Table 1.

Phosphatase genes identified as putative regulators of autophagy

Symbol Family Gene full name ID Score 
Screen 1     
ACP6 AP Acid phosphatase 6, lysophosphatidic 51205 3.47 
PTPRH PTP Protein tyrosine phosphatase, receptor type, H 5794 3.47 
PPAPDC1A Other LP Phosphatidic acid phosphatase type 2 domain-containing 1A 196051 3.33 
ENTPD3 NP Ectonucleoside triphosphate diphosphohydrolase 3 956 3.30 
G6PC3 CP Glucose 6 phosphatase, catalytic, 3 92579 3.30 
ACP5 AP Acid phosphatase 5, tartrate resistant 54 3.13 
DUSP21 DUSP Dual-specificity phosphatase 21 63904 3.08 
KIAA1524 PPP-M CIP2A 57650 3.05 
HINT2 NP Histidine triad nucleotide binding protein 2 84681 2.97 
PPP1R14A PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 14A 94274 2.97 
PTPN18 PTP Protein tyrosine phosphatase, nonreceptor type 18 (brain derived) 26469 2.97 
PTPN3 PTP Protein tyrosine phosphatase, nonreceptor type 3 5774 2.97 
MTMR14 PIP Myotubularin-related protein 14, Jumpy, FLJ22405 64419 2.88 
LPPR2 Other LP Lipid phosphate phosphatase-related protein type 2 64748 2.88 
PIP3AP PIP Phosphatidylinositol-3-phosphate–associated protein; PIP3AP 378766 2.88 
SSH3 DUSP Slingshot homologue 3 (Drosophila melanogaster) 54961 2.88 
DUSP16 DUSP Dual-specificity phosphatase 16 80824 2.80 
NUDT10 PP Nudix (nucleoside diphosphate–linked moiety X)-type motif 10 170685 2.80 
NUDT11 PP Nudix (nucleoside diphosphate–linked moiety X)-type motif 11 55190 2.80 
PPP1CA PPP Protein phosphatase 1, catalytic subunit, α isoform 5499 2.80 
PPP1R1B PPP Protein phosphatase 1, regulatory (inhibitor) subunit 1B; DARPP-32 84152 2.80 
PPP1R3F PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 3F 89801 2.80 
ANP32C Other M Acidic (leucine rich) nuclear phosphoprotein 32 family, member C 23520 2.72 
CHP Other M Calcium binding protein P22 11261 2.72 
DUSP9 DUSP Dual-specificity phosphatase 9 1852 2.72 
PPM1J PPP Protein phosphatase, Mg2+/Mn2+ dependent, 1J 333926 2.72 
PPP1R16B PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 26051 2.72 
PTPRN PTP Protein tyrosine phosphatase, receptor type, N 5798 2.72 
CHTF18 NP Chromosome transmission fidelity factor 18 homologue 63922 2.63 
DUSP4 DUSP Dual-specificity phosphatase 4 1846 2.63 
NT5C2 NP 5-Nucleotidase, cytosolic II 22978 2.63 
PPP1R14B PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 14B 26472 2.63 
PPP1R1A PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 1A 5502 2.63 
PPP3R1 PPP-M Protein phosphatase 3, regulatory subunit B, α 5534 2.63 
SGPP1 Other P Sphingosine-1-phosphate phosphatase 1 81537 2.63 
ACPP AP Acid phosphatase, prostate 55 2.55 
ATP6V0E2 Other P ATPase, H+ transporting V0 subunit e2 155066 2.55 
PTPN20B PTP Protein tyrosine phosphatase, nonreceptor type 20B 26095 2.55 
ILKAP PPP Integrin-linked kinase–associated serine/threonine phosphatase 2C 67444 2.55 
PALD Other P Paladin; KIAA1274 27143 2.55 
PPP3CB PPP Protein phosphatase 3, catalytic subunit, β isozyme 19056 2.55 
PPP3R2 PPP-M Protein phosphatase 3, regulatory subunit B, β 5535 2.55 
PPP2R3B PPP-M Protein phosphatase 2, regulatory subunit B, β 28227 2.55 
ALPP AlkP Alkaline phosphatase, placental 250 2.47 
DUSP14 DUSP Dual-specificity phosphatase 14 11072 2.47 
DUSP2 DUSP Dual-specificity phosphatase 2 1844 2.47 
DUSP22 DUSP Dual-specificity phosphatase 22 56940 2.47 
G6PC CP Glucose-6-phosphatase, catalytic subunit 2538 2.47 
PHACTR4 PPP-M Phosphatase and actin regulator 4 65979 2.47 
PPM1A PPP Protein phosphatase, Mg2+/Mn2+ dependent, 1A 5494 2.47 
PPP1R14D PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 14D 54866 2.47 
TPTE2 PIP Transmembrane phosphoinositide 3-phosphatase and tensin homologue 2 93492 2.47 
ATP6V0E Other P ATPase, H+ transporting, lysosomal 9 kD, V0 subunit e1 8992 2.38 
CDC14A DUSP CDC14 cell division cycle 14 homologue A (Saccharomyces cerevisiae) 8556 2.38 
NAP1L2 Other Nucleosome assembly protein 1–like 2 4674 2.38 
OCRL Other Oculocerebrorenal syndrome of Lowe 4952 2.38 
PFKFB1 CP 6-Phosphofructo-2-kinase/fructose-2, 6-biphosphatase 1 5207 2.38 
PPP4R1 PPP-M Serine/threonine protein phosphatase 4 regulatory subunit 1 9989 2.30 
G6PC2 CP Glucose-6-phosphatase, catalytic, 2 57818 2.22 
NUDT14 PP Nudix (nucleoside diphosphate–linked moiety X)-type motif 14 256281 2.22 
PNKP NP Polynucleotide kinase 3-phosphatase 11284 2.22 
Screen 2     
PPP2R1A PPP-M Protein phosphatase 2, regulatory subunit A, α 5518 2.50 
PPM1G PPP Protein phosphatase, Mg2+/Mn2+ dependent, 1G 5496 2.50 
PPP1R12A PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 12A 4659 2.50 
PPP1R3A PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 3A 5506 3.00 
PPP2R3A PPP-M Protein phosphatase 2, regulatory subunit B, α 5523 3.00 
PTPRJ PTP Protein tyrosine phosphatase, receptor type, J 5795 3.00 
MTM1 PIP Myotubularin 1 4534 3.00 
ANP32B Other M Acidic (leucine rich) nuclear phosphoprotein 32 family, member B 10541 3.00 
DUSP5 DUSP Dual-specificity phosphatase 5 1847 3.25 
MTMR6 PIP Myotubularin-related protein 6 9107 3.25 
PPP1CC PPP Protein phosphatase 1, catalytic subunit, γ isoform 5501 3.25 
PTPRE PTP Protein tyrosine phosphatase, receptor type, E 5791 3.25 
PTEN PIP Phosphatase and tensin homologue 5728 3.25 
G6PC2 CP Glucose-6-phosphatase, catalytic, 2 57818 3.33 
CTDSP1 Other P CTD (C-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1 58190 3.33 
PSPH PPP Phosphoserine phosphatase 5723 3.33 
SGPP2 Other LP Sphingosine-1-phosphate phosphatase 2 130367 3.50 
Symbol Family Gene full name ID Score 
Screen 1     
ACP6 AP Acid phosphatase 6, lysophosphatidic 51205 3.47 
PTPRH PTP Protein tyrosine phosphatase, receptor type, H 5794 3.47 
PPAPDC1A Other LP Phosphatidic acid phosphatase type 2 domain-containing 1A 196051 3.33 
ENTPD3 NP Ectonucleoside triphosphate diphosphohydrolase 3 956 3.30 
G6PC3 CP Glucose 6 phosphatase, catalytic, 3 92579 3.30 
ACP5 AP Acid phosphatase 5, tartrate resistant 54 3.13 
DUSP21 DUSP Dual-specificity phosphatase 21 63904 3.08 
KIAA1524 PPP-M CIP2A 57650 3.05 
HINT2 NP Histidine triad nucleotide binding protein 2 84681 2.97 
PPP1R14A PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 14A 94274 2.97 
PTPN18 PTP Protein tyrosine phosphatase, nonreceptor type 18 (brain derived) 26469 2.97 
PTPN3 PTP Protein tyrosine phosphatase, nonreceptor type 3 5774 2.97 
MTMR14 PIP Myotubularin-related protein 14, Jumpy, FLJ22405 64419 2.88 
LPPR2 Other LP Lipid phosphate phosphatase-related protein type 2 64748 2.88 
PIP3AP PIP Phosphatidylinositol-3-phosphate–associated protein; PIP3AP 378766 2.88 
SSH3 DUSP Slingshot homologue 3 (Drosophila melanogaster) 54961 2.88 
DUSP16 DUSP Dual-specificity phosphatase 16 80824 2.80 
NUDT10 PP Nudix (nucleoside diphosphate–linked moiety X)-type motif 10 170685 2.80 
NUDT11 PP Nudix (nucleoside diphosphate–linked moiety X)-type motif 11 55190 2.80 
PPP1CA PPP Protein phosphatase 1, catalytic subunit, α isoform 5499 2.80 
PPP1R1B PPP Protein phosphatase 1, regulatory (inhibitor) subunit 1B; DARPP-32 84152 2.80 
PPP1R3F PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 3F 89801 2.80 
ANP32C Other M Acidic (leucine rich) nuclear phosphoprotein 32 family, member C 23520 2.72 
CHP Other M Calcium binding protein P22 11261 2.72 
DUSP9 DUSP Dual-specificity phosphatase 9 1852 2.72 
PPM1J PPP Protein phosphatase, Mg2+/Mn2+ dependent, 1J 333926 2.72 
PPP1R16B PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 26051 2.72 
PTPRN PTP Protein tyrosine phosphatase, receptor type, N 5798 2.72 
CHTF18 NP Chromosome transmission fidelity factor 18 homologue 63922 2.63 
DUSP4 DUSP Dual-specificity phosphatase 4 1846 2.63 
NT5C2 NP 5-Nucleotidase, cytosolic II 22978 2.63 
PPP1R14B PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 14B 26472 2.63 
PPP1R1A PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 1A 5502 2.63 
PPP3R1 PPP-M Protein phosphatase 3, regulatory subunit B, α 5534 2.63 
SGPP1 Other P Sphingosine-1-phosphate phosphatase 1 81537 2.63 
ACPP AP Acid phosphatase, prostate 55 2.55 
ATP6V0E2 Other P ATPase, H+ transporting V0 subunit e2 155066 2.55 
PTPN20B PTP Protein tyrosine phosphatase, nonreceptor type 20B 26095 2.55 
ILKAP PPP Integrin-linked kinase–associated serine/threonine phosphatase 2C 67444 2.55 
PALD Other P Paladin; KIAA1274 27143 2.55 
PPP3CB PPP Protein phosphatase 3, catalytic subunit, β isozyme 19056 2.55 
PPP3R2 PPP-M Protein phosphatase 3, regulatory subunit B, β 5535 2.55 
PPP2R3B PPP-M Protein phosphatase 2, regulatory subunit B, β 28227 2.55 
ALPP AlkP Alkaline phosphatase, placental 250 2.47 
DUSP14 DUSP Dual-specificity phosphatase 14 11072 2.47 
DUSP2 DUSP Dual-specificity phosphatase 2 1844 2.47 
DUSP22 DUSP Dual-specificity phosphatase 22 56940 2.47 
G6PC CP Glucose-6-phosphatase, catalytic subunit 2538 2.47 
PHACTR4 PPP-M Phosphatase and actin regulator 4 65979 2.47 
PPM1A PPP Protein phosphatase, Mg2+/Mn2+ dependent, 1A 5494 2.47 
PPP1R14D PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 14D 54866 2.47 
TPTE2 PIP Transmembrane phosphoinositide 3-phosphatase and tensin homologue 2 93492 2.47 
ATP6V0E Other P ATPase, H+ transporting, lysosomal 9 kD, V0 subunit e1 8992 2.38 
CDC14A DUSP CDC14 cell division cycle 14 homologue A (Saccharomyces cerevisiae) 8556 2.38 
NAP1L2 Other Nucleosome assembly protein 1–like 2 4674 2.38 
OCRL Other Oculocerebrorenal syndrome of Lowe 4952 2.38 
PFKFB1 CP 6-Phosphofructo-2-kinase/fructose-2, 6-biphosphatase 1 5207 2.38 
PPP4R1 PPP-M Serine/threonine protein phosphatase 4 regulatory subunit 1 9989 2.30 
G6PC2 CP Glucose-6-phosphatase, catalytic, 2 57818 2.22 
NUDT14 PP Nudix (nucleoside diphosphate–linked moiety X)-type motif 14 256281 2.22 
PNKP NP Polynucleotide kinase 3-phosphatase 11284 2.22 
Screen 2     
PPP2R1A PPP-M Protein phosphatase 2, regulatory subunit A, α 5518 2.50 
PPM1G PPP Protein phosphatase, Mg2+/Mn2+ dependent, 1G 5496 2.50 
PPP1R12A PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 12A 4659 2.50 
PPP1R3A PPP-M Protein phosphatase 1, regulatory (inhibitor) subunit 3A 5506 3.00 
PPP2R3A PPP-M Protein phosphatase 2, regulatory subunit B, α 5523 3.00 
PTPRJ PTP Protein tyrosine phosphatase, receptor type, J 5795 3.00 
MTM1 PIP Myotubularin 1 4534 3.00 
ANP32B Other M Acidic (leucine rich) nuclear phosphoprotein 32 family, member B 10541 3.00 
DUSP5 DUSP Dual-specificity phosphatase 5 1847 3.25 
MTMR6 PIP Myotubularin-related protein 6 9107 3.25 
PPP1CC PPP Protein phosphatase 1, catalytic subunit, γ isoform 5501 3.25 
PTPRE PTP Protein tyrosine phosphatase, receptor type, E 5791 3.25 
PTEN PIP Phosphatase and tensin homologue 5728 3.25 
G6PC2 CP Glucose-6-phosphatase, catalytic, 2 57818 3.33 
CTDSP1 Other P CTD (C-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1 58190 3.33 
PSPH PPP Phosphoserine phosphatase 5723 3.33 
SGPP2 Other LP Sphingosine-1-phosphate phosphatase 2 130367 3.50 

MCF7-EGFP-LC3 breast carcinoma cells were transfected with a human phosphatome siRNA library targeting 318 genes. After 56 h in normal culture conditions (screen 1) or after treatment for additional 3 h with siramesine (screen 2), the cells were scored for EGFP-LC3 puncta accumulation on the scale from 0 to 5, where control siRNA scored 1 and siramesine scored 5 (Fig. S1). The candidates were requested to reach a score ≥2 in screen 1 and a score ≤4 in screen 2 with a minimum of 2/3 siRNAs in three independent screens. The score values represent means of three independent screens performed with two independent siRNAs. P < 0.0001 in all cases when compared to control siRNA (screen 1) or siramesine (screen 2). AlkP, alkaline phosphatase; AP, acid phosphatase; CP, carbohydrate phosphatase; DUSP, dual-specificity phosphatase; LP, lipid phosphatase; M, modulator; NP, nucleotide phosphatase; P, phosphatase; PIP, phosphatidylinositol phosphatase; PPP, phosphoprotein phosphatase; PTP, phosphotyrosine phosphatase.

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