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1 DOI: 1.138/ncb1 Control Atg7 / NAC (mm) Control Atg7 / NAC (mm) Lamin B Gstm1 Figure S1 Neither the translocation of into the nucleus nor the induction of antioxidant proteins in autophagydeficient hepatocytes was suppressed by treatment with the antioxidant reagent Nacetylcysteine (NAC). Hepatocytes isolated from Atg7 F/F (control) and Atg7 F/F :Mx1 (Atg7 / ) mice at day post pipcinjection were treated with NAC (, 1 or 1 mm) for hr. cell lysates and nuclear fractions were prepared and subjected to immunoblot analysis with the antibodies indicated. Bands corresponding to endogenous,, Gstm1,,, and Lamin B are shown. The data represent three separate experiments Macmillan Publishers Limited. All rights reserved.

2 (kda) 1 3 MBPPull down assay MBP 1 MBP MBPM3 3 MBPM MBPM7 GSTDC MBP MBP MBP PB1 Zinc UBA MBP LRS MBP Amino acids MBP MBPM7 MBPM GSTDC MBPM3 37 Figure S Identification of the interg region in. The deletionmutation constructs of are illustrated in the left panel and the pulldown assay is shown in the right panel. MBP and its deletion mutants M3, M, and M7 conjugated with amylose resins were incubated with purified recombinant GSTDC. The pulleddown complexes were subjected to SDSPAGE and visualized by CBB staining. Bands corresponding to MBP, M3, M, M7, and GSTDC are indicated. 1 Macmillan Publishers Limited. All rights reserved.

3 a b IP: FLAG MBPPull down assay 1 MBPM83 MBPM8 3 MBPM8 (K3A) MBPM8 (E37A) MBPM8 (V38A) MBPM8 (D39A) 7 MBPM8 (P3A) 8 MBPM8 (S3A) 9 MBPM8 (T3A) 1 MBPM8 (G33A) 11 1 MBPM8 (E3A) MBPM8 (L3A) 13 MBPM8 (Q3A) MBPM8 (S37A) 1 MBPM8 (L38A) 1 FLAG 3 (P3A) (S3A) (T3A) GSTDC MBPM8 and its mutants MBPM83 (E3A) 7 (L3A) 8 (D39A) c d IP: FLAG GSTPull down assay 1 GST GSTDC (wt) 3 GSTDC (Y33A) GSTDC (S33A) GSTDC (R38A) GSTDC (N38A) GSTDC (R1A) GSTDC (R83A) GSTDC (S8A) 1 GSTDC (Q3A) 11 GSTDC (SA) 1 GSTDC (SA) 13 MBPM8 (3337) GSTDC and its mutants MBPM8 1 FLAG FLAG 3 FLAG (Y33A) FLAG (S33A) FLAG (R38A) FLAG (N38A) 7 FLAG (R1A) 8 FLAG (R83A) 9 FLAG (S8A) 1 FLAG (Q3A) 11 FLAG (SA) FLAG FLAG 1 FLAG (SA) Figure S3 The similar binding mode between and. (a) List of the pointmutation constructs of and the corresponding pulldown assay. The experiments were carried out as in Figure 1b. GST DC, MBPM8 and its point mutants, and MBPM83 are indicated. (b) Immunoprecipitation assays. Each FLAGtagged and mutant with the specified point mutation was expressed in Hek93T cells. The cell lysates were immunoprecipitated with antiflag antibody. The resulting immunoprecipitates were subjected to SDS PAGE and analyzed by immunoblotting with antiflag and anti antibodies. Bands corresponding to, endogenous, and are indicated. The data shown are representative of three separate experiments. (c) Pulldown assay with MBPM8 and GSTDC or the point mutants. Each GSTDC and mutant conjugated with glutathionesepharose B was incubated with purified recombinant MBPM8. The pulleddown complexes were subjected to SDS PAGE and visualized by CBB staining. GSTDC, its mutants, and MBPM8 are indicated. (d) Immunoprecipitation assays. Each FLAGtagged and point mutant listed was expressed in Hek93T cells. The cell lysates were immunoprecipitated with antiflag antibody. The resulting immunoprecipitates were subjected to SDSPAGE and analyzed by immunoblotting with antiflag and anti antibodies. The bands corresponding to FLAG, endogenous,, and are indicated. The data shown are representative of three independent experiments Macmillan Publishers Limited. All rights reserved.

4 IP: T3A Lactacystin Ubiquitinated IgG H.C. antiubiquitin anti endo. anti anti Figure S The overproduction of inhibits the ubiquitination of. FLAGtagged and the mutant defective in interg with ( T3A) were overproduced in wildtype primary mouse hepatocytes employing the adenovirus system. At 8 hr post infection, the cells were cultured in the absence (lanes 1, 3 and ) or presence (lanes, and ) of 1 µm lactacystin for hr. The cell lysates were immunoprecipitated with anti antibody, then subjected to SDSPAGE and analyzed by immunoblotting with anti and antiubiquitin antibodies. The bands corresponding to, ubiquitinated,, endogenous, and are shown. Three separate experiments were used to provide the data. 1 Macmillan Publishers Limited. All rights reserved.

5 a Relative luciferase activity c Endo. KIR K7AD9A w.t Lamin B KIR + ++ K7AD9A + ++ b Relative RNA 1 1 deltakir K7AD9A Gstm1 deltakir K7AD9A Cypa deltakir K7AD9A Figure S The competitive activity of oligomerizationdefective mutant K7AD9A against. (a) Luciferase assay. The expression plasmids for,, and wildtype, KIR, or K7AD9A were transfected into Hepa1 cells along with pare reporter plasmid and prltk as an internal control. At 3 hr after transfection, the luciferase activity was measured according to the manufacturer s instructions. Assays were performed twice in triplicate. (b) Quantitation of the mrna levels of the detoxification enzymes, Gstm1 and Cypa in hepatocytes overexpressing, KIR, and K7AD9A. RNAs were prepared from noninfected or infected hepatocytes and reverse transcribed into their respective cdnas, which were used as templates in realtime PCR analyses. The values were normalized to the amount of each mrna in the noninfected hepatocytes. Note that targets were greatly induced upon overexpression of the mutant though less efficient than wildtype. The experiments were performed three times. (c) Immunoblot analysis. FLAGtagged, KIR, and K7AD9A were overproduced in wildtype primary mouse hepatocytes by the adenovirus system. At 8 hr after infection, total cell lysates and nuclear fractions were prepared and subjected to immunoblot analysis with the antibodies specified. The bands corresponding to, endogenous,,,, and Lamin B are shown. The data are representative of three independent experiments. 1 Macmillan Publishers Limited. All rights reserved.

6 a b KIR T3A E3A KIR T3A E3A Endo. 3. * Level of. Lamin B Exp. 1 Exp. Relative intensity KIR T3A E3A Endo. KIR T3A E3A KIR T3A E3A Relative intensity ** Level of nuclear. Lamin B Exp. 3 Exp.. KIR T3A E3A Figure S Stabilization of and the transcriptional activation via. (a) Immunoblot analysis. FLAGtagged and its mutants defective in interg with were overproduced in wildtype primary mouse hepatocytes by the adenovirus system. At 8 hr after infection, total cell lysates and nuclear fractions were prepared and subjected to immunoblot analysis with the antibodies specified. The bands corresponding to, endogenous,,,,, and Lamin B are shown. Representative data from four independent immunoblot analyses are shown. (b) Quantitative densitometry of immunoblotting data in (a) was performed and the ratios between and and nuclear and Lamin B, respectively were plotted; *P<., **P< Macmillan Publishers Limited. All rights reserved.

7 a F/F b F/F:Mx1: / c F/F:Mx1: / d F/F:Mx1: / e F/F:Mx1: / Figure S7 Electron microscopic analysis. (ae) Electron micrographs of Atg7 F/F (control) (a) and Atg7deficient (F/F:Mx1: / ) (be) livers. The boxed regions in figures b and d are enlarged and shown as figures c and e, respectively. Note that the glycogen area (asterisks) that is easily detected in control liver is occupied by abundant smooth ER and that numerous peroxisomes (some are indicated by arrows in c and d) are accumulated in the peripheral area. Figures d and e show a typical inclusion body that is observed in Atg7deficient livers. Bars: a and b, µm; c and d, 1 µm; e,. µm Macmillan Publishers Limited. All rights reserved.

8 a F/F / F/F:Mx1 F/F:Mx1: / (kda) b *** *** Gstm1 38 Gstm1/Cytoplasmic proteins (%) F/F / F/F:Mx1 F/F:Mx1: / Figure S8 Glutathione Stransferase m1 is most remarkable cytosolic protein in autophagydeficient livers. (a) The cytosolic fraction (1 µg) prepared from indicated genotype mouse livers were analysed by SDSPAGE followed by CBB staining. A kdaprotein whose amount was markedly increased in Atg7deficient livers and repressed by additional loss of was trypsinized and subsequently analysed by mass spectrometry. As the result, the protein was specified as glutathione Stransferase m1 (Gstm1). (b) The occupancy of Gstm1 in the cytosolic proteins estimated by intensity of CBB stain. Data are displayed as mean ± SD values of 3 independent experiments. ***P<.1 (Student s ttest) Macmillan Publishers Limited. All rights reserved.

9 a endo. wildtype hepatocytes Soluble Insoluble c Absorbance wildtype hepatocytes.1 Atg7double knockout hepatocytes Soluble Insoluble Absorbance Atg7double knockout hepatocytes b wildtype hepatocytes Relative RNA Gstm Cypa Atg7double knockout hepatocytes Relative RNA 3 1 Gstm Cypa Figure S9 The effect of exogenous expression of on the cell viability in wildtype and Atg7double knockout (DKO) hepatocytes. (a) Immunoblot analyses of exogenously expressed. Hepatocytes isolated from wildtype or Atg7 F/F :Mx1: / mice at day post pipc injection were infected by adenovirus or adenovirus. At 7 hr after infection, each hepatocytes were separated into detergent (.% Tx1)soluble (Soluble) and insoluble (Insoluble) fractions. Each of total, soluble, and insoluble fractions was subjected to SDSPAGE and analyzed by immunoblotting with antibodies against,, and. The bands corresponding to endogenous,,, and are indicated. Note enough expression of exogenous in both genotype hepatocytes. (b) Quantitation of mrna levels of targets in overexpressedhepatocytes by RTPCR. RNAs were prepared from noninfected hepatocytes or the hepatocytes infected as shown in (a) and then each RNA was conducted to cdna synthesis followed by realtime PCR analyses. The values are normalized to the amount of each mrna in noninfected hepatocytes. (c) Viability of overexpressed hepatocytes. Viability of the hepatocytes infected as shown in (a) was measured using Cell Counting Kit8 according to the manufacturer s protocol (Dojindo Laboratories, Inc., Kumamoto, Japan). Note that exogenous expression of showed statistically insignificant effect on the viability of both genotypes (i.e., wildtype and Atg7 DKO) hepatocytes under at least present experimental conditions Macmillan Publishers Limited. All rights reserved.

10 HS Degradation in the S Proteasome SH HS SH HS HS DLG Motif (Latch) Ub Ub LxxQ DIDLG Ub Ub Ub Classical Regulation E TGE ED SH SH Electrophilic/ Oxidative Stress ETGE Motif (Hinge) Regulation Repressed Autophagy or Increased Induction of Autophagy Cytoplasm HS HS DLG ETGE SH SH Electrophile S S Electrophile Electrophile Electrophile S S ETGE S S Electrophile Electrophile Transcription of Cytoprotective Genes Maf ARE DLG M Komatsu et al., Supplementary Figure S1 Figure S1 Schematic representation of the pathway. Canonical pathway (left). Novel regulation of the pathway by (right). Note that the present study provides evidence that the hinge and latch mechanism actually operates in vivo Macmillan Publishers Limited. All rights reserved.

11 11 Fig.1a Fig.1e Fig.3b Fig.a Fig.b Fig.a Fig.a Fig.1d IP Flag Flag IP IP IP Flag Fig.3d Lamin B LC3 LC3 Gstm1 Lamine B Figure S11 Uncropped image blots. 1 Macmillan Publishers Limited. All rights reserved.

12 Supplementary table 1. Data collection and refinement statistic of DCKIR complex DCKIR Data collection Space group P 1 Cell dimensions a=b, c (Å), γ ( ) 1.9,.7, 1 Wavelength (Å) 1. Resolution (Å).8(.9.8)* R sym.1(.37) I/σ(I) 19.3(.1) Completeness (%) 1(1) Redundancy.1(.) Refinement Resolution (Å).8 No. reflections 8 R work /R free.178/.3 No. protein residues 9 No. peptide residues 8 No. sulfate ion 9 No. water 37 R.m.s. deviations Bond lengths (Å). Bond angles ( ) 1. Ramachandran plot statistics Most favored 8.% Additional allowed.8% Generously allowed.8% Disallowed regions.% *Highest resolution shell is shown in parenthesis 1 Macmillan Publishers Limited. All rights reserved.

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