TBC1D9

TBC1D9 is a Ca²⁺-sensing, ubiquitin-recognizing TBC domain protein that functions as an upstream activator of TBK1 during selective autophagy. It binds ubiquitin-coated substrates—including intracellular bacteria and damaged mitochondria—through its ubiquitin-binding region (UBR) in a Ca²⁺-dependent manner, and its knockout abolishes TBK1 activation and subsequent ULK1 complex recruitment during both xenophagy and mitophagy (PMID:32034138). TBC1D9 also directly interacts with ATG8/LC3 family proteins via a LIR motif and colocalizes with LC3-positive autophagy membranes, consistent with a role as a selective autophagy adaptor (PMID:22354992).

1. 2012 Medium

   Whether TBC domain-containing Rab GAPs participate in autophagy was unknown; a systematic interaction screen revealed that TBC1D9 directly binds ATG8/LC3 family members and colocalizes with LC3-positive membranes, establishing it as a candidate autophagy-linked adaptor.

   Evidence Pulldown/binding assays with ATG8 modifiers and colocalization imaging in mammalian cells

   PMID:22354992

   Open questions at the time

   • TBC1D9 was one of 14 hits; no functional follow-up specific to TBC1D9 was performed
   • The biological consequence of TBC1D9–LC3 binding was not tested
   • No substrate-targeting or cargo-recognition mechanism was defined
2. 2020 High

   How TBC1D9 is activated and what downstream signaling it controls were unknown; knockout and domain-mutant analyses demonstrated that Ca²⁺-dependent ubiquitin recognition by TBC1D9 is required for TBK1 activation and ULK1 complex recruitment during both xenophagy and mitophagy, placing TBC1D9 as a Ca²⁺-sensing signal integrator upstream of TBK1.

   Evidence TBC1D9-KO cells, Ca²⁺ chelation, Co-IP with ubiquitin-positive bacteria, immunofluorescence, UBR and Ca²⁺-binding motif mutant analysis across xenophagy and mitophagy contexts

   PMID:32034138

   Open questions at the time

   • Whether TBC1D9 retains or uses Rab GAP catalytic activity during autophagy has not been tested
   • The structural basis of Ca²⁺-dependent ubiquitin recognition is unresolved
   • Contribution of the LIR motif versus the UBR to cargo selectivity has not been dissected in vivo

• It remains unknown whether TBC1D9 functions as a bona fide Rab GAP in autophagy signaling, which Rab substrates (if any) it acts on, and how the Ca²⁺-binding, ubiquitin-binding, and LIR-dependent interactions are coordinated to drive selective autophagy.
• No Rab GAP activity has been demonstrated for TBC1D9
• No structural model of TBC1D9 exists
• In vivo relevance in animal models has not been established