Systematic Analysis of Human Cells Lacking ATG8 Proteins Uncovers Roles for GABARAPs and the CCZ1/MON1 Regulator C18orf8/RMC1 in Macroautophagic and Selective Autophagic Flux

ABSTRACT

Selective autophagy and macroautophagy sequester specific organelles/substrates or bulk cytoplasm, respectively, inside autophagosomes as cargo for delivery to lysosomes. The mammalian ATG8 orthologues (MAP1LC3A/B/C and GABARAP/L1/L2) are ubiquitin (UB)-like proteins conjugated to the autophagosome membrane and are thought to facilitate cargo receptor recruitment, vesicle maturation, and lysosomal fusion. To elucidate the molecular functions of the ATG8 proteins, we engineered cells lacking genes for each subfamily as well as all six mammalian ATG8s. Loss of GABARAPs alone attenuates autophagic flux basally and in response to macroautophagic or selective autophagic stimuli, including parkin-dependent mitophagy, and cells lacking all ATG8 proteins accumulate cytoplasmic UB aggregates, which are resolved following ectopic expression of individual GABARAPs. Autophagosomes from cells lacking GABARAPs had reduced lysosomal content by quantitative proteomics, consistent with fusion defects, but accumulated regulators of late endosome (LE)/autophagosome maturation. Through interaction proteomics of proteins accumulating in GABARAP/L1/L2-deficient cells, we identified C18orf8/RMC1 as a new subunit of the CCZ1-MON1 RAB7 guanine exchange factor (GEF) that positively regulates RAB7 recruitment to LE/autophagosomes. This work defines unique roles for GABARAP and LC3 subfamilies in macroautophagy and selective autophagy and demonstrates how analysis of autophagic machinery in the absence of flux can identify new regulatory circuits.

KEYWORDS:

• macroautophagy
• selective autophagy
• ATG8
• autophagosome maturation
• mitophagy

View publisher note:

Article of Significant Interest Selected from This Issue by the Editors

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at https://doi.org/10.1128/MCB.00392-17.

ACKNOWLEDGMENTS

We thank Jennifer Waters, Talley Lambert, and Anna Jost of the Nikon Imaging Center (NIC) at Harvard Medical School for imaging support and technical assistance, Hunter Elliott and David Richmond of the Imaging and Data Analysis Core (IDAC) for data analysis support, Maria Ericsson and the HMS Electron Microscopy Facility for EM/immunogold support, Joseph Mancias for technical support with autophagosome isolation/proteomics and gel filtration analysis, Christian Munch for maintaining the Velos LTQ and running CompPASS samples on the instrument, Alban Ordureau for cloning of mtKeima into the pHAGE lentiviral expression backbone, and Takeda Oncology for the gift of ATG8 antibodies.

This work was supported by research grants to J.W.H. from the NIH (R37-NS083524 and RO1-GM095567) and an NIH grant (K01DK098285) to J.A.P. L.P.V. was supported by a Damon Runyon postdoctoral fellowship.

L.P.V. and J.W.H. conceived the study and prepared the manuscript. L.P.V. performed the experiments. J.A.P. provided proteomics support. E.L.H. provided proteomics data analysis support.