Table I Autophagic activity screen in yeast strains defective of the orthologs of the genes encoding for the common autophagosome associated proteins

The common proteins localizing to autophagosomes of MCF7 cells independent of the stimuli.

ProteinGene ID (human)Yeast orthologAutophagic activityaReferencedeGFP-IPe
Nitrogen starvationbRapamycinc
Alanyl tRNA synthetaseAARSALA1f+
Annexin A4ANXA432g
Annexin A5ANXA532g++
Archain 1ARCN1RET2f++
ADP-ribosylation factor 1ARF1ARF2126.1 ± 16.032g++
Argininosuccinate synthase 1ASS1ARG1115.8 ± 11.6++
5-Aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolaseATICADE1799.7 ± 13.532g
Biliverdin reductase BBLVRB++
γ-Glutamyl cyclotransferaseC7orf24
Calcyclin-binding proteinCACYBP32g+
Calpain, small subunit 1CAPNS132g+
Chaperonin containing TCP1, subunit 2CCT2CCT2f++
Chaperonin containing TCP1, subunit 5CCT5CCT5f++
Chaperonin containing TCP1, subunit 8CCT8CCT8f++
Cofilin 1CFL1COF1f++
Chromatin modifying protein 6CHMP6
Coatomer protein complex, subunit ζ1COPZ1RET3f+
Copine IIICPNE3
Cellular retinoic acid-binding protein 2CRABP2+
Cystatin BCSTB
DestrinDSTN++
Eukaryotic translation elongation factor 1γEEF1GTEF456.2 ± 16.384.3 ± 19.1++
Eukaryotic translation elongation factor 2EEF2EFT2104.5 ± 23.2++
Enolase 1ENO1ENO195.8 ± 38.034h++
Fatty acid synthaseFASNCEM1101.4 ± 14.2++
Fructose-1,6-bisphosphatase 1FBP1FBP199.2 ± 16.934h+
FK506-binding protein 4, 59 kDaFKBP4FPR186.2 ± 17.032+
Glucose-6-phosphate dehydrogenaseG6PDZWF1108.3 ± 12.8++
GABAA receptor-associated protein-like 2GABARAPL2ATG826.1 ± 21.444.7 ± 26.358+
GDP dissociation inhibitor 2GDI232g++
Guanine nucleotide-binding protein, β polypeptide 2-like 1GNB2L1ASC1148.0 ± 21.5210.7 ± 43.1+
Glucose phosphate isomeraseGPIPGI1f++
Glutathione reductaseGSRGLR190.7 ± 9.1
Hypoxanthine phosphoribosyltransferase 1HPRT1+
Heat shock protein 90-kDa α, class A member 1HSP90AA1HSC82100.0 ± 15.9++
Heat shock protein 90-kDa α, class B member 1HSP90AB1HSP8290.6 ± 6.8++
Heat shock 27-kDa protein 1HSPB1++
KIAA1609KIAA1609++
LIM and SH3 protein 1LASP132g+
Lectin, galactoside-binding, soluble, 3LGALS3++
Microtubule-associated protein 1 light chain 3βMAP1LC3BATG826.1 ± 21.444.7 ± 26.358
Malate dehydrogenase 1MDH134h
Macrophage migration inhibitory factorMIF++
Purine nucleoside phosphorylaseNPPNP146.0 ± 5.930.1 ± 10.6
Aminopeptidase, puromycin-sensitiveNPEPPSAAP1101.4 ± 34.432g+
Platelet-activating factor acetylhydrolase 1b, catalytic subunit 3PAFAH1B3
Poly(rC)-binding protein 1PCBP1PBP2103.4 ± 8.833++
Phosphatidylethanolamine-binding protein 1PEBP132g+
Profilin 1PFN1PFY1f++
Profilin 2PFN2
Phosphogluconate dehydrogenasePGDGND1111.5 ± 25.2
Phosphoglycerate dehydrogenasePHGDHSER3398.7 ± 31.8++
Pyruvate kinase, musclePKM2CDC19f++
Peptidylprolyl isomerase APPIACPR194.9 ± 16.334h++
Protein phosphatase 3, catalytic subunit, α isoformPPP3CACMP2102.7 ± 11.1+
Peroxiredoxin 1PRDX1TSA196.8 ± 11.634h++
Peroxiredoxin 2PRDX2TSA196.8 ± 11.634h++
Peroxiredoxin 6PRDX6PRX190.9 ± 6.034h++
Proteasome subunit, α type, 2PSMA2PRE8f45g+
Proteasome subunit, α type, 3PSMA3PRE10f45g
Proteasome subunit, α type, 5PSMA5PUP2f45g+
Proteasome subunit, α type, 6PSMA6SCL1f45g+
Proteasome subunit, α type, 7PSMA7PRE6f45g+
Proteasome subunit, β type, 1PSMB1PRE7f45g
Proteasome subunit, β type, 2PSMB2PRE1f45g+
Proteasome subunit, β type, 3PSMB3PUP3f45g
Proteasome subunit, β type, 4PSMB4PRE4f45g
Proteasome subunit, β type, 5PSMB5PRE2f45g
Proteasome subunit, β type, 6PSMB6PRE3f45g
Proteasome subunit, β type, 7PSMB7PUP1f45g
Proteasome 26 S subunit, ATPase, 6PSMC6RPT4f45g
Proteasome activator subunit 1PSME145g++
Proteasome activator subunit 2PSME245g++
Ras homolog enriched in brain 1RHEB1RHB136.3 ± 11.137.2 ± 4.259g
Ribosomal protein S21RPS21RPS21B85.5 ± 4.3
Ribosomal protein SARPSARPS0A90.8 ± 32.7+
S100 calcium-binding protein A11S100A11++
S100 calcium-binding protein A13S100A13
SH3 domain binding glutamic acid-rich protein likeSH3BGRL
Sequestosome 1SQSTM141++
Spermidine synthaseSRMSPE3119.1 ± 23.132g
Stress-induced-phosphoprotein 1STIP1STI1113.4 ± 24.3++
Tumor protein D52-like 2TPD52L2++
Triosephosphate isomerase 1TPI1TPI1f++
Tubulin, βTUBBTUB2f++
Tubulin, β 2CTUBB2C++
ThioredoxinTXNTRX2101.2 ± 29.7+
Thioredoxin reductase 1TXNRD132g
Ubiquitin-like modifier activating enzyme 1UBE1UBA1f
Ubiquitin-conjugating enzyme E2NUBE2NUBC13106.5 ± 19.4++
Tryptophanyl-tRNA synthetaseWARSWRS1f32g+
Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, β polypeptideYWHAB32g++
Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, ζ polypeptideYWHAZBMH298.7 ± 20.7++
Zinc and ring finger 2ZNRF2
Additional proteins associated to autophagosomal clusters
    CAP, adenylate cyclase-associated protein 1CAP1SRV250.4 ± 11.142.4 ± 10.4++
    Vacuolar protein sorting 35 homologVPS35VPS3512.4 ± 3.236.3 ± 21.1++
  • a As measured by the alkaline phosphatase (ALP) activity assay. The values represent triplicates, and the standard deviations are indicated. The numbers marked in bold type indicate significant changes in the value obtained by ALP assay compared with randomly chosen control KO strains (p < 0.05, one-way analysis of variance).

  • b Nitrogen starvation (3 h).

  • c Rapamycin treatment (0.5 μg/ml; 3 h).

  • d Proteins previously described in autophagosomes are referenced.

  • e Identified in one (+) or two (++) eGFP-IPs of cells treated with HBSS or rapamycin in addition to concanamycin A.

  • f Knockout strain not viable.

  • g Autophagy-related proteins but so far not linked to the autophagosome are referenced.

  • h Rat ortholog.