Molecular Vision: Brennan, Mol Vis 2012; 18:1773-1786. Table 2

Table 2. Identified autophagy genes and their functions.

Induction	Role in Autophagy	Reference
Beclin 1	Member of PtdIns 3-kinase complex, involved in activation of macroautophagy	[31]
TSC1	Acts as a gtpase-activating protein for Rheb, thus inhibiting TOR	[32]
UVRAG	Member of PtdIns 3-kinase complex, regulates macroautophagy	[33]
AEG1	Gene encodes oncogenic protein that induces macroautophagy independent of Beclin-1 and PtdIns 3-kinase	[34]
Omi/HtrA2	Degrades the Bcl-2 family-related protein Ha × −1 to allow macroautophagy induction	[35]
Pten	Dephosphorylates PdtIns(3,4,5)P3 inhibiting PDK1 and PKB/Akt activity	[36,37]
Atg14	Component of PtdIns 3-kinase complex, targets this complex toward autophagic machinery	[38]
Bif-1	Interacts with Beclin 1 via UVRAG and is required for macroautophagy	[39]
HMGB1	Binds beclin-1 to displace Bcl-2 inhibiting apoptosis and promoting macroautophagy	[40]
RalB	Activation of phagophore assembly through ULK1-Beclin1-Vps34 complex assembly and Exo84 interaction	[41]
RB1CC1/FIP200	Component of Ulk1 complex, required for phagophore formation, phosphorylation of Ulk1/2	[42]
FoxO1	Regulates macroautophagy independent of transcriptional control	[43]
FoxO3	Stimulates macroautophagy through transcriptional control of autophagy genes	[44]
PERK/eif2α3K	Phosphorylated due to ER stress which induces LC3 conversion and macroautophagy	[45,46]
Expansion/Closure
MAPK1	MAPK/ERK regulates the maturation of autophagosomes	[47]
Atg12	Ubiquitin-like protein, conjugates Atg5, member of ATG12–5–16 complex, essential for Map1LC3B/Atg8 activation, involved in mitochondrial homeostasis	[48,49]
WIPI1/Atg18	Binds PI3P by WD40 β-propeller domain, involved in retrograde movement of Atg9	[50,[51]
Atg3	E2 ubiquitin ligase, conjugates PE to Map1LC3B after Atg7 processing of c-terminus of cleaved Map1LC3B/Atg8, can be conjugated to Atg12	[49,[52]
Atg5	Contains ubiquitin-folds, member of ATG12–5–16 complex	[48]
Map1LC3b/Atg8	Atg8 homolog, involved in autophagosome biogenesis and cargo recruitment to autophagosomes, marker of autophagosomes	[53–55]
Atg4a	Cysteine Protease of Yeast Atg8 homologs, required for Map1LC3B /Atg8 activation, able to deconjugate PE of processed Map1LC3B	[55,56]
Rab33B	Binds Atg16L1, involved in autophagosome maturation by regulation of autophagosome to lysosome fusion, OATL1 binding partner	[57,58]
Fusion/Degradation
FYCO1	Rab7 effector, binds Map1LC3B and phosphatidylinositol-3-phosphate, coordinates plus-end directed autophagosome transport	[26,59]
Rab7	Transport of early to late endosomes, docking protein for amphisome to lysosome fusion	[26,60–62]
Rab9	Involved in trafficking from late endosomes to the trans-golgi, believed to be a key component of the ATG5/7 alternative macroautophagy pathway	[60,63]
VAMP7	SNARE protein, required for autophagosome formation, autophagosome maturation via facilitation of autophagosome to lysosome fusion	[64,65]
VCP	AAA+ ATPase, required for autophagosome maturation, mutations to vcp results in accumulation of ubiquitin-containing autophagosomes	[66,67]
PSEN1	Protease, part of the γ-secretase complex, involved in lysosomal degradation	[68]
Mitophagy
ERK2	Localizes to the mitochondria, regulates mitophagy	[69]
BNIP3L/NIX	Bcl2 related, necessary for selective mitochondrial clearance	[70]
Pink1	Decreased MMP causes altered Pink1 processing, results in spanning of Pink1 across the outer mitochondrialmembrane, recruiting Parkin for mitophagy	[71]
PARL	Mitochondrial protease that regulates PINK1 localization and stability	[72]
Chaperone Mediated Autophagy
Lamp2	Lysosomal membrane receptor for chaperone-mediated autophagy allowing translocation of substrates across the lysosomal membrane.	[73]
BAG3	Directs Hsp70 misfolded protein substrates to dynein targeting them to aggresomes for selective degradation	[74]
Hsc70–4	Aids in targeting of cytosolic proteins to the lysosome for degradation	[75]
hsp90	Assists in LAMP-2A stabilization of during its lateral mobility in the lysosomal membrane	[76]
Adaptor Proteins
NBR1	Binds ubiquitinated proteins allowing degradation by macroautophagy	[77,78]
P62	Interacts with Atg8 via its LIR domain, adaptor for degradation of ubiquitin-labeled molecules	[78,79]
Autophagy Inhibitors
mTOR	Serine/threonine kinase that controls cells growth and metabolism in response to nutrients, growth factors, cellular energy and stress	[80,81]
c-Jun	transcription factor, Inhibits mammalian macroautophagy induced by starvation	[82]
p8/Nupr1	Inhibits macroautophagy by repressing the transcriptional activity of FoxO3	[83]
PKB/Akt	Upstream regulator of mtor	[84]
PARK7/DJ1	Overxpression suppresses macroautophagy through the JNK pathway	[85]