Supporting Information Park et al. 10.1073/pnas.1300460110 SI Materials and Methods using a cetyltrimethylammonium bromide-based miniscale pro- Molecular Biology. The cDNA of AP-1 μ-adaptin 2 (AP1M2)was tocol as reported previously (6). For seedling observation, seeds obtained from the RIKEN Plant Science Center and isolated by were germinated on solid medium [2.15 g/L MS salts, 1 g/L MES, PCR using primers AP1M2-forward (F) and AP1M2-reverse (R). 1% (wt/vol) sucrose (pH 5.6)] in the same growth condition as Internal tags [myelocytomatosis viral oncogene homolog (myc) or described above. Segregation of antibiotics resistance was counted 3×HA (hemagglutinin)] were introduced by a PCR approach us- on PPT-supplemented (15 mg/L) and/or KAN-supplemented ing the primers shown in Table S3. Each tagging site is shown in (30 mg/L) medium. Fig. S1. AP1M2 with internal myc (AP1M2:myc) was ligated to the binary vector (XbaI/blunt end) pCsV1300 with cassava vein mosaic Transient Expression and in Vivo Targeting of Reporter Cargo Proteins. virus promoter (pCsVMV) to generate pCsVMV::AP1M2:myc.For Plasmid DNA was introduced into protoplasts from leaf tissues by × the polyethylene glycol-mediated transformation method as de- AP1M2pro:::AP1M2:3 HA::AP1M23UTR, a binary plasmid contain- fi ing AP1M2 cis-regulatory sequences was generated as follows: scribed previously (7). The expression and traf cking of GFP- a genomic fragment corresponding to the 3′ UTR region of fused cargoes, vacuolar sorting receptor (VSR)1:HA (8), and fi HA:δ-adaptin (1) were examined by Western blot analysis or At1g60780 (approximately 0.3 kb) was PCR-ampli ed and fl subcloned into the pGreenIIBASTA plasmid (EcoRV/PstI). by confocal uorescence microscopy at different time points. Next, a genomic fragment including the promoter and 5′ UTR fi Western Blot Analysis and Coimmunoprecipitation. For immunoblot of At1g60780 (approximately 1.5 kb) was PCR-ampli ed and analysis, protein extracts were prepared with lysis buffer [50 mM Tris further subcloned into the pGreenIIBASTA::AP1M23UTR plasmid fi × (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100] supple- (Acc65I/XhoI). PCR-ampli ed AP1M2:3 HA was inserted into mented with an EDTA-free protease inhibitors mixture (Roche the pGreenIIBASTA::AP1M2pro::AP1M23UTR plasmid (XhoI/ × Diagnostics). Antibodies of anti-GFP (rabbit; 1:1,000; Clontech), EcoRV). For 35S::AP1M1:3 myc,aAP1M1 genomic fragment anti-binding protein (BiP) (rabbit; 1:3,000) (8), anti-tubulin (mouse; was isolated from the Arabidopsis thaliana genome and followed 1:5,000; Sigma-Aldrich), anti-myc (1:1,000; Cell Signaling), anti– by insertion of the three times repeated myc epitope (BamH1) γ-adaptin (rabbit; 1:1,000), anti–α-adaptin (rabbit; 1:1,000) (9), or (F. El Kasmi, M. Werner, and G.J., Entwicklungsgenetik, ZMBP, –γ γ × anti -subunit of coatmer complex ( COP) (rabbit; 1:2,000; University of Tübingen, Tübingen, Germany). AP1M1:3 myc was Agrisera), anti-VSR (rabbit, 1:1,000) (8), anti-actin (MP Bio- subclonedintothe35Sexpressionvector(SmaI/XbaI).ForGST: medicals), and peroxidase (POD)-conjugated anti-HA (1:1,000, α α -adaptin, HA: -adaptin (1) was blunted after digestion with Acc65I Roche Diagnostics) were used to detect the indicated proteins. and further ligated to the SmaI-cleaved pGEX-5X-3 plasmid POD-conjugated secondary antibodies (1:7,000, Sigma-Aldrich) γ γ fi (GE Healthcare). For GST: -adaptin, -adaptin was ampli ed by were used in all immunoblot analyses. Membranes were devel- γ γ PCR using primers -F and -R and ligated to the pGEX-5X-1 oped using a chemiluminescence detection system (Fusion Fx7 (EcoRI/XhoI; GE Healthcare). For maltose-binding protein Imager; PEQlab) or an LAS3000 image capture system (Fujifilm). fi (MBP):AP1M2, AP1M2 was PCR-ampli ed using primers AP1M2- For coimmunoprecipitation experiments, protein extracts from F2andAP2M2-R2andligatedtopMAL-c2X(BamHI/XbaI).For protoplasts were prepared in immunoprecipitation buffer [20 mM the list of primers used, see Table S3. Hepes (pH 7.5), 125 mM potassium acetate, 2.5 mM magnesium acetate Mg(OAc)2,1mMEDTA,1mMEGTA,1mMDTT,0.1% Plant Material, Growth Condition, and Transformation. Arabidopsis — — Triton X-100, 0.1% NP-20, 1 mM protease inhibitor mixture]. thaliana ecotype Columbia (Col) or Wassilewskija (Ws) plants Protein extract was incubated with anti-myc (Cell signaling tech- were grown on soil or on Murashige and Skoog (MS) plates at 23 °C nology) or anti-T7 (Novagen) antibody at 4 °C for 3 h and followed in continuous light. For protoplast preparation, Arabidopsis thali- by incubation with protein A–agarose beads (Repligen) for 1 h, ana plants were grown on MS plates for 3 wk at 23 °C under long- except for the experiment shown in Fig. S6C, in which protein day condition. Wild-type (WT) or heterozygous plants of either G–agarose was used instead. The beads were washed three times with ap1m2-1 [resistant to both kanamycin (KAN) and phosphino- immunoprecipitation buffer and subjected to Western blot analysis. thricin (PPT); purchased from the Versailles Arabidopsis Stock Center] and or hap13 (resistant to phosphinothricin) (2) were Cell Fractionation. Total protein was extracted from WT (Ws) and transformed with Agrobacterium tumefaciens, using the floral-dip ap1m2-1 mutant seedlings, using a fractionation buffer [20 mM method (3). GFP:ARA7 (4) and PIN-FORMED 2 (PIN2):GFP Hepes (pH 7.5), 125 mM potassium acetate, 2.5 mM Mg(OAc)2, (5) transgenic plants were crossed with AP1M2::AP1M2:3×HA 125mMsucrose,1mMEDTA,1mMEGTA,1mMDTT,1mM transgenic plants or heterozygous plants of ap1m2-1. protease inhibitor mixture]. After discarding cell debris, the super- natant (approximately 15 mg) was ultracentrifuged at 195,000 × g Genetic Analysis. T1 plants grown on soil from bulk-harvested for 1 h at 4 °C. Resulting soluble (supernatant) and membrane seeds were selected for transformants either with a 1:1,000 diluted fractions were subjected to immunoblot analysis. BASTA (183 g/L glufosinate; AgrEvo) or with hygromycin (20 mg/L; Duchefa). Selected resistant plants were genotyped. Pull-Down Assay. Recombinant proteins GST:γ-adaptin and MBP: PCR genotyping was as follows: for ap1m2-1, FLAG-LB4 and RP AP1M2 were purified from BL21(DE3) bacterial cells, using for a T-DNA insertion, amplifying a 0.7-kb fragment, and LP glutathione–agarose beads (Thermo Scientific) and amylase resin and RP for an endogenous AP1M2;forhap13,LB1aand (New England Biolabs), respectively, and further incubated with RP-h13 for a T-DNA insertion, amplifying a 0.9-kb fragment, protein extracts from seedlings, using pull-down buffer [20 mM ×- and LP and RP-h13 for an endogenous AP1M2;forAP1M2:3 Hepes (pH 7.5), 125 mM potassium acetate, 2.5 mM Mg(OAc)2, HA, primers HAs and M2-as, which amplify a 1-kb fragment; for 1 mM EDTA, 1 mM EGTA, 0.1% Triton X-100, 0.1% NP-20, AP1M2:myc, primers mycs and M2-as, which amplify a 0.8-kb 1 mM PMSF, protease mixture]. The beads were washed three fragment; and for AP1M1:3×myc, primers mycs and M1-as, times with the same volume of pull-down buffer and subjected to which amplify a 0.8-kb fragment. Genomic DNA was isolated immunoblot analysis. Park et al. www.pnas.org/cgi/content/short/1300460110 1of11 Semiquantitative RT-PCR Analysis of Transcripts. To determine the EtOH; Invitrogen) or 20 μM wortmannin (20 mM stock solution transcript level in the mutant plants, total RNA was isolated from in DMSO) for 1 h, followed by fixation or immediate observa- the 7-d-old seedlings grown on plates using an RNeasy Mini Kit tion. For FM4-64, 2 μM FM4-64 was added to 5-d-old seedlings (Qiagen). Total RNA (2 μg) was reverse-transcribed using (4 mM stock solution in H2O; Invitrogen). For simultaneous SuperScript II (Invitrogen) with random primers mixed with oligo treatment with BFA and FM4-64, BFA was followed by addition (dT) primers. Equal amount of cDNA was used for PCR with of FM4-64. For BFA washout, BFA-treated seedlings for 1 h gene specific primers listed in Table S3. PCR products were an- were transferred to new liquid medium and fixed 30 min after the alyzed by ethidium bromide staining. transfer. For concanamycin A (ConcA) treatment, protoplasts Anti–γ-Adaptin Antibody Generation. To generate anti–γ-adaptin isolated from WT seedlings were treated at indicated concen- antibody, the full-length γ-adaptin was expressed as a fusion trations (1 mM stock solution in DMSO, Invitrogen). For cy- protein with MBP using the pMAL-c2 vector (New England cloheximide (CHX) treatment, 50 μM CHX was added to Biolabs). Recombinant MBP:γ-adaptin was expressed in E. coli seedlings for 1 h (50 mM stock solution in H2O; Sigma-Aldrich). BL21(DE3) strain and purified using amylose resin (New England Biolabs). MBP:γ-adaptin was used to immunize rabbits and anti- Ultrastructure Analysis. Root tips of 5-d-old seedlings were high- body was affinity-purified using recombinant proteins. To con- pressure-frozen in 1-hexadecene (Merck Sharp and Dohme) firm the specificity of the anti–γ-adaptin antibody, protein extracts using a Bal-Tec HPM 010 high-pressure freezer (Balzers). Frozen from protoplasts transformed with HA:γ-adaptin were used in samples were freeze-substituted in acetone containing 2.5% (wt/ Western blot analysis (1). vol) osmium tetroxide (2 d at −90 °C, 6 h at −60 °C, 6 h at −30 °C, and 1 h at 0 °C) and finally embedded in epoxy resin (Roth). Immunohistochemistry. Immunostaining of root tissues was per- Ultrathin sections were stained with 2% (wt/vol) uranyl acetate in formed as reported previously (10).