Key resources table.
| Reagent type or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain (Saccharomyces cerevisiae) |
Wild-type strains (BY4741; BY4742; SEY6210; SUB62; W303-1B) |
Other | See additional information |
Provided by Daniel Finley (Harvard Medical School), Audrey P. Gasch (University of Wisconsin) and Mark Hochstrasser (Yale University); allS. cerevisiae strains are listed in Supplementary file 1-Table S1 |
| Strain (Arabidopsis
thaliana) |
Wild type ecotype Columbia-0 (Col-0) |
Arabidopsis Biological Resource Center (ABRC) |
CS60000 | N/A |
| Genetic reagent (S. cerevisiae) |
Yeast GFP clone collection strains (PRE10-GFP; RPN5-GFP; BLM10-GFP) |
Thermo Fisher Scientific; PMID 14562095 |
See additional information |
All S. cerevisiae strains are listed in Supplementary file 1-Table S1 |
| Genetic reagent (S. cerevisiae) |
Yeast gene knockout collection strains (multiple) |
GE Healthcare; PMID 10436161 |
See additional information |
All S. cerevisiae strains are listed in Supplementary file 1-Table S1 |
| Genetic reagent (S. cerevisiae) |
GFP-ATG8; GFP-APE1;OM45-GFP; PEX14-GFP;RPL25-GFP |
PMID 15138258; PMID 25042851 |
YTS187; KL095; KL099; KL282; KL285 |
Provided by Stefan Jentsch (Max Planck Institut für Biochemie) and Daniel J. Klionsky (University of Michigan); all S. cerevisiae strains are listed in Supplementary file 1-Table S1 |
| Genetic reagent (S. cerevisiae) |
PHO8Δ60 | PMID 7741731 | TN124 | Provided by Daniel J. Klionsky (University of Michigan); all S. cerevisiae strains are listed in Supplementary file 1-Table S1 |
| Genetic reagent (S. cerevisiae) |
rpn11-m1; rpn11-m5 | PMID 18172023; PMID 19773362; PMID 23936414 |
N/A | Provided by Agnès Delahodde (Université Paris-Sud); all S. cerevisiae strains are listed in Supplementary file 1-Table S1 |
| Genetic reagent (S. cerevisiae) |
PRE1-TEV-ProA; RPN11-TEV-ProA |
PMID: 12408819 | SDL133; SDL135 |
Provided by Daniel Finley (Harvard Medical School); allS. cerevisiae strains are listed in Supplementary file 1-Table S1 |
| Genetic reagent (A. thaliana) |
atg7-2 | GABI-Kat, Universität Bielefeld; PMID 20136727 |
GABI_655_B06 | N/A |
| Genetic reagent (A. thaliana) |
pa200-2; pa200-3 | ABRC; PMID 20516081 | SALK_095870; SALK_070184 |
N/A |
| Genetic reagent (A. thaliana) |
PAG1:PAG1-GFP pag1-1 | PMID 26004230 | SALK_114864 forpag1-1 |
N/A |
| Genetic reagent (A. thaliana) |
RPN5a:RPN5a-GFP rpn5a-2 | PMID 26004230 | SALK_010840 forrpn5a-2 |
N/A |
| Genetic reagent (A. thaliana) |
35S:GFP-ATG8a | PMID 16040659 | N/A | N/A |
| Genetic reagent (A. thaliana) |
UBQ10:mCherry-ATG8a | PMID 21984698 | N/A | N/A |
| Genes (A. thaliana and S. cerevisiae) |
See additional information |
Saccharomyces Genome Database or the Arabidopsis Information Resource |
See additional information |
All gene accession numbers are listed in Supplementary file 1-Table S2 |
| Antibody | Anti-FLAG (mouse monoclonal) |
Sigma-Aldrich | F3165, RRID:AB_259529 |
1:10,000 |
| Antibody | Anti-GFP (mixture of mouse monoclonals) |
Sigma-Aldrich | 11814460001, RRID:AB_390913 |
1:5000 |
| Antibody | Anti-H3 (rabbit polyclonal) |
Abcam | AB1791, RRID:AB_302613 |
1:3000 |
| Antibody | Anti-HA (mouse monoclonal) |
Covance | MMS-101R, RRID:AB_2314672 |
1:5000 |
| Antibody | Anti-mCherry (mouse monoclonal) |
Abcam |
AB125096, RRID:AB_11133266 |
1:1000 |
| Antibody | Anti-Pre4 (rabbit polyclonal) | Other | N/A | 1:1,000; provided by Daniel Finley (Harvard Medical School) |
| Antibody | Anti-Rpn5 (rabbit polyclonal) | PMID 19252082 | N/A | 1:3000 |
| Antibody | Anti-Rpn8 (rabbit polyclonal) | Other | N/A | 1:1,000; provided by Daniel Finley (Harvard Medical School) |
| Antibody | Anti-Rpt1 (rabbit polyclonal) | Other | N/A | 1:1,000; provided by Daniel Finley (Harvard Medical School) |
| Antibody | Goat anti-mouse HRP conjugate |
Sercare | 074–1806, RRID:AB_2307348 |
1:10,000 |
| Antibody | Goat anti-rabbit HRP conjugate |
Sercare | 074–1506, RRID:AB_2721169 |
1:10,000 |
| Recombinant DNA reagent |
pAG424GPD-ccdB;
pAG424GPD-ccdB-HA |
Addgene; PMID 17583893 | 14152; 14248 | Provided by Susan Lindquist (Whitehead Institute for Biomedical Research) via Addgene |
| Recombinant DNA reagent |
RNQ1-mCherry | PMID 18756251 |
pESC::GAL1-
RNQ1-mCherry |
Provided by Shay Ben-Aroya (Bar-Ilan University) |
| Recombinant DNA reagent |
mCherry-BLM10 | This paper |
pAG424::GPD1-
mCherry-BLM10 |
The mCherry-BLM10 coding sequence (CDS) cloned into pAG424GPD-ccdB |
| Recombinant DNA reagent |
mCherry-SPG5 | This paper |
pAG424::GPD1-
mCherry-SPG5 |
The mCherry-SPG5 CDS cloned into pAG424GPD-ccdB |
| Recombinant DNA reagent |
RPN11-FLAG | This paper |
pAG424::GPD1-
RPN11-FLAG |
The RPN11-FLAG CDS cloned into pAG424GPD-ccdB |
| Recombinant DNA reagent |
BRE5-HA | This paper |
pAG424::GPD1-
BRE5-HA |
The BRE5 CDS cloned into pAG424GPD-ccdB-HA |
| Recombinant DNA reagent |
NAT3-HA and derivatives |
This paper |
pAG424::GPD1-NAT3-
HA and derivatives |
The NAT3 CDS (and derivatives) cloned into pAG424GPD-ccdB-HA |
| Recombinant DNA reagent |
UBP3-HA and derivatives |
This paper |
pAG424::GPD1-UBP3-
HA and derivatives |
The UBP3 CDS (and derivatives) cloned into pAG424GPD-ccdB-HA |
| Sequence-based reagent |
See additional information |
Integrated DNA Technologies |
See additional information |
All oligonucleotide primer sequences are listed in Supplementary file 1-Table S3 |
| Recombinant protein |
6His-TEV protease | Other | N/A | Provided by E. Sethe Burgie (Washington University in St. Louis) |
| Commercial assay or kit |
LightCycler 480 SYBR Green I Master Mix |
Roche Diagnostics | 04707516001 | N/A |
| Commercial assay or kit |
Pierce BCA protein assay kit |
Thermo Fisher Scientific | 23225 | N/A |
| Commercial assay or kit |
SuperSignal West Pico Plus Chemiluminescent Substrate |
Thermo Fisher Scientific | 34578 | N/A |
| Chemical compound | 2-deoxyglucose | Sigma-Aldrich | D8375 | N/A |
| Chemical compound | Canavanine sulphate salt | Sigma-Aldrich | C9758 | N/A |
| Chemical compound | Carbonyl-cyanide-3- chlorophenylhydrazone |
Sigma-Aldrich | C2759 | N/A |
| Chemical compound | Concanamycin A | Santa Cruz Biotechnology | SC-202111A | N/A |
| Chemical compound | LFP | GenScript; PMID 16337593 | See additional information |
Custom synthesis |
| Chemical compound | MG132 | Selleckchem | S2619 | N/A |
| Chemical compound |
N-succinyl-LLVY-7-amido- 4-methylcoumarin |
Sigma-Aldrich | S6510 | N/A |
| Chemical compound | p-fluorophenylalanine | Sigma-Aldrich | F5251 | N/A |
| Chemical compound | p-nitrophenol | Sigma-Aldrich | 1048 | N/A |
| Chemical compound |
p-nitrophenyl phosphate disodium salt hexahydrate |
Sigma-Aldrich | N4645 | N/A |
| Software | Adobe Illustrator CC; Adobe Photoshop CC |
Adobe Systems | N/A | N/A |
| Software | Nikon Elements Imaging Software |
Nikon | N/A | N/A |
| Software | Total Lab Quant | Non-linear Dynamics | N/A | N/A |
| Other | Immobilon-P PVDF Transfer Membrane |
EMD Millipore | IPVH00010 | N/A |
| Other | Murashige and Skoog basal salt micronutrient solution |
Sigma-Aldrich | M0529 | N/A |
| Other | Nickel-nitrilotriacetic acid-agarose beads |
Qiagen | 30230 | N/A |
| Other | Protease inhibitor cocktail |
Sigma-Aldrich | P9599 | N/A |
| Other | Rabbit whole molecule IgG antigen affinity gel |
MP Biomedicals | 0855961 | N/A |
| Other | Yeast nitrogen base without amino acids and ammonium sulphate |
Sigma-Aldrich | Y1251 | N/A |