Dataset Information

CTLH E3 Ligase Regulates the Degradation of HMG-CoA Synthase 1 Through the Pro/N-end Rule Pathway

ABSTRACT: Supporting raw MS data for paper (doi: 10.1016/j.molcel.2024.04.026) by Yi S.A. et al, titled "CTLH E3 Ligase Regulates the Degradation of HMG-CoA Synthase 1 Through the Pro/N-end Rule Pathway". Index of RAW files uploaded: - Related to Supplementary Table 1 (HA-9-81-X | WT (1), ATG7KO (2), RB1CC1 (3): whole proteome (Unimod: 35; 2016; 4)). - Related to Supplementary Table 2 - Proteome (HA-1-50: whole proteome (Unimod: 35; 2016; 4)). - Related to Supplementary Table 2 - PhosphoSites (HA-1-50_Phos: phospho proteome (Unimod: 35; 21; 2016; 4)) - Related to Supplementary Table 3 (Yis-1-49: whole proteome (Unimod: 35; 2016; 4))

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Heeseon An Alban Ordureau

PROVIDER: MSV000090814 | MassIVE | Tue Nov 29 20:21:00 GMT 2022

REPOSITORIES: MassIVE

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Publications

mTORC1-CTLH E3 ligase regulates the degradation of HMG-CoA synthase 1 through the Pro/N-degron pathway.

Yi Sang Ah SA Sepic Sara S Schulman Brenda A BA Ordureau Alban A An Heeseon H

Molecular cell 20240523 11

Mammalian target of rapamycin (mTOR) senses changes in nutrient status and stimulates the autophagic process to recycle amino acids. However, the impact of nutrient stress on protein degradation beyond autophagic turnover is incompletely understood. We report that several metabolic enzymes are proteasomal targets regulated by mTOR activity based on comparative proteome degradation analysis. In particular, 3-hydroxy-3-methylglutaryl (HMG)-coenzyme A (CoA) synthase 1 (HMGCS1), the initial enzyme i ...[more]

PMID: 38788716

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Project description:Supporting raw MS data for paper (doi: 10.1016/j.cell.2024.05.018) by Sinha N.K. et al, titled "The ribotoxic stress response drives UV-mediated cell death". Index of MS files and labels Table S1 - HaCaT Timecourse. 1-1 - Proteome (AO3604-3627 | Unimod:35; 2016; 4 | 126 -UT_01; 127n - UT_02; 127c - UT_03; 128n -1min_01; 128c - 1min_02; 129n - 1min_03; 129c - 1min_04; 130n - 5min_01; 130c - 5min_02; 131n - 5min_03; 131c - 15min_01; 132n - 15min_02; 132c - 15min_03; 133n - 30min_01; 133c - 30min_02; 134n - 30min_03) 1-2 - Phospho (AO3628-3651 | Unimod:35; 2016; 4; 21 | 126 -UT_01; 127n - UT_02; 127c - UT_03; 128n -1min_01; 128c - 1min_02; 129n - 1min_03; 129c - 1min_04; 130n - 5min_01; 130c - 5min_02; 131n - 5min_03; 131c - 15min_01; 132n - 15min_02; 132c - 15min_03; 133n - 30min_01; 133c - 30min_02; 134n - 30min_03) Table S2 - MCF10a KO and inhibitor (Set1 - ZAK & Set 2 - GCN2). 2-1-1 - Proteome (Set 1 - AO4019-4042 | Unimod:35; 2016; 4 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_ZAKi01; 128c - WT_UT_ZAKi02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_ZAKi01; 130c - WT_UV_ZAKi02; 131n - ZAK-KO_UT_DMSO01; 131c - ZAK-KO_UT_DMSO02; 132n - ZAK-KO_UT_ZAKi01; 132c - ZAK-KO_UT_ZAKi02; 133n - ZAK-KO_UV_DMSO01; 133c - ZAK-KO_UV_DMSO02; 134n - ZAK-KO_UV_ZAKi01; 134c -ZAK-KO_UV_ZAKi02) 2-1-2 - Proteome (Set 2 - AO4049-4072 | Unimod:35; 2016; 4 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_GCN2i01; 128c - WT_UT_GCN2i02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_GCN2i01; 130c - WT_UV_GCN2i02; 131n - GCN2-KO_UT_DMSO01; 131c - GCN2-KO_UT_DMSO02; 132n - GCN2-KO_UT_GCN2i01; 132c - GCN2-KO_UT_GCN2i02; 133n - GCN2-KO_UV_DMSO01; 133c - GCN2-KO_UV_DMSO02; 134n - GCN2-KO_UV_GCN2i01; 135n -GCN2-KO_UV_GCN2i02) 2-2-1 - Phospho (Set 1 - AO4013-4019 | Unimod:35; 2016; 4; 21 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_ZAKi01; 128c - WT_UT_ZAKi02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_ZAKi01; 130c - WT_UV_ZAKi02; 131n - ZAK-KO_UT_DMSO01; 131c - ZAK-KO_UT_DMSO02; 132n - ZAK-KO_UT_ZAKi01; 132c - ZAK-KO_UT_ZAKi02; 133n - ZAK-KO_UV_DMSO01; 133c - ZAK-KO_UV_DMSO02; 134n - ZAK-KO_UV_ZAKi01; 134c -ZAK-KO_UV_ZAKi02) 2-2-2 - Phospho (Set 2 - AO4043-4048 | Unimod:35; 2016; 4; 21 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_GCN2i01; 128c - WT_UT_GCN2i02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_GCN2i01; 130c - WT_UV_GCN2i02; 131n - GCN2-KO_UT_DMSO01; 131c - GCN2-KO_UT_DMSO02; 132n - GCN2-KO_UT_GCN2i01; 132c - GCN2-KO_UT_GCN2i02; 133n - GCN2-KO_UV_DMSO01; 133c - GCN2-KO_UV_DMSO02; 134n - GCN2-KO_UV_GCN2i01; 135n -GCN2-KO_UV_GCN2i02) Table S3 - HaCaT Kinase inhibitors (Set 1 & Set 2). 3-1-1 - Proteome (Set 1 - AO3766-3777 | Unimod:35; 2016; 4 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Nil)_UT01; 129n - ZAKi(Nil)_UT02; 129c - ZAKi(Nil)_UV01; 130n - ZAKi(Nil)_UV02; 130c - p38i_UT01; 131n - p38i_UT02; 131c - p38i_UV01; 132n - p38i_UV02; 132c - JNKi_UT01; 133n - JNKi_UT02; 133c - JNKi_UV01; 134n - JNKi_UV02) 3-1-2 - Proteome (Set 2 - AO3778-3789 | Unimod:35; 2016; 4 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Vem)_UT01; 129n - ZAKi(Vem)_UT02; 129c - ZAKi(Vem)_UV01; 130n - ZAKi(Vem)_UV02; 130c - GCN2i_UT01; 131n - GCN2i_UT02; 131c - GCN2i_UV01; 132n - GCN2i_UV02; 132c - ATRi_UT01; 133n - ATRi_UT02; 133c - ATRi_UV01; 134n - ATRi_UV02) 3-2-1 - Phospho (Set 1 - AO3754-3759 | Unimod:35; 2016; 4; 21 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Nil)_UT01; 129n - ZAKi(Nil)_UT02; 129c - ZAKi(Nil)_UV01; 130n - ZAKi(Nil)_UV02; 130c - p38i_UT01; 131n - p38i_UT02; 131c - p38i_UV01; 132n - p38i_UV02; 132c - JNKi_UT01; 133n - JNKi_UT02; 133c - JNKi_UV01; 134n - JNKi_UV02) 3-2-2 - Phospho (Set 2 - AO3760-3765 | Unimod:35; 2016; 4; 21 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Vem)_UT01; 129n - ZAKi(Vem)_UT02; 129c - ZAKi(Vem)_UV01; 130n - ZAKi(Vem)_UV02; 130c - GCN2i_UT01; 131n - GCN2i_UT02; 131c - GCN2i_UV01; 132n - GCN2i_UV02; 132c - ATRi_UT01; 133n - ATRi_UT02; 133c - ATRi_UV01; 134n - ATRi_UV02). Tabel S4 - ZAK affinity purification. 4-1 - Label-free ZAK pulldown (mNG-ZAK-WT labeled files | Unimod:35; 4| Untreated or ANS treated cells) Additional file: AO4072_GCN2_RSP10_tMS2: Targeted RPS10-Kgg search | Unimod:35; 2016; 4; 492 | TMT label as 2-1-2.

Project description:We investigate molecular effects of glucosamine supplements, a popular safe alternative to non-steroidal anti-inflamatory drugs for decreasing pain, inflammation and keeping joints healthy. Numerous publications state an array of different molecular effects upon glucosamine treatment. We question whether these differences resulted mainly from focusing on a specific sub proteome or because different cell lines or tissues were used in the previous studies. To address this question global MS- and transcription array-based glucosamine drug profiling were performed on lymphocyte derived cell lines. We combined global label free MS-based protein quantitation with an open search strategy to obtain the best possible proteome coverage. Our result in large part support previous findings in a variety of cell models. Glucosamine induce O-GlcNAcylation but we also observe global changes in acetylation, methylation, phosphorylation. Furthermore, we mapped novel O-GlcNAc sites, on ER lumen proteins, regulated upon glucosamine treatment which provides novel insights into the role of glucosamine in ER stress. Preprocessing of MS data: All Q-Exactive data were calibrated using polycyclodi-methylsiloxane (PCMs—outgassed material from semiconductors) present in the ambient air and Bis(2-Ethylhexyl)(Phthalate) (DEHP—from plastic)1, 2 using both MaxQuant version 1.3.0.53 and modular VEMS mVEMS4. mVEMS4 further allows alternative parent ion annotations for each MS/MS spectrum which is needed if two peptide elution profiles overlap in the m/z and retention time dimension. By allowing alternative parent ion annotation for each MS/MS spectrum, provides a space efficient data format. Furthermore these alternative parent ion annotations were taken into account during the search. Database dependent search of MS data: All data were searched with MaxQuant version 1.3.0.53 and VEMS5. Mass accuracy was set to 10 ppm for peptides and 10 mDa for peptide fragments. Four missed cleavages were specified and the database UniProtKB/TrEMBL were used including permutated protein sequences, leaving Lys and Arg in place, together with common contaminants such as human keratins, bovine serum proteins and proteases6. Fixed modification of carbamidomethyl cysteine was included in the search parameters. In MaxQuant the following variable modifications were considered: Met-loss (UNIMOD 765), Oxidized methionine (UNIMOD 885), O-GlcNAc (HexNAc, UNIMOD 43). In VEMS a list of variable 36 modifications were considered for all data against the full protein database were performed. Protein N-terminal Met-loss is not in the list of VEMS modifications since VEMS by default always looks for N-terminal Met-loss. The modifications Phosphate-ribosylation (UNIMOD 1356), ADP ribose (UNIMOD 213), hydroxylation (UNIMOD 35) and Myristoylation (UNIMOD 45) were not frequent at a 1% FDR threshold and the search was therefore repeated excluding these modifications.