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CYRI/FAM49B negatively regulates RAC1-driven cytoskeletal remodelling and protects against bacterial infection

Nature Microbiology volume 4, pages 1516–1531 (2019)Cite this article

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Abstract

Salmonella presents a global public health concern. Central to Salmonella pathogenicity is an ability to subvert host defences through strategically targeting host proteins implicated in restricting infection. Therefore, to gain insight into the host–pathogen interactions governing Salmonella infection, we performed an in vivo genome-wide mutagenesis screen to uncover key host defence proteins. This revealed an uncharacterized role of CYRI (FAM49B) in conferring host resistance to Salmonella infection. We show that CYRI binds to the small GTPase RAC1 through a conserved domain present in CYFIP proteins, which are known RAC1 effectors that stimulate actin polymerization. However, unlike CYFIP proteins, CYRI negatively regulates RAC1 signalling, thereby attenuating processes such as macropinocytosis, phagocytosis and cell migration. This enables CYRI to counteract Salmonella at various stages of infection, including bacterial entry into non-phagocytic and phagocytic cells as well as phagocyte-mediated bacterial dissemination. Intriguingly, to dampen its effects, the bacterial effector SopE, a RAC1 activator, selectively targets CYRI following infection. Together, this outlines an intricate host–pathogen signalling interplay that is crucial for determining bacterial fate. Notably, our study also outlines a role for CYRI in restricting infection mediated by Mycobacterium tuberculosis and Listeria monocytogenes. This provides evidence implicating CYRI cellular functions in host defence beyond Salmonella infection.

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Fig. 1: The Ity15 pedigree displays increased susceptibility to S. Typhimurium infection.
Fig. 2: A mutation in Cyri confers susceptibility to S. Typhimurium infection in the Ity15 pedigree.
Fig. 3: CYRI binds to the small GTPase RAC1 in a GTP-dependent manner.
Fig. 4: CYRI regulates cell morphology and actin cytoskeletal dynamics in a RAC1-dependent manner.
Fig. 5: CYRI negatively regulates SopE-mediated cellular effects.
Fig. 6: CYRI expression in haematopoietic cells confers resistance to S. Typhimurium infection.
Fig. 7: The Salmonella bacterial effector SopE negatively regulates CYRI.

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Data availability

The data that support the findings of this study are available from the corresponding authors on reasonable request.

Code availability

All commercial and custom codes used to generate data presented in this study are available from the corresponding authors on reasonable request.

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Acknowledgements

We thank L. Larivière, E. Flamant, L. Rached-D’Astous, J. Kim, F. Pampaloni and M. Sader for technical assistance, N. Prud’homme and P. D’Arcy for mouse breeding and screening, S.-J. Pilon for histopathology scoring, and K. Koch and T. Maculins for reviewing the manuscript. We also acknowledge A. Malliri for reagents and G. White for the preparation of the PAK-CRIB peptide. This work was supported by the Canadian Institutes of Health Research (grant no. MOP133700 to D.M.), the DFG-funded Collaborative Research Centre on Selective Autophagy (grant no. SFB 1177), the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742720), the DFG-funded Cluster of Excellence ‘Macromolecular Complexes’ (grant no. EXC115), the DFG-funded SPP 1580 program ‘Intracellular Compartments as Places of Pathogen-Host-Interactions’, and by the LOEWE program Ubiquitin Networks (Ub-Net) and the LOEWE Centre for Gene and Cell Therapy Frankfurt, which are both funded by the State of Hessen, Germany (to I.D.). Funding was provided to M.M.E. by Le Fonds de Recherche Santé du Québec and to H.M. by the Alexander von Humboldt foundation as a Humboldt research fellowship for postdoctoral researchers.

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Author notes

  1. These authors contributed equally: Kyoko E. Yuki, Hadir Marei, Evgenij Fiskin, Megan M. Eva.

  2. These authors jointly supervised this work: Danielle Malo, Ivan Dikic.

Authors and Affiliations

  1. Department of Human Genetics, McGill University, Montreal, Quebec, Canada

    Kyoko E. Yuki, Megan M. Eva, Jeremy A. Schwartzentruber, Jacek Majewski, Silvia M. Vidal & Danielle Malo

  2. McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada

    Kyoko E. Yuki, Megan M. Eva, Angelica A. Gopal, Judith N. Mandl, Silvia M. Vidal & Danielle Malo

  3. Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany

    Hadir Marei, Evgenij Fiskin & Ivan Dikic

  4. Department of Physiology, McGill University, Montreal, Quebec, Canada

    Angelica A. Gopal & Judith N. Mandl

  5. Institut Armand-Frappier, Centre INRS, Laval, Quebec, Canada

    Mathieu Cellier

  6. Department of Medicine, McGill University, Montreal, Quebec, Canada

    Danielle Malo

  7. Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany

    Ivan Dikic

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Contributions

K.E.Y., H.M., E.F., M.M.E., S.M.V., M.C., D.M. and I.D. designed the conceptual framework of the study and experiments. K.E.Y. and M.M.E. contributed to ENU mutation identification and performed all in vivo and ex vivo experiments involving Cyri mutant and conditional alleles and analysed the data. H.M. designed, performed and analysed all biochemical and cell biology assays. E.F. designed, performed and analysed all mass spectrometry and in vitro Salmonella-infection experiments and performed some biochemical assays. J.A.S. and J.M. performed the analyses of exome sequences. A.A.G. and J.N.M. designed, performed and analysed the experiments with neutrophil mobility assays. D.M. and I.D. supervised the project. All authors wrote the manuscript.

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Correspondence to Danielle Malo or Ivan Dikic.

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Supplementary Figs. 1–13, Supplementary Tables 1–5, Supplementary Notes and Supplementary References.

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Supplementary File 1

Ubiquitylation sites quantified from three replicate SILAC-diGly proteomics experiments in HeLa Flp-In T-REx GFP–SopE cells, as described in Fig. 7.

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Statistics for main and supplementary figures.

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Yuki, K.E., Marei, H., Fiskin, E. et al. CYRI/FAM49B negatively regulates RAC1-driven cytoskeletal remodelling and protects against bacterial infection. Nat Microbiol 4, 1516–1531 (2019). https://doi.org/10.1038/s41564-019-0484-8

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