Table 2.

Major cellular functions involving components of the autophagy machinery

Functions	Protein	Autophagic Role	References
Related to membrane biology
Cytokine secretion	ATG7	Elongation	Henault et al., 2012, Li et al., 2016
	ULK1	Initiation
Cytokinesis	BECN1	Nucleation	Thoresen et al., 2010, You et al., 2016
	BIF-1	Nucleation
	UVRAG	Initiation
	VPS15	Nucleation
	VPS34	Nucleation
	ULK1	Initiation
Endocytosis	BECN1	Nucleation	Lee et al., 2011, Liang et al., 2008, McKnight et al., 2014, Pirooz et al., 2014, Rohatgi et al., 2015, Shravage et al., 2013, Thoresen et al., 2010
	BIF-1	Nucleation
	RAB7A	Fusion
	UVRAG	Initiation
	VPS15	Nucleation
	VPS34	Nucleation
ER-to-GA anterograde transport	ULK1	Initiation	Joo et al., 2016, Wang et al., 2018
	ULK2	Initiation
Exosome secretion	ATG12	Elongation	Guo et al., 2017, Jaé et al., 2015, Murrow et al., 2015, Shrivastava et al., 2015
	ATG16L1	Elongation
	ATG3	Elongation
	ATG5	Elongation
	ATG7	Elongation
	RAB7A	Fusion
GA-to-ER retrograde transport	VPS34	Nucleation	He et al., 2013
	UVRAG	Initiation
Granule exocytosis	ATG4B	Elongation	DeSelm et al., 2011, Patel et al., 2013
	ATG5	Elongation
	ATG7	Elongation
	LC3	Cargo selection
	RAB7A	Fusion
LAP	ATG12	Elongation	Martinez et al., 2015, Martinez et al., 2016, Sanjuan et al., 2007
	ATG16L1	Elongation
	ATG3	Elongation
	ATG4B	Elongation
	ATG5	Elongation
	ATG7	Elongation
	BECN1	Nucleation
	LC3	Cargo selection
	RUBCN	Nucleation
	UVRAG	Initiation
	VPS34	Nucleation
Melanogenesis	UVRAG	Initiation	Yang et al., 2018
Non-canonical protein secretion	ATG5	Elongation	Dupont et al., 2011, Kimura et al., 2017, Zhang et al., 2015
	RAB7A	Fusion
Pathogen controla	ATG12	Elongation	Hwang et al., 2012, Kimmey et al., 2015, Mauthe et al., 2016, Selleck et al., 2015, Zhao et al., 2008
	ATG13	Initiation
	ATG16L1	Elongation
	ATG5	Elongation
	ATG7	Elongation
	FIP200	Initiation
	LC3	Cargo selection
	NDP52	Cargo selection
	p62	Cargo selection
Pathogen replicationb and release	LC3	Cargo selection	Al-Younes et al., 2011, Alirezaei et al., 2015, Sin et al., 2017, Wong et al., 2008
Phagocytosis	ATG16L1	Elongation	Tung et al., 2010, Xiong et al., 2015
	ATG9	Initiation
Vision cycle	ATG5	Elongation	Muniz-Feliciano et al., 2017, Kim et al., 2013
Others
ADCD	AMBRA1	Nucleation	Elgendy et al., 2014, Gao et al., 2011, Goodall et al., 2016, Haller et al., 2014, Imagawa et al., 2016, Lee et al., 2012, Rubinstein et al., 2011, Singh et al., 2010, Strappazzon et al., 2016
	ATG12	Elongation
	ATG13	Initiation
	ATG14	Nucleation
	ATG5	Elongation
	ATG7	Elongation
	ATG9	Initiation
	BECN1	Nucleation
	IRGM	Unclear
	p62	Cargo selection
	VPS34	Nucleation
Cell proliferation	ATG3	Elongation	Afzal et al., 2015, O’Sullivan et al., 2016, Pei et al., 2015
	ATG5	Elongation
	ATG7	Elongation
	UVRAG	Initiation
Centrosome functions	BECN1	Nucleation	Park et al., 2014
DNA repair	UVRAG	Initiation	Yang et al., 2016, Zhao et al., 2012
Immunological memory	ATG5	Elongation	Puleston et al., 2014, Xu et al., 2014
	ATG7	Elongation
PRR signaling	ATG7	Elongation	Henault et al., 2012, Sorbara et al., 2013
	ATG16L1	Elongation
	BECN1	Nucleation
	LC3	Cargo selection
	RUBCN	Nucleation

ADCD, autophagy-dependent cell death; ER, endoplasmic reticulum; GA, Golgi apparatus; LAP, LC3-associated phagocytosis; PRR, pattern recognition receptor.

^aPartially unrelated to membrane biology

^bReferring to the replication of pathogens in the cytoplasm of infected cells