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Modulation of membrane phosphoinositide dynamics by the phosphatidylinositide 4-kinase activity of the Legionella LepB effector

Nature Microbiology volume 2, Article number: 16236 (2017) Cite this article

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Abstract

Legionella pneumophila, the causative bacterium for Legionnaires’ disease, hijacks host membrane trafficking for the maturation of the Legionella-containing vacuole (LCV). The LCV membrane mainly contains PtdIns4P, which is important for anchoring many secreted Legionella effectors onto the LCV. Here, we identify a cryptic functional domain (LepB_NTD) preceding the well-characterized RabGAP domain in the Legionella Dot/Icm type IV secretion system effector LepB. LepB_NTD alone is toxic to yeast and can disrupt the Golgi in mammalian cells. The crystal structure reveals an unexpected kinase fold and catalytic motif important for LepB_NTD function in eukaryotes. Cell biology-guided biochemical analyses uncovered a lipid kinase activity in LepB_NTD that specifically converts PtdIns3P into PtdIns(3,4)P2. PtdIns(3,4)P2 is efficiently hydrolysed into PtdIns4P by another Dot/Icm effector SidF that is known to possess phosphoinositide phosphatase activity. Consistently, SidF is capable of counteracting the cellular functions of LepB_NTD. Genetic analyses show a requirement for LepB kinase activity as well as lipid phosphatase activity of SidF for PtdIns4P biosynthesis on the LCV membrane. Our study identifies an unprecedented phosphatidylinositide 4-kinase activity from bacteria and highlights a sophisticated manipulation of host phosphoinositide metabolism by a bacterial pathogen.

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Figure 1: Identification of LepB_NTD, which can inhibit yeast growth and disrupt the Golgi structure in mammalian cells.
Figure 2: Crystal structure reveals that LepB_NTD is an active atypical kinase.
Figure 3: LepB_NTD functions as a phosphatidylinositide 4-kinase to convert PtdIns3P into PtdIns(3,4)P2.
Figure 4: LepB and SidF can function sequentially to synthesize PtdIns4P from PtdIns3P in vitro and in vivo.

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  • 14 July 2017

    In the PDF version of this article previously published, the year of publication provided in the footer of each page and in the 'How to cite' section was erroneously given as 2017, it should have been 2016. This error has now been corrected. The HTML version of the article was not affected.

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Acknowledgements

The authors thank B. Storrie, A.K. Chen, J. Lippincott-Schwartz, X. Chen and X. Wang for providing plasmids or reagents. The authors also thank Y. Ding, Y. Ren and members of the Shao laboratory for technical assistance and discussions. This work was supported by the National Key Research and Development Project on Protein Machinery and its Control and Regulation of Biological Processes (2016YFA0501500), the China National Science Foundation Program for Distinguished Young Scholars (31225002) and Program for International Collaborations (31461143006), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB08020202) and the National Basic Research Program of China 973 Program (2014CB849602) to F.S. The research was supported in part by an International Early Career Scientist grant from the Howard Hughes Medical Institute and the Beijing Scholar Program to F.S.

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Author notes

  1. Na Dong and Miao Niu: These authors contributed equally to this work.

Authors and Affiliations

  1. National Institute of Biological Sciences, Beijing, 102206, China

    Na Dong, Miao Niu, Liyan Hu, Qing Yao, Rui Zhou & Feng Shao

  2. Graduate Program in Chinese Academy of Medical Sciences and Beijing Union Medical College, Beijing, 100730, China

    Miao Niu

  3. National Institute of Biological Sciences, Collaborative Innovation Center for Cancer Medicine, Beijing, 102206, China

    Feng Shao

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Contributions

F.S. and N.D. conceived the study. N.D. and M.N. designed and performed the functional experiments. L.H. and Q.Y. determined the structure. R.Z. provided technical assistance. N.D. and F.S. analysed the data and wrote the manuscript. All authors discussed the results and commented on the manuscript.

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Correspondence to Na Dong or Feng Shao.

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Dong, N., Niu, M., Hu, L. et al. Modulation of membrane phosphoinositide dynamics by the phosphatidylinositide 4-kinase activity of the Legionella LepB effector. Nat Microbiol 2, 16236 (2017). https://doi.org/10.1038/nmicrobiol.2016.236

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