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A Chlamydia effector combining deubiquitination and acetylation activities induces Golgi fragmentation

Nature Microbiology volume 3, pages 1377–1384 (2018)Cite this article

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Abstract

Pathogenic bacteria are armed with potent effector proteins that subvert host signalling processes during infection1. The activities of bacterial effectors and their associated roles within the host cell are often poorly understood, particularly for Chlamydia trachomatis2, a World Health Organization designated neglected disease pathogen. We identify and explain remarkable dual Lys63-deubiquitinase (DUB) and Lys-acetyltransferase activities in the Chlamydia effector ChlaDUB1. Crystal structures capturing intermediate stages of each reaction reveal how the same catalytic centre of ChlaDUB1 can facilitate such distinct processes, and enable the generation of mutations that uncouple the two activities. Targeted Chlamydia mutant strains allow us to link the DUB activity of ChlaDUB1 and the related, dedicated DUB ChlaDUB2 to fragmentation of the host Golgi apparatus, a key process in Chlamydia infection for which effectors have remained elusive. Our work illustrates the incredible versatility of bacterial effector proteins, and provides important insights towards understanding Chlamydia pathogenesis.

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Fig. 1: Identification of specialized and dual-function CE-clan enzymes.
Fig. 2: Molecular dissection of dual deubiquitinase/acetyltransferase activities.
Fig. 3: ChlaDUB function is required for C. trachomatis Golgi fragmentation.
Fig. 4: ChlaDUB deubiquitinase activity is responsible for C. trachomatis Golgi fragmentation.

Data availability

The data that support the findings in this study are available from the corresponding author on request. Coordinates and structure factors for the ChlaDUB1~Ub, ChlaDUB1~CoA and C.a. ChlaDUB structures have been deposited with the protein data bank, accession codes 6GZS, 6GZT and 6GZU respectively.

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Acknowledgements

We thank members of our laboratories for reagents and advice, particularly Lee Dolat (Duke University) for his contribution to some preliminary Chlamydia infection work. Access to DLS was supported in part by the EU FP7 infrastructure grant BIOSTRUCT-X (contract no. 283570). Work in the D.K. lab was funded by the Medical Research Council (grant no. U105192732), the European Research Council (grant no. 724804), and the Lister Institute for Preventive Medicine. J.N.P. was supported on an EMBO Long-Term Fellowship. Work in the R.H.V. lab was funded by the National Institute of Health (grant no. R01AI100759 to R.H.V.) and the National Institute of Allergy and Infectious Diseases (grant no. STI CRC U19 AI084044 to R.J.B. and R.H.V.). E.B. was supported by North West Cancer Research. B.S. was supported by the Medical Research Council.

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Author notes

  1. These authors contributed equally: Robert J. Bastidas, Erithelgi Bertsoulaki.

Authors and Affiliations

  1. Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK

    Jonathan N. Pruneda, Kirby N. Swatek & David Komander

  2. Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA

    Robert J. Bastidas & Raphael H. Valdivia

  3. Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK

    Erithelgi Bertsoulaki, Michael J. Clague & Sylvie Urbé

  4. Division of Structural Studies, MRC Laboratory of Molecular Biology, Cambridge, UK

    Balaji Santhanam

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Contributions

Conceptualization was by J.N.P. and D.K. The investigation was carried out by J.N.P., R.J.B., E.B., K.N.S. and B.S. The methodology was done by R.J.B., R.H.V., M.J.C. and S.U. The writing was by J.N.P. and D.K. Funding acquisition was by D.K., R.H.V., R.J.B., S.U. and M.J.C.

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Correspondence to David Komander.

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Pruneda, J.N., Bastidas, R.J., Bertsoulaki, E. et al. A Chlamydia effector combining deubiquitination and acetylation activities induces Golgi fragmentation. Nat Microbiol 3, 1377–1384 (2018). https://doi.org/10.1038/s41564-018-0271-y

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