Bacillus subtilis. Mol. Microbiol. 49, 1509–1522 (2003).

    Article  CAS  Google Scholar 

  28. Shi, K. et al. Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis. Proc. Natl Acad. Sci. USA 102, 18596–18601 (2005).

    Article  CAS  Google Scholar 

  29. Kozlowicz, B. K. et al. Molecular basis for control of conjugation by bacterial pheromone and inhibitor peptides. Mol. Microbiol. 62, 958–969 (2006).

    Article  CAS  Google Scholar 

  30. Declerck, N. et al. Structure of PlcR: Insights into virulence regulation and evolution of quorum sensing in Gram-positive bacteria. Proc. Natl Acad. Sci. USA 104, 18490–18495 (2007).

    Article  CAS  Google Scholar 

  31. Bouillaut, L. et al. Molecular basis for group-specific activation of the virulence regulator PlcR by PapR heptapeptides. Nucleic Acids Res. 36, 3791–3801 (2008).

    Article  CAS  Google Scholar 

  32. Baker, M. D. & Neiditch, M. B. Structural basis of response regulator inhibition by a bacterial anti-activator protein. PLoS Biol. 9, e1001226 (2011).

    Article  CAS  Google Scholar 

  33. Parashar, V., Aggarwal, C., Federle, M. J. & Neiditch, M. B. Rgg protein structure-function and inhibition by cyclic peptide compounds. Proc. Natl Acad. Sci. USA 112, 5177–5182 (2015).

    Article  CAS  Google Scholar 

  34. Makthal, N. et al. Structural and functional analysis of RopB: a major virulence regulator in Streptococcus pyogenes. Mol. Microbiol. 99, 1119–1133 (2016).

    Article  CAS  Google Scholar 

  35. Talagas, A. et al. Structural insights into streptococcal competence regulation by the cell-to-cell communication system ComRS. PLoS Pathog. 12, e1005980 (2016).

    Article  Google Scholar 

  36. Deng, Y. et al. ApnI, a transmembrane protein responsible for subtilomycin immunity, unveils a novel model for lantibiotic immunity. Appl. Environ. Microbiol. 80, 6303–6315 (2014).

    Article  Google Scholar 

  37. Zahler, S. A., Korman, R. Z., Rosenthal, R. & Hemphill, H. E. Bacillus subtilis bacteriophage SPbeta: localization of the prophage attachment site, and specialized transduction. J. Bacteriol. 129, 556–558 (1977).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Wang, Q. S. et al. The macromolecular crystallography beamline of SSRF. Nucl. Sci. Tech. 26, 12–17 (2015).

    Google Scholar 

  39. Wang, Q.-S. et al. Upgrade of macromolecular crystallography beamline BL17U1 at SSRF. Nucl. Sci. Tech. 29, 68 (2018).

    Article  Google Scholar 

  40. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  41. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235–242 (2011).

    Article  CAS  Google Scholar 

  42. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    Article  CAS  Google Scholar 

  43. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).

    Article  CAS  Google Scholar 

  44. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).

    Article  Google Scholar 

  45. Wach, A. PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12, 259–265 (1996).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank the staff of the BL17U1/BL19U1/BL19U2 beamline of the NCPSS at the Shanghai Synchrotron Radiation Facility for assistance during data collection and research associates at the Center for Protein Research, Huazhong Agricultural University, for technical support. We thank Z. Dong and Y. Deng for helpful discussions and gene disruption in prophages. We also thank Q. Tang for help with the DNA I footprinting assay. This work was supported by funds from the National Key R&D Program of China (2018YFA0507700), the National Natural Science Foundation of China (grant no. 81601742 for T.Z.) and the Fundamental Research Funds for the Central Universities (Program No. 2662014BQ028 for T.Z. and 2662017PY031 for P.Y.).

Author information

Author notes

  1. These authors contributed equally: Qiang Wang, Zeyuan Guan.

Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China

    Qiang Wang, Zeyuan Guan, Kai Pei, Jing Wang, Zhu Liu & Ping Yin

  2. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China

    Donghai Peng

  3. College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China

    Tingting Zou

Authors
  1. Qiang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zeyuan Guan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kai Pei
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jing Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zhu Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ping Yin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Donghai Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Tingting Zou
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Q.W., Z.G., P.Y., Z.L., D.P. and T.Z. designed the project and analysed data. Q.W. and Z.G. contributed to protein production and crystallization. Q.W. and K.P. performed EMSA, AUC, SLS, ITC, size-exclusion chromatography, and crosslinking and DNase I footprinting assays. Q.W., J.W. and T.Z performed gene disruption and in vivo experiments. Z.L. performed SAXS measurements. Q.W., Z.G. and T.Z. wrote the paper. All authors contributed to editing of the manuscript.

Corresponding author

Correspondence to Tingting Zou.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

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

Supplementary information

Supplementary Information

Supplementary Figures 1–15, Supplementary Tables 1–4.

Reporting Summary

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, Q., Guan, Z., Pei, K. et al. Structural basis of the arbitrium peptide–AimR communication system in the phage lysis–lysogeny decision. Nat Microbiol 3, 1266–1273 (2018). https://doi.org/10.1038/s41564-018-0239-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41564-018-0239-y

This article is cited by

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology