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

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]
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 [5355]
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]
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 [26,6062]
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]
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]