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Nε-fatty acylation of multiple membrane-associated proteins by Shigella IcsB effector to modulate host function

Nature Microbiology volume 3, pages 996–1009 (2018)Cite this article

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Abstract

Shigella flexneri, an intracellular Gram-negative bacterium causative for shigellosis, employs a type III secretion system to deliver virulence effectors into host cells. One such effector, IcsB, is critical for S. flexneri intracellular survival and pathogenesis, but its mechanism of action is unknown. Here, we discover that IcsB is an 18-carbon fatty acyltransferase catalysing lysine Nε-fatty acylation. IcsB disrupted the actin cytoskeleton in eukaryotes, resulting from Nε-fatty acylation of RhoGTPases on lysine residues in their polybasic region. Chemical proteomic profiling identified about 60 additional targets modified by IcsB during infection, which were validated by biochemical assays. Most IcsB targets are membrane-associated proteins bearing a lysine-rich polybasic region, including members of the Ras, Rho and Rab families of small GTPases. IcsB also modifies SNARE proteins and other non-GTPase substrates, suggesting an extensive interplay between S. flexneri and host membrane trafficking. IcsB is localized on the Shigella-containing vacuole to fatty-acylate its targets. Knockout of CHMP5—one of the IcsB targets and a component of the ESCRT-III complex—specifically affected S. flexneri escape from host autophagy. The unique Nε-fatty acyltransferase activity of IcsB and its altering of the fatty acylation landscape of host membrane proteomes represent an unprecedented mechanism in bacterial pathogenesis.

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Fig. 1: Ectopic expression of IcsB is toxic to yeast and disrupts the actin cytoskeleton in mammalian cells, which requires the putative catalytic motif.
Fig. 2: IcsB disrupts RhoGTPase membrane cycling by modifying its C-terminal tail.
Fig. 3: IcsB is an 18-carbon N-fatty acyltransferase that modifies lysine residues in the C-terminal PBR of RhoGTPases.
Fig. 4: Chemical proteomics reveals that IcsB targets multiple host membrane proteins for lysine Nε-fatty acylation.
Fig. 5: IcsB is localized on Shigella-containing vacuoles and modifies its substrates on the membrane location.
Fig. 6: Fatty acylation of CHMP5 by IcsB is important for Shigella escape from host autophagy.

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Acknowledgements

We thank R. Isberg for providing Yersinia strains, G. Praefcke for the pRSF-FTase plasmid, and the Proteomics Resource Center at The Rockefeller University for mass spectrometry analysis. We also thank members of the Shao laboratory for technical assistance and stimulating discussions. This work was supported by the Basic Science Center Project of the National Natural Science Foundation of China (81788101), National Key Research and Development Program of China (2017YFA0505900 and 2016YFA0501500) and Strategic Priority Research Program of the Chinese Academy of Sciences (XDB08020202) to F.S. H.C.H. acknowledges support from NIH-NIGMS grant R01 GM087544. The research was also supported in part by an International Early Career Scientist grant from the Howard Hughes Medical Institute and Beijing Scholar Program to F.S.

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Author notes

  1. Yan Zhou

    Present address: Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China

  2. These authors contributed equally: Wang Liu, Yan Zhou, Tao Peng.

Authors and Affiliations

  1. College of Life Science, Peking University, Beijing, China

    Wang Liu

  2. Peking University–Tsinghua University–National Institute of Biological Sciences Joint Graduate Program, National Institute of Biological Sciences, Beijing, China

    Wang Liu

  3. National Institute of Biological Sciences, Beijing, China

    Wang Liu, Yan Zhou, Ping Zhou, Xiaojun Ding, Zilin Li, Haoyu Zhong, Yue Xu, She Chen & Feng Shao

  4. College of Life Sciences, Beijing Normal University, Beijing, China

    Yan Zhou

  5. School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China

    Tao Peng

  6. Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY, USA

    Tao Peng & Howard C. Hang

  7. Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China

    Feng Shao

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Contributions

F.S. conceived the study. Y.Z. performed initial studies on the identification of RhoGTPases as the substrate of IcsB and its fatty acyltransferase activity. W.L. established the SunTag labelling of T3SS effectors, analysed the proteomic hits of IcsB, and performed the localization and autophagy studies. P.Z. and Z.L. provided technical assistance to Y.Z. and W.L. H.Z. and Y.X. performed the plaque assay. T.P. and H.C.H. were responsible for the chemical proteomic analyses. X.D. and S.C. carried out the mass spectrometry experiments. Y.Z., W.L., T.P., S.C., H.C.H. and F.S. analysed the data. W.L., Y.Z. and F.S. wrote the manuscript. All authors discussed the results and commented on the manuscript.

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Correspondence to Howard C. Hang or Feng Shao.

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Supplementary information

Supplementary Information

Supplementary Figures 1–7.

Reporting Summary

Supplementary Table 1

SILAC chemical proteomic analyses IcsB-modified proteins in IcsB-transfected cells.

Supplementary Table 2

SILAC chemical proteomic analyses IcsB-modified proteins in Shigella-infected cells.

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Liu, W., Zhou, Y., Peng, T. et al. Nε-fatty acylation of multiple membrane-associated proteins by Shigella IcsB effector to modulate host function. Nat Microbiol 3, 996–1009 (2018). https://doi.org/10.1038/s41564-018-0215-6

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