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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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.
The authors declare no competing interests.
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Supplementary Tables 1–3, Supplementary Figures 1–5
Data associated with the 2k macroarray and the Arabidopsis thaliana myristoylome
Complete human myristoylome
Protein N-Gly termini isolated from humans
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) doi:10.1038/s41589-018-0077-5
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