Table 1.

Non-autophagic Functions of Core Components of the Autophagy Apparatus

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

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

^aReferring to bacteria replicating in the cytoplasm of infected cells