Table 2.
ATG mRNAs expression regulated by translation machinery.
| Protein Studied | Model | Autophagy evaluation | Autophagy flux assessment | Additional observations | References |
|---|---|---|---|---|---|
| 4E-BP1 | LHMB-AR PrEC sh4E-BP1 |
↑LC3-II, ↑acridine orange | (37) #122 | ||
| 4E-BP1 | HL60 or HeLa parthenolide HEK293 Parthenolide + sh4E-BP1 HeLa Parthenolide + plasmid 4E-BP1 |
↑LC3-II, ↑GFP-LC3 ↑LC3-II ↓LC3-II |
↓ 4EB-P1 ↓Ⓟ 4E-BP1 |
(38) #127 | |
| 4EB-P1 | HCT-1116 hypoxia |
↑ translation 35 lysosomal mRNAs ↑ acridine orange ↑ LysoTracker+ ↑ LC3-II ↓p62 |
↑Ⓟ eIF2α; ↓Ⓟ 4EB-P1 ↑ translation EIF4EBP3 and EIF2AK3; EIF4E, RPS6K subunits |
(39) #40 | |
| 4E-BP1 Akt S6K1 |
HepG2.2.15 si4E-BP1 siAkt or Akt inhibitors siS6K1 |
↑LC3-II ↓LC3-II ↓GFP-LC3 puncta ↑p62 ↓LC3-II |
CQ ↑ LC3-II CQ ≠ LC3-II |
(40) #161 | |
| eIF4E | T-ALL Jurkat selenite selenite +sieIF4E |
↑LC3-II ↑GFP-LC3 puncta ↑ATF4 on MAP1LC3B and CHOP promoters ↓GFP-LC3 puncta ↓ATF4 on MAP1LC3B and CHOP promoters |
Baf A1 ↑LC3-II ↑p62 |
↑CHOP, ↑Ⓟ eIF4E ↓ATF4 + si_p38 or p38 inhibitors prevent selenite effects |
(41) #124 |
| eIF4E eIF2α |
NB-4 selenite selenite+ sieIF2α selenite+ plasmid eIF4E |
↓LC3-II, ↑p62 ↓GFP-LC3 puncta ↓ATF4 on MAP1LC3B promoter ↑LC3-II, ≠GFP-LC3 ↑LC3-II ↑GFP-LC3 puncta ↑ATF4 on MAP1LC3B promoter |
↑CHOP, ↑ATF4 ↑Ⓟ eIF2α, ↓Ⓟ eIF4E ↓CHOP ↑CHOP |
(42) #43 | |
| eIF5A eIF4A3 | MCF-7 sieIF5A sieIF5A +Torin-1 |
↓GFP-LC3 puncta ↓autophagosome (TEM) ↓ATG3 ↓GFP-LC3 puncta |
Baf A1 ↑LC3-II | (43) | |
|
iff-2 (eIF5A homlog) |
C. elegans iff-2 RNAi | ↓GFP::LGG-1 puncta | (43) | ||
| eIF4G1 eIF4G2 | MCF10A or HEK293T sheIF4G1 or sh eIF4G2 |
↑LC3-II ↑GFP-LC3 puncta ↑MDC+ Vesicles | (44) #216 | ||
| eIF4G1 | MCF10A sheIF4G1 γ irradiation |
↑LC3-II ↑GFP-LC3 puncta | (45) #2 | ||
| RACK1 | HT1080 siRACK1 HepG2, Hep3B, U2OS, HeLa, MCF-7 and MDAMB231 |
↑LC3-II ↑LAMP1 and LAMP2 ↑GFP-LC3 puncta and colocalization with LysoTracker ↑BCL-XL and BECN1 interaction ↓p62 ↑polysomal fraction on MAP1LC3 and BCL-XL mRNA |
Baf A1 ↑LC3-II ↑p62 |
(46) #126 | |
| RPS27L | MB231 or SK-BR3+ siRPS27L | ↑LC3-II ↑EGFP-LC3 puncta ↓p62 |
+CQ or Baf A1: ↑LC3-II and ↑p62 | ↑DEPTOR, ↓Ⓟ S6K1 and Ⓟ 4EBP1 ↓Ⓟ S6K1 and Ⓟ 4EBP1 |
(47) #131 |
| MEFs RSP27L−/− | ↑LC3-II ↓p62 |
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| HuD | βTC6 or U2OS siHuD plasmid HuD |
≠ATG5 mRNA; ↓ATG5 ↓LC3-II ↓GFP-LC3 puncta ↓autophagosomes (TEM) ≠ATG5 mRNA ↑ATG5 ↑LC3-II ↑GFP-LC3 puncta |
+miR-181 ↓EGFP-3'UTR Atg5 mRNA ↑EGFP-3'UTR Atg5 mRNA |
(48) #125 | |
| HuR | HSC-LX2 or HSC-T6 erastin+ siHuR HSC-LX2 or HSC-T6 erastin+ plasmid HuR |
↓LC3-II ↓BECN1 ↑p62 ↑LC3-II ↑BECN1 ↑autophagosome (TEM), ↓p62 |
CQ: ↑LC3-II | RIP: 3'UTR BECN1 mRNA enrichment | (49) |
| HuR | L-02 or Hep3B siHuR |
↓ATG5, ATG12 and ATG16 ↓polysome association to ATG5, ATG12 and ATG16 mRNAs ↓LC3-II ↓Autophagosome and autolysosome (TEM) ↓GFP-LC3 puncta |
colchicine modest ↑LC3-II | RIP: 3'UTR ATG5, ATG12, ATG16 mRNAs enrichment | (50) #36 |
| HuR | HK-2 hypoxia HK-2 hypoxia+ shHuR |
↑LC3-II, ATG7 and ATG16 ↓LC3-II, ATG7 and ATG16 |
↑TUNEL+ cells RIP: ATG7, ATG16 mRNAs enrichment |
(51) | |
| HuR | MCF-7 starvation MCF-7, MDA-MB 231, PC3, HaCat siHur |
↑LC3-II, ↑BECN1, ↑polysomes association of BECN1 mRNA & HuR, ↓LC3-II ↓BECN1 ↓BECN1 mRNA |
RIP: 3'UTR BEC1 mRNA enrichment | (52) | |
| HuR | Intestinal epithelium IE_HuR−/− mice | ↓LC3-II ↓BECN1, ↓ATG16L1 ↓ATG7 | RIP: ATG16 mRNA enrichment |
(53) | |
| IECs siHuR |
↓LC3-II ↓ATG16L1 ↓ newly synthesized ATG16L1 |
||||
| ZFP36 | HSC-LX2 or HSC-T6 erastin + plasmid ZFP36 |
↓ LC3-II ↓GFP-LC3 puncta ↓ ATG16L1 ↓ ATG5-ATG12 ↓ Autophagosome (TEM) ↓ATG16 mRNA, ↑SQSTM11 mRNA |
RIP: ATG16 mRNA enrichment Luc-3'ÚTR Atg16 mRNA: ↓Luc activity |
(54) | |
| HSC-LX2 or HSC-T6 erastin + plasmid FXBW7 |
↑ LC3-II, ↑ ATG16L1, ↑ ATG5-ATG12 ↑ Autophagosome (TEM) |
||||
| hnRNPA1 | HCT-116 sihnRNPA1 plasmid hnRNPA1 |
↓BECN1, ≠ Becn1 mRNA ↑BECN1, ≠ Becn1 mRNA |
Luc-3′ÚTR Becn1 mRNA: ↓Luc activity Luc-3′ÚTR Becn1 mRNA: ↑ Luc activity Biotin-3′UTR Benc1 mRNA RIP: Becn1 mRNA enrichment |
(55) | |
| Orb | Drosophila germarium Orb mutant | ↑Atg12 (mRNA); ↑Atg12 and Atg8 (protein); ↑LysoTracker+ structures |
RIP: Atg12 mRNA enrichment | (56) #8 | |
| Dhh1 (DDX6) | Yeast Δdhh1 nutrient replete |
↑ Atg3, Atg7, Atg8, Atg19, Atg20, Atg22 and Atg24 mRNA | GFP- ATG8 processing assay Δdhh1+ starvation: ↑ GFP free | (57) #123 | |
| Mouse ESC DDX6 +/− |
↑Map1lc3 mRNA ↑LC3-II ↓LC3 puncta ↓p62 |
||||
| HeLa+ siDDX6 |
↑ MAP1LC3 mRNA ↑ LC3 puncta |
||||
| HeLa+ plasmid DDX6 | ↓MAP1LC3 mRNA ↓ LC3-II ↓LC3 puncta ↑p62 |
||||
| Dhh1 (DDX6) Eap1 | Yeast Δdhh1 Nitrogen starvation HEK293A DDX6 −/− Amino acid starvation |
↓Atg1, Atg13 (protein) ≠ ATG1 and ATG13 mRNAs ↓ATG16L1 ↑ATG16L1 mRNA |
Pgi-GFP processing assay: ↓ free GFP |
(58) #24 ó 1 | |
| Psp2 | Yeast Δpsp2+ Nitrogen starvation | ↓Atg1 ≠ ATG1 mRNA ↓polysomes association of ATG1 mRNA, ↓Atg13 | Pgi-GFP processing assay: ↓ free GFP Pho8Δ60 assay: ↓ vacuolar Pho8Δ60 |
RIP: ATG1 & ATG13 mRNA enrichment | (59) #274 |
| ATF4 CHOP |
MEFs ATF4 −/− leucine starvation | ≠ Atg16l1, Map1lc3b, Atg12, Atg3, Becn1, Gabarapl2, p62, Nbr1, Atg7 mRNAs | ↑Ⓟ eIF2α | (60) #3 | |
| MEFs CHOP −/− leucine starvation | ≠ Atg10, Gabarap, Atg5, p62, Nbr1, Atg7 mRNAs | ↑Ⓟ eIF2α | |||
| PERK ATF4 |
LNCaP Tunicamycin |
↑ LC3-II mTagRFP-mWasabi-LC3: ↑ red punctate ↑MAP1LC3B, GABARAPL1, WIPI1, MAPLC3B2, MAPLC3A, ATG13, ATG16L1, GAGARAP, ATG12, ATG5, ATG3, BECN1 mRNA |
BafA1: ↑ LC3-II mTagRFP-mWasabi-LC3: ↑ yellow puncta LDH sequestration assay: ↑ sequestration rate LLPD assay: ↑ Valine release |
(61) #128 | |
| LNCaP Tunicamycin siATF4 |
↓MAP1LC3B, GABARAPL1, WIPI1, MAPLC3B2, MAPLC3A, ATG13 mRNA | ↓↓ Valine release | |||
| eIF2α ATF4 |
MEFs eIF2Aα non-phosphorylable mutant or ATF4−/− Rapamycin |
↓Map1lc3 and Atg5 mRNA ↓LC3-II and LC3 puncta |
GFP-LC3 processing assay: ↓ free GFP |
(62) #130 |