Supplemental Data. Furlan et al. Plant Cell (2017) /tpc
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1 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc..00.
2 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc..00.
3 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc..00. Supplemental Figure. PUB displays autoubiquitination activity in vitro. (A) In vitro autoubiquitination assay with MBP-PUB and the inactive W0A mutant using His-UBA and His-UBC. MPB-PUB was incubated with the indicated components for h, resolved by PAGE and analysed by immunoblot (IB) with the indicated anti-bodies. (B) In vitro autoubiquitination sites identified on PUB. MS spectra of peptides with a diglycine footprint found on GST-PUB after in vitro autoubiquitination assay using His-UBA and His-UBC.
4 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc Supplemental Figure. PUBprom:GFP-PUB complements the pub pub pub phenotype. (A) Primary root lengths seedlings measured seven days after transplanting onto media containing µm flg or DMSO as control. A homozygous T line carrying a single copy of the PUBprom:GFP-PUB construct in the pub pub pub background was used. Data shown as mean of three independent experiments +/- SD (n 0). Asterisk indicates significantly different values between wild-type and pub pub pub with p<0.0 (one way ANOVA, Tukey post hoc test). (B) PUB accumulation is induced by flg in the PUBprom:GFP-PUB/pub pub pub line. Protein expression was induced by flg (µm) treatment in two week-old seedlings carrying a PUBprom:GFP-PUB construct. Total protein samples were analysed by IB using anti-gfp. Coomassie brilliant blue (CBB) is shown as loading control.
5 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc Supplemental Figure. Post-translational modification of PUB and PUB. (A) Protein expression from experiments in Figure a. cmyc-nyfp-mpk or cmyc-nyfp- MPK were coexpressed with HA-cYFP-PUB W0A as indicated in Figure A. Total proteins were analysed by IB with anti-cmyc and anti-ha. Equal loading shown by coomassie brilliant blue (CBB). (B) PUB does not ubiquitinate MPK or MPK in vitro. In vitro ubiquitination assay with MBP-PUB and GST-MPK or GST-MPK using His-UBA and His-UBC and incubated for h. Proteins were analysed by IB with anti-gst, anti-ubiquitin and anti-pub. (C) PUB is also phosphorylated by MPK in vitro. Recombinant MBP-PUB or MBP- PUB were incubated alone or with activated MPK, MPK and MPK and separated by PAGE (MAPKs indicated by asterisk). Autophosphorylation and trans-phosphorylation were visualized with radioactive ATP and autoradiography. The artificial kinase substrate, myelin basic protein (MBP), was used to adjust equal MPK activities (right panel). The protein loading control is shown by CBB staining.
6 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc..00. Supplemental Figure. In vitro and in vivo phosphorylation sites of PUB.
7 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc..00. (A) LC-MS/MS analysis spectra of PUB phosphorylated tryptic peptides from in vitro phosphorylation assay with MPK. To obtain phosphorylated PUB, GST-PUB was incubated alone or with activated GST-MPK, GST-MPK and untagged MPK. (B) LC-MS/MS analysis spectra of PUB phosphorylated tryptic peptides from in vivo samples. UBQ0prom:GFP-PUB transgenic seedlings grown for days in liquid media were treated with µm flg or water (mock) and harvested after 0min. GFP-PUB was immune-purified resolved by PAGE and gel bands were analysed by LC-MS/MS. Phosphorylated peptides were not detected in the control samples.
8 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc..00. Supplemental Figure. Phylogenetic relations between Arabidopsis PUB proteins class II and III.
9 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc..00. Alignment was performed using MAFFT and manually edited and used for phylogenetic analysis using maximum likelihood with 000 random drawn samples (bootstraps). Bootstrap values greater than 0. are shown at the corresponding node. The phylogenetic tree was rooted using AtCHIP as outgroup. Highlighted are PUB proteins with a conserved threonine followed by proline at position (orange circle) and (red arrowhead). Scale bar denotes 0. amino acid substitutions per site. 0 Supplemental Figure. PUB stabilization is MPK dependent. Luc-PUB fusion was coexpressed with MPK or MPK in mpk protoplasts. Protein levels of YFP-MPK and YFP-MPK of experiments shown in Figure B. Proteins were analyzed by IB using anti-gfp.
10 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc Supplemental Figure. Transgenic lines express comparable levels of transcript of PUB WT and mutant variants. (A) Quantitative real-time PCR of selected T homozygous transgenic lines carrying UBQ0prom:GFP-PUB WT and variants W0A, T/A and T/E. Samples were taken from adult plants and PPA (ATG0) was used as a reference gene. Data shown as mean +/- SD (n=). (B) Analysis of the relative amounts of PUB and mutant variants (line A). The band intensity of PUB WT was determined, set to 00% and the relative amounts for the other lines were calculated. Data shown as mean +/- SEM of four independent experiments. Letters indicate significantly different values at p<0.0 (one way ANOVA, Tukey post hoc test). (C) Representative immunoblot showing accumulation of PUB WT and W0A, T/A and T/E variants in transgenic lines A used to calculate relative protein amounts in (B). 0
11 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc Supplemental Figure. PUB homo- and hetero-oligomerizes. (Supports Figure.) (A) Protein levels of split luciferase experiments shown in Figure F. N- and C-terminal fragments of luciferase fused to PUB U-box WT, TA, TW and TI variants were analyzed by IB with anti-luc. (B) Protein levels of split luciferase experiments shown in Figure G. N- and C-terminal fragments of luciferase fused to PUB U-box WT, W0A, IR and F0E variants were analyzed by IB with anti-luc. (C) Model of the PUB U-box dimer highlighting exchanged residues. Front protomer shown in cartoon style (turquoise) and back protomer shows electrostatic surface charges. (D) Protein levels of split luciferase experiments shown in Figure H. N- and C-terminal luciferase fusion proteins of PUB U-box coexpressed with MKK KR (inactive) or MKK DD (constitutive active) were analyzed by IB with anti-luc. Activation of MPK and MPK was confirmed using anti-erk/.
12 Supplemental Data. Furlan et al. Plant Cell (0) 0.0/tpc..00. Supplemental Tables Table : Primers for genotyping Gene Locus `-Forward-` `-Reverse-` PUB AtG0 ATGTCCATGGGGAAGGAATAG AATGCCCGTCGTGGATATC PUB AtG0 CAATCTTGGTGCACCCTAAAC TTTTCATCAGCAGGGATATGC PUB AtG0 GACGACGTCGTATCAAAGGAC TCGATTGAGGATTGATCGATC MPK AtG0 ATTTTTGTCAACAATGGCCTG TCTGCCTTTTCACGGAATATG Table : Primers used for SDM on PUB and PUB U-box in entry vectors Mutation `-Forward-` `-Reverse-` Type II enzyme F0E ATATATGAAGACGAGTTCC ATATATGAAGACGAACTC BpiI TTTGTCCAATCTCTCT GGAAGGAATCTCTATCT IR ATATATGAAGACCGAGTTT ATATATGAAGACGAAACT BpiI CCACCGGAATAAC CGCACCGGATCT W0A ATATATGAAGACGCGCTCT ATATATGAAGACAAGAG BpiI TTTCCGGTAAGA CGCCTTCTCGATG TI ATATATGAAGACATTCCAA ATATATGAAGACTTTGGA BpiI ACCACAC ATAAGATCAGTT TA ATATATGGTCTCGGCGCC ATATATGGTCTCGGCGC BsaI GAACCACACTCTTCGCC CAGATCAGTTTCGGTTAT G TE ATATATGGTCTCGAGCCC ATATATGGTCTCGGGCT BsaI AACCACACTCTTC CAAGATCAGTTTCG TA ATATATGAAGACAGCTCCA ATATATGAAGACTTGGAG BpiI TE AAACCTCCGATC ATATATGAAGACGAGCCC AAACCTCCGATCTG Table : Primers for cloning CTGGGATCCTCTC ATATATGAAGACTTGGG CTCTGGGATCCTCTCT BpiI Diagnostic none none HaeII none HaeII BanII none BanII Gene Plasmid `-Forward-` `-Reverse-` PUB Ubox pentrc GGCCATTUATGGATCAAGAGAT AGAGA GGTGATTUCTAGATGCGAAGA TGAC no stop PUB pmal CATGTCGACATGGATCAAGAGA TAGAGA CATCTGCAGTCAAGCAGGATA CGAAT PUB pmal CATGAATTCATGAATATATATAC CATCTGCAGTTAGATCTTTGGC GTACA Exo0B petb GAATTCGATGGCTGAAGCCGGT GACGA Table : qrt-pcr CCTTTG CTCGAGTCAACTTGAGCTTTCC TTGA Gene `-Forward-` `-Reverse-` PPA TAACGTGGCCAAAATGATGC GTTCTCCACAACCGCTTGGT PUB TGCAATTGGGAGTTGTAGCA GATTCCCTCCAAACCCTAGC 0
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