Table 1.

Summary of the relevant deubiquitinases and their effects in several autophagic processes.

Deubiquitinase	Autophagy Type	Targets	Effects	References
AMSH	Microautophagy and endosomal microautophagy	ESCRT-0	Stabilization of ESCRT proteins, MVE formation	[91,92]
CSN6	Lysosomal degradation	Cathepsin-L (CTSL)	Positive transcriptional regulation of CTSL	[87]
Cyld	Autolysosome and crinosome formation, MVE-lysosome fusion, vRed, Cvt, ALP, Vid pathways	α- and β-tubulin	Microtubule assembly and maintaining microtubule dynamics	Data available about the regulation of microtubules [83,97,98,99,100]
Doa4	vRed and Vid pathways	Ypq1, Cot1, Zrt3, Vid27?	Opposite effect of Rsp5/Tul1 mediated degradation of Ypq1, Cot1, Zrt3, possible binding partner of Vid27	[15,16,95]
Otub1	Macroautophagy	DEPTOR	Stabilizes DEPTOR which inhibits mTOR, macroautophagy induction	[73]
Ubp3	Macroribophagy	60S ribosomes	Positive regulation of 60S ribosome macroautophagic degradation by its deubiquitination	[81]
Usp8/Ubp5	Microautophagy and endosomal microautophagy, macromitophagy	ESCRT-0, Parkin	Stabilization of ESCRT proteins, MVE formation, Parkin stabilization	Usp8 data only available [73,88,89,90,91]
Usp10	Macroautophagy	Atg6/Beclin1	Activation and stabilization of Atg6/Beclin1, positive regulation of autophagosome formation	[73]
Usp13	Macroautophagy	Atg6/Beclin1	Activation and stabilization of Atg6/Beclin1, positive regulation of autophagosome formation	[73]
Usp14	Macroautophagy	Atg6/Beclin1, MAPT, UVRAG	Destabilizes Atg6/Beclin1, rescues MAPT and UVRAG from proteasomal degradation	[73,82]
Usp20	Macroautophagy	Atg1/Ulk1	Positive effect on macroautophagy by stabilization of Atg1/Ulk1	[73]
Usp30	Macromitophagy	Mitochondrial surface proteins	Opposite effect of Parkin mediated macromitophagy	[78,79,80]
Usp32/Ubp12	Autolysosome and crinosome formation, MVE-lysosome fusion, vRed, Cvt, ALP, Vid pathways	Rab7/Ypt7	Positive regulation of Rab7/Ypt7 recycling and recruitment to the membrane of late endosomal compartment	Usp32 data about late endosomal effect only available [94]
Usp33	Macroautophagy	RALB	Stabilizes RALB, the Atg6/Beclin1 interacting protein, positively regulates autophagosome formation	[73]
Usp36	Macroautophagy, macromitophagy	direct effect on H2B, indirect effect on Atg6/Beclin1 and Atg14L	Positive transcriptional regulation of Atg6/Beclin and Atg14L	[76]
?	Macroautophagy	LC3/Atg8	LC3/Atg8 stabilization, opposite effect of Ubp6 and Birc6	[74]