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Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern

Nature Chemical Biology volume 14, pages 671–679 (2018)Cite this article

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Abstract

An organism’s entire protein modification repertoire has yet to be comprehensively mapped. N-myristoylation (MYR) is a crucial eukaryotic N-terminal protein modification. Here we mapped complete Homo sapiens and Arabidopsis thaliana myristoylomes. The crystal structures of human modifier NMT1 complexed with reactive and nonreactive target-mimicking peptide ligands revealed unexpected binding clefts and a modifier recognition pattern. This information allowed integrated mapping of myristoylomes using peptide macroarrays, dedicated prediction algorithms, and in vivo mass spectrometry. Global MYR profiling at the genomic scale identified over a thousand novel, heterogeneous targets in both organisms. Surprisingly, MYR involved a non-negligible set of overlapping targets with N-acetylation, and the sequence signature marks for a third proximal acylation—S-palmitoylation—were genomically imprinted, allowing recognition of sequences exhibiting both acylations. Together, the data extend the N-end rule concept for Gly-starting proteins to subcellular compartmentalization and reveal the main neighbors influencing protein modification profiles and consequent cell fate.

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Fig. 1: The NMT recognition site is characterized by four distinct pockets, a bottleneck, and an outer salt bridge.
Fig. 2: MS MYR diagnoses.
Fig. 3: Impact and imprinting of S-palmitoylation at the genomic scale.
Fig. 4: Modification pattern of proteins starting with glycine.
Fig. 5: Sequential action of the various enzymes involved in N-terminal maturation of Met-Gly-starting polypeptide chains.

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Acknowledgements

This work was funded by Agence Nationale de la Recherche (ANR-2010-BLAN-1611-01) and Fondation ARC (SFI2011120111203841). The team benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS). C.D., B.C., and S.C. were supported by postdoctoral fellowships (CNRS). We thank W. Majeran and C. Micalella for initial help with sample preparation and in vitro assays and all members of the group for stimulating discussions. The 2016 innovative experimental training Master class students hosted in the Gif laboratory actively contributed to early crystallographic attempts of one NMT complex. C. Duyckaerts (APHP) and Hopital Pitié Salpêtrière (Université Pierre et Marie Curie, Paris) kindly allowed access to human tissue samples from Neuro-CEB (http://www.neuroceb.org/) and M.-A. Loriot and A. Al Ali to sample preparation. J. Bignon (CNRS, Gif) allowed access to human cell culture facility. This work used the facilities and expertise of the SICaPS mass spectrometry platform at I2BC (Gif). We thank ESRF staff for help with data collection.

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Author notes

  1. Coralie L. Ebert

    Present address: The Weizmann Institute, Rehovot, Israel

  2. These authors contributed equally: Benoit Castrec, Cyril Dian.

Authors and Affiliations

  1. Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette cedex, France

    Benoit Castrec, Cyril Dian, Sarah Ciccone, Coralie L. Ebert, Willy V. Bienvenut, Carmela Giglione & Thierry Meinnel

  2. Institut de Chimie des Substances Naturelles, CNRS Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette cedex, France

    Jean-Pierre Le Caer

  3. Laboratoire d’Informatique, École Polytechnique, Palaiseau, France

    Jean-Marc Steyaert

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Contributions

C.D. performed NMT cloning, purification, and structural analysis. B.C. and S.C. performed in vitro assays. W.V.B. and J.P.L.C performed mass spectrometry measurements and analysis. C.L.E. and J.-M.S. built the SVM classifiers. C.G. and T.M. designed the research, supervised the overall project, analyzed the data, and wrote the manuscript.

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Correspondence to Carmela Giglione or Thierry Meinnel.

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Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–3, Supplementary Figures 1–5

Reporting Summary

Supplementary Dataset 1

Data associated with the 2k macroarray and the Arabidopsis thaliana myristoylome

Supplementary Dataset 2

Complete human myristoylome

Supplementary Dataset 3

Protein N-Gly termini isolated from humans

Supplementary Dataset 4

Protein N-Gly termini from Arabidopsis thaliana

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Castrec, B., Dian, C., Ciccone, S. et al. Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern. Nat Chem Biol 14, 671–679 (2018). https://doi.org/10.1038/s41589-018-0077-5

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