KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| α-Met4 | Mike Tyers’s lab | N/A |
| α-K11 polyubiquitin linkage (Clone 2A3/2E6) | Genentech | N/A |
| α-Ub P4D1 | Santa Cruz Biotechnology | sc-8017, RRID:AB_628423 |
| α-HA (Y-11 ) | Santa Cruz Biotechnology | sc-805, RRID:AB_631618 |
| α-streptavidin | Abcam | ab7239, RRID:AB_305786 |
| α-tubulin | Abcam | ab210797 |
| HRP-conjugated goat anti-human IgG, Fcγ | Jackson | 109–005-008, |
| fragment specific-488 | ImmunoResearch | RRID: AB_2337534 |
| HRP-conjugated goat α-mouse | Thermo Fisher | P-21129, RRID:AB_2539816 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Lys-C | Meizhiyuan | N/A |
| Trypsin | Meizhiyuan | N/A |
| TRIzol reagent | Invitrogen | 15596026 |
| RNase-free DNase I | Promega | M6101 |
| Dynabeads mRNA DIRECT Kit | Invitrogen | 61011 |
| random hexamer primers | SYBR | N/A |
| DNA polymerase I | SYBR | N/A |
| T4 DNA polymerase | SYBR | N/A |
| Pfu polymerase | NEB | N/A |
| [13C6] L-lysine | Cambridge Isotope Labs | CLM-2247-H |
| [13C6/15N4] L-arginine | Cambridge Isotope Labs | CNLM-539-H |
| K11 diubiquitin | Boston Biochem | UC-40B |
| K48 diubiquitin | Boston Biochem | UC-200B |
| K63 diubiquitin | Boston Biochem | UC-300B |
| K11 tetra-ubiquitin chains | Boston Biochem | UC-45 |
| K48 tetra-ubiquitin chains | Boston Biochem | UC-210B |
| Dynabeads™ Protein G for Immunoprecipitation | Life technologies | 10004D |
| Ni-NTA agarose | Qigen | 30250 |
| Immobilon-NC Transfer Membrane | Millipore | HATF04700 |
| Streptavidin Dip and Read biosensors | ForteBio | 18–5019 |
| Phenylmethanesulfonyl fluoride (PMSF) | Sigma-Aldrich | P7626 |
| N-ethylmaleimide | Sigma-Aldrich | E3876–25G |
| 0.5 mm glass beads | Biospec Products Inc | 1107900–105 |
| Hepes | Fisher Scientific | BP-310 |
| Deoxycholic Acid | Sigma | D-6750 |
| EDTA | Fisher Scientific | S-311 |
| NaCl | Fisher Scientific | S-640 |
| Triton | Fisher Scientific | BP-151 |
| LiCI | Sigma | L-9650 |
| NP-40 | Boston Bioproducts | P-877 |
| Tris | Invitrogen | 15504 |
| L-Methionine | Sigma | M-5308 |
| Formaldehyde | Sigma | F-8775 |
| Glycogen | Acros Organics | 422950010 |
| RNase A | Sigma | R-5503 |
| Proteinase K | Thermo | 26160 |
| Antifoam Y-30 | Sigma | A-5758 |
| Protein A Sepharose/Salmon Sperm blocked | Millipore | 16–157 |
| Microtube screw cap | Olympus plastics | 21–266 |
| 1.5 mL Bioruptor Microtubes with Caps for | ||
| Bioruptor Pico | Diagenode | C30010016 |
| iTaq Universal SYBR Green SuperMix | Biorad | 1725120 |
| Dynabeads™ MyOne™ Streptavidin C1 | Thermo Fisher Shanghai Leon Chemical | 65002 |
| IISGIGVGGIAVLSPMLISEVAPK | Ltd. Shanghai Leon Chemical | N/A |
| TLSDYNIQK (Ub, unmodified 1, Light & Heavy) | Ltd. | N/A |
| LISEEDLGM*QIFVK(GG)TLTGK (Ub, K6 | Shanghai Leon Chemical | |
| oxidative, Light & Heavy) | Ltd. | N/A |
| LISEEDLGMQIFVK(GG)TLTGK (K6, Light & | Shanghai Leon Chemical | |
| Heavy) | Ltd. | N/A |
| TLTGK(GG)TITLEVESSDTIDNVK (K11, Light & | Shanghai Leon Chemical | |
| Heavy) | Ltd. | N/A |
| TITLEVESSDTIDNVK(GG)SK (K27, Light & | Shanghai Leon Chemical | |
| Heavy) | Ltd. Shanghai Leon Chemical | N/A |
| SK(GG)IQDK (K29, Light & Heavy) | Ltd. Shanghai Leon Chemical | N/A |
| IQDK(GG)EGIPPDQQR (K33, Light & Heavy) | Ltd. Shanghai Leon Chemical | N/A |
| LIFAGK(GG)QLEDGR (K48, Light & Heavy) | Ltd. | N/A |
| TLSDYNIQK(GG)ESTLHLVLR (K63, Light & | Shanghai Leon Chemical | |
| Heavy) | Ltd. | N/A |
| Deposited Data | ||
| Raw data | This study | http://www.proteomexchange.org |
| Experimental Models: Organisms/Strains | ||
| S. cerevisiae: Strain background: BY4741 | ATCC | ATCC 4040002 |
| SUB592 | Spence J, et al., 2000 | N/A |
| JMP024 (WT) | Xu P, et al., 2009 | N/A |
| JMP025 (Ub K11R) | Xu P, et al., 2009 | N/A |
| PY283 | Kaiser P, et al., 2000 | N/A |
| PX001 : JMP024, met4::3HA-MET4 | This study | N/A |
| PX002: JMP025, met4::3HA-MET4 | This study | N/A |
| PX003: JMP024, met4::3HA-MET4 K163R | This study | N/A |
| PX004: JMP024, met4::3HA-MET4, met30:: | ||
| natNT2, met32:: hphNTI | This study | N/A |
| PK2308: JMP024 (WT) | ||
| med14::MED14–3HA::KAN | This study | N/A |
| PK2309: JMP025 (K11R) | ||
| med14::MED14–3HA::KAN | This study | N/A |
| Recombinant DNA | ||
| pET28(a) Avi-6xHis-SUMO-Met4 (amino acids | ||
| 76–160) | This study | N/A |
| pBirAcm plasmid coding for BirA | This study | N/A |
| pAL01 base (6xHis- Med15 1–651 Δ239–271, Δ373–483) | This study | N/A |
| Oligonucleotides | ||
| Primers for MET3, see Table S6 | This study | N/A |
| Primers for MET17, see Table S6 | This study | N/A |
| Primers for CYS4, see Table S6 | This study | N/A |
| Primers for SAM2, see Table S6 | This study | N/A |
| Primers for CCW12, see Table S6 | This study | N/A |
| Primers for CDC19, see Table S6 | This study | N/A |
| Primers for 18SrRNA, see Table S6 | This study | N/A |
| Software and Algorithms | ||
| Trans-Proteomic Pipeline | Pedrioli PG, et al., 2010 | N/A |
| Sequest-Sorcerer algorithm (version 4.0.4 build) | Eng JK, et al., 1994 | N/A |
| SILVER | Chang C, et al., 2014 | N/A |
| MaxQuant (1.5.3.0) | Cox, J., et al., 2008 | N/A |
| Xcalibur v2.0 | Thermo Finnigan | N/A |
| ForteBio Data Analysis 9.0 | Pall ForteBio | N/A |
| Other | ||
| Capillary column 75 μm i.d. × 15 cm; C18, 3 μm | Beijing SpectraPeaks | N/A |