Subtractive CRISPR screen identifies the ATG16L1/vacuolar ATPase axis as required for non-canonical LC3 lipidation

Rachel Ulferts, Elena Marcassa, Lewis Timimi, Liam C Lee, Andreas Daley, Beatriz Montaner, Suzanne D. Turner, Oliver Florey, J Kenneth Baillie, Rupert Beale

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Although commonly associated with autophagosomes, LC3 can also be recruited to membranes by covalent lipidation in a variety of non-canonical contexts. These include responses to ionophores such as the M2 proton channel of influenza A virus. We report a subtractive CRISPR screen that identifies factors required for non-canonical LC3 lipidation. As well as the enzyme complexes directly responsible for LC3 lipidation in all contexts, we show the RALGAP complex is important for M2-induced, but not ionophore drug-induced, LC3 lipidation. In contrast, ATG4D is responsible for LC3 recycling in M2-induced and basal LC3 lipidation. Identification of a vacuolar ATPase subunit in the screen suggests a common mechanism for non-canonical LC3 recruitment. Influenza-induced and ionophore drug-induced LC3 lipidation lead to association of the vacuolar ATPase and ATG16L1 and can be antagonized by Salmonella SopF. LC3 recruitment to erroneously neutral compartments may therefore represent a response to damage caused by diverse invasive pathogens.

Original languageEnglish
Article number109899
Pages (from-to)1 - 11
Number of pages11
JournalCell Reports
Volume37
Issue number4
Early online date26 Oct 2021
DOIs
Publication statusE-pub ahead of print - 26 Oct 2021

Keywords / Materials (for Non-textual outputs)

  • Autophagosomes/genetics
  • Autophagy-Related Proteins/genetics
  • CRISPR-Cas Systems
  • HCT116 Cells
  • HEK293 Cells
  • Humans
  • Influenza A virus/genetics
  • Lipoylation
  • Microtubule-Associated Proteins/genetics
  • Salmonella/genetics
  • Viral Matrix Proteins/genetics
  • Viroporin Proteins/genetics

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