A comprehensive platform for the analysis of ubiquitin-like protein modifications using in vivo biotinylation

Research output: Contribution to journalJournal article

  • Lucia Pirone
  • Wendy Xolalpa
  • Jón Otti Sigurdsson
  • Juanma Ramirez
  • Coralia Pérez
  • Monika González
  • Ainara Ruiz de Sabando
  • Félix Elortza
  • Manuel S Rodriguez
  • Ugo Mayor
  • Olsen, Jesper Velgaard
  • Rosa Barrio
  • James D Sutherland

Post-translational modification by ubiquitin and ubiquitin-like proteins (UbLs) is fundamental for maintaining protein homeostasis. Efficient isolation of UbL conjugates is hampered by multiple factors, including cost and specificity of reagents, removal of UbLs by proteases, distinguishing UbL conjugates from interactors, and low quantities of modified substrates. Here we describe bioUbLs, a comprehensive set of tools for studying modifications in Drosophila and mammals, based on multicistronic expression and in vivo biotinylation using the E. coli biotin protein ligase BirA. While the bioUbLs allow rapid validation of UbL conjugation for exogenous or endogenous proteins, the single vector approach can facilitate biotinylation of most proteins of interest. Purification under denaturing conditions inactivates deconjugating enzymes and stringent washes remove UbL interactors and non-specific background. We demonstrate the utility of the method in Drosophila cells and transgenic flies, identifying an extensive set of putative SUMOylated proteins in both cases. For mammalian cells, we show conjugation and localization for many different UbLs, with the identification of novel potential substrates for UFM1. Ease of use and the flexibility to modify existing vectors will make the bioUbL system a powerful complement to existing strategies for studying this important mode of protein regulation.

Original languageEnglish
Article number40756
JournalScientific Reports
Volume7
Number of pages17
ISSN2045-2322
DOIs
Publication statusPublished - 2017

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