Letter

An extracellular network of Arabidopsis leucine-rich repeat receptor kinases

  • Nature volume 553, pages 342346 (18 January 2018)
  • doi:10.1038/nature25184
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Abstract

The cells of multicellular organisms receive extracellular signals using surface receptors. The extracellular domains (ECDs) of cell surface receptors function as interaction platforms, and as regulatory modules of receptor activation1,2. Understanding how interactions between ECDs produce signal-competent receptor complexes is challenging because of their low biochemical tractability3,4. In plants, the discovery of ECD interactions is complicated by the massive expansion of receptor families, which creates tremendous potential for changeover in receptor interactions5. The largest of these families in Arabidopsis thaliana consists of 225 evolutionarily related leucine-rich repeat receptor kinases (LRR-RKs)5, which function in the sensing of microorganisms, cell expansion, stomata development and stem-cell maintenance6,7,8,9. Although the principles that govern LRR-RK signalling activation are emerging1,10, the systems-level organization of this family of proteins is unknown. Here, to address this, we investigated 40,000 potential ECD interactions using a sensitized high-throughput interaction assay3, and produced an LRR-based cell surface interaction network (CSILRR) that consists of 567 interactions. To demonstrate the power of CSILRR for detecting biologically relevant interactions, we predicted and validated the functions of uncharacterized LRR-RKs in plant growth and immunity. In addition, we show that CSILRR operates as a unified regulatory network in which the LRR-RKs most crucial for its overall structure are required to prevent the aberrant signalling of receptors that are several network-steps away. Thus, plants have evolved LRR-RK networks to process extracellular signals into carefully balanced responses.

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Acknowledgements

We thank A. Pasha for uploading the CSILRR interaction dataset to the Bio-Analytic Resource for Plant Biology, Y. Dagdas for comments on the manuscript, C. K. Garcia for the pECIA2/14 vectors, E. Özkan for his protocols, Y. Saijo, K. Tori and M. Butenko for the pepr1/2, erl2 and hsl2 mutant lines, respectively, and A. Bindeus for help with programming software. This work was supported by grants from the Austrian Academy of Sciences through the Gregor Mendel Institute (Y.B. and W.B.); the Natural Sciences and Engineering Research Council of Canada Discovery Grants to D.S.G. and D.D.; a Canada Research Chair in Plant-Microbe Systems Biology (D.D.) or Comparative Genomics (D.S.G.); and the Centre for the Analysis of Genome Evolution and Function (D.D. and D.S.G.). This research was also funded by the Gatsby Charitable Foundation (C.Z.) and the European Research Council (grant ‘PHOSPHinnATE’) (C.Z.). E.S.-L. is supported by a Hertha Firnberg Programme post-doctoral fellowship (T-947) from the FWF Austrian Science Fund. M.S. is supported by a post-doctoral fellowship (STE 2448/1) from the Deutsche Forschungsgemeinschaft (DFG). This work was supported by the National Science Foundation (IOS-1557796) to M.S.M. P.S.-B. acknowledges funding from the Austrian Federal Ministry of Science, Research & Economy, and the City of Vienna through the Vienna Biocenter Core Facilities (VBCF). We would like to thank P. Serrano Drozdowskyj, A. Aszodi and A. Gyenesei from the VBCF Biocomputing facility for developing the Platero software. We also thank the VBCF Plant Sciences facilities for the plant growth chambers.

Author information

Author notes

    • Elwira Smakowska-Luzan
    • , G. Adam Mott
    •  & Katarzyna Parys

    These authors contributed equally to this work.

Affiliations

  1. Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria

    • Elwira Smakowska-Luzan
    • , Katarzyna Parys
    • , Jixiang Kong
    • , Karin Grünwald
    • , Natascha Weinberger
    • , Santosh B. Satbhai
    • , Dominik Mayer
    • , Wolfgang Busch
    • , Mathias Madalinski
    •  & Youssef Belkhadir
  2. Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, Ontario, Canada

    • G. Adam Mott
    • , Mehdi Layeghifard
    • , Nicholas J. Provart
    • , Darrell Desveaux
    •  & David S. Guttman
  3. The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK

    • Martin Stegmann
    •  & Cyril Zipfel
  4. Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA

    • Timothy C Howton
    •  & M. Shahid Mukhtar
  5. Protein Technologies Facility, Vienna Biocenter Core Facilities (VBCF), Vienna, Austria

    • Jana Neuhold
    • , Anita Lehner
    •  & Peggy Stolt-Bergner
  6. Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, California 92037, USA

    • Santosh B. Satbhai
    •  & Wolfgang Busch
  7. Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria

    • Dominik Mayer
    •  & Mathias Madalinski
  8. Institute of Molecular Biotechnology GmbH (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria

    • Dominik Mayer
    •  & Mathias Madalinski
  9. Centre for the Analysis of Genome Evolution & Function, 25 Willcocks St., University of Toronto, Toronto, Ontario, Canada

    • Nicholas J. Provart
    • , Darrell Desveaux
    •  & David S. Guttman

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Contributions

E.S.-L., G.A.M., K.G. and Y.B conceived and designed the experiments for the CSI screen. J.N. and A.L. cloned and expressed all the ECDs with inputs from E.S.-L., P.S.-B. and Y.B.; E.S.-L. performed all the ECD interaction assays. T.C.H. conceived, designed and performed the Y2H assays under the supervision of M.S.M.; G.A.M., E.S.-L. and K.P. characterized and tested all the T-DNA insertion lines under the supervision of D.D., D.S.G. and Y.B.; G.A.M., E.S.-L., K.P., N.W., K.G. and J.K. genotyped and bulked all the T-DNA insertion lines. G.A.M. analysed and implemented the computational and statistical analysis of all the data with inputs from D.S.G. and Y.B.; M.L. and G.A.M. conceived, designed and performed the network analysis with inputs from D.D., D.S.G., N.J.P. and Y.B.; M.S. designed and performed the BAK1–FLS2 co-immunoprecipitation assays under the supervision of C.Z.; K.P. organized and performed the APEX–PEPRs co-immunoprecipitation experiment with guidance from E.S.-L.; E.S.-L. and K.G. generated the apex bak1 double-mutant and 35S::APEX transgenic lines. S.B.S. and W.B. contributed and characterized the fir T-DNA mutant. E.S.-L. conceived, organized and performed the physiological assays with brassinosteroids, Pep2 and flg22. D.M. and M.M. devised the synthesis of the flg22 and Pep2 peptides. G.A.M. and Y.B. wrote the manuscript with major input from E.S.-L., M.S.M., C.Z., D.D. and D.S.G.; all authors commented and agreed on the manuscript.

Competing interests

The Gregor Mendel Institute, the University of Toronto and The Sainsbury Laboratory have filed a patent application on the use of the technical and computational approaches described in this work, in which E.S.-L., G.A.M., M.L., K.G., C.Z., D.D., D.S.G. and Y.B. are listed as inventors.

Corresponding authors

Correspondence to Darrell Desveaux or David S. Guttman or Youssef Belkhadir.

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

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