Overexpression of PTP4A
phosphatases are associated with advanced
cancers, but their
biological functions are far from fully understood due to limited knowledge about their physiological substrates. VCP is implicated in lysophagy via collaboration with specific cofactors in the ELDR complex. However, how the ELDR complex assembly is regulated has not been determined. Moreover, the functional significance of the penultimate and conserved Tyr805 phosphorylation in VCP has not been established. Here, we use an unbiased substrate trapping and mass spectrometry approach and identify VCP/p97 as a bona fide substrate of PTP4A2. Biochemical studies show that PTP4A2 dephosphorylates VCP at Tyr805, enabling the association of VCP with its C-terminal cofactors UBXN6/UBXD1 and PLAA, which are components of the ELDR complex responsible for lysophagy, the autophagic clearance of damaged lysosomes. Functionally, PTP4A2 is required for cellular homeostasis by promoting lysophagy through facilitating ELDR-mediated K48-linked
ubiquitin conjugate removal and autophagosome formation on the damaged lysosomes. Deletion of Ptp4a2 in vivo compromises the recovery of
glycerol-injection induced
acute kidney injury due to impaired lysophagy and sustained lysosomal damage. Taken together, our data establish PTP4A2 as a critical regulator of VCP and uncover an important role for PTP4A2 in maintaining lysosomal homeostasis through dephosphorylation of VCP at Tyr805. Our study suggests that PTP4A2 targeting could be a potential therapeutic approach to treat
cancers and other degenerative diseases by modulating lysosomal homeostasis and macroautophagy/autophagy.Abbreviations:
AAA+: ATPases associated with diverse cellular activities; AKI:
acute kidney injury; CBB:
Coomassie Brilliant Blue; CRISPR: clustered regularly interspaced short palindromic repeats; ELDR: endo-lysosomal damage response; GFP:
green fluorescent protein; GST: glutathione S-
transferase; IHC: immunohistochemistry; IP: immunoprecipitation; LAMP1:
lysosomal-associated membrane protein 1; LC-MS: liquid chromatography-mass spectrometry;
LGALS3/Gal3:
galectin 3; LLOMe:
L-leucyl-L-leucine methyl
ester; MAP1LC3/LC3:
microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; PLAA:
phospholipase A2, activating
protein; PTP4A2:
protein tyrosine phosphatase 4a2; PUB: NGLY1/PNGase/UBA- or UBX-containing
protein; PUL: PLAP, Ufd3, and Lub1; TFEB:
transcription factor EB; UBXN6/UBXD1: UBX domain protein 6; UPS:
ubiquitin-
proteasome system; VCP/
p97: valosin containing protein; VCPIP1:
valosin containing protein interacting
protein 1; YOD1: YOD1
deubiquitinase.