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For: Paulo JA, O'Connell JD, Everley RA, O'Brien J, Gygi MA, Gygi SP. Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources. J Proteomics 2016;148:85-93. [PMID: 27432472 DOI: 10.1016/j.jprot.2016.07.005] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/26/2016] [Accepted: 07/07/2016] [Indexed: 12/18/2022]
Number Cited by Other Article(s)
1
Parmar S, Zuniga NR, Rossio V, Liu X, Paulo JA. Temporal Proteomic Profiling of Pheromone-Induced Cell Cycle Re-Entry in Saccharomyces cerevisiae. Proteomics 2025;25:e202400455. [PMID: 40259487 DOI: 10.1002/pmic.202400455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 04/23/2025]
2
MacDonald JA, Bradshaw GA, Jochems F, Bernards R, Letai A. Apoptotic priming in senescence predicts specific senolysis by quantitative analysis of mitochondrial dependencies. Cell Death Differ 2025;32:802-817. [PMID: 39762561 DOI: 10.1038/s41418-024-01431-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 11/20/2024] [Accepted: 12/04/2024] [Indexed: 05/21/2025]  Open
3
Raiff A, Zhao S, Bekturova A, Zenge C, Mazor S, Chen X, Ru W, Makaros Y, Ast T, Ordureau A, Xu C, Koren I. TOM20-driven E3 ligase recruitment regulates mitochondrial dynamics through PLD6. Nat Chem Biol 2025:10.1038/s41589-025-01894-4. [PMID: 40263465 DOI: 10.1038/s41589-025-01894-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 03/27/2025] [Indexed: 04/24/2025]
4
Awasthi BW, Paulo JA, Burkhart DL, Smith IR, Collins RL, Harper JW, Gygi SP, Haigis KM. The network response to Egf is tissue-specific. iScience 2025;28:112146. [PMID: 40171493 PMCID: PMC11960661 DOI: 10.1016/j.isci.2025.112146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/29/2024] [Accepted: 02/27/2025] [Indexed: 04/03/2025]  Open
5
McKenna MJ, Kraus F, Coelho JP, Vasandani M, Zhang J, Adams BM, Paulo JA, Harper JW, Shao S. ARMC1 partitions between distinct complexes and assembles MIRO with MTFR to control mitochondrial distribution. SCIENCE ADVANCES 2025;11:eadu5091. [PMID: 40203102 PMCID: PMC11980836 DOI: 10.1126/sciadv.adu5091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2024] [Accepted: 03/04/2025] [Indexed: 04/11/2025]
6
Gu S, Maurya S, Lona A, Borrega Roman L, Salanga C, Gonzalez DJ, Kufareva I, Handel TM. Traffic control: Mechanisms of ligand-specific internalization and intracellular distribution of CCR5. Mol Pharmacol 2025;107:100020. [PMID: 40199068 DOI: 10.1016/j.molpha.2025.100020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 01/30/2025] [Accepted: 01/31/2025] [Indexed: 04/10/2025]  Open
7
Hossain MK, Unger L, Larsen U, Altankhuyag A, Legøy TA, Paulo JA, Vethe H, Ghila L. Mapping the initial effects of carcinogen-induced oncogenic transformation in the mouse bladder. Exp Cell Res 2025;446:114452. [PMID: 39988124 DOI: 10.1016/j.yexcr.2025.114452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 01/31/2025] [Accepted: 02/14/2025] [Indexed: 02/25/2025]
8
Liu X, Dawson SL, Gygi SP, Paulo JA. Isobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometer. J Proteome Res 2025;24:1414-1424. [PMID: 39937051 DOI: 10.1021/acs.jproteome.4c01107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2025]
9
Gonzalez-Lozano MA, Schmid EW, Whelan EM, Jiang Y, Paulo JA, Walter JC, Harper JW. EndoMAP.v1, a Structural Protein Complex Landscape of Human Endosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.07.636106. [PMID: 39975243 PMCID: PMC11839024 DOI: 10.1101/2025.02.07.636106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
10
Sooklim C, Paemanee A, Ratanakhanokchai K, Wiwatratana D, Soontorngun N. Integrated omic analysis of a new flavor yeast strain in fermented rice milk. FEMS Yeast Res 2025;25:foaf017. [PMID: 40153366 PMCID: PMC11995695 DOI: 10.1093/femsyr/foaf017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2024] [Revised: 03/11/2025] [Accepted: 03/26/2025] [Indexed: 03/30/2025]  Open
11
Pham BQ, Yi SA, Ordureau A, An H. mTORC1 regulates the pyrimidine salvage pathway by controlling UCK2 turnover via the CTLH-WDR26 E3 ligase. Cell Rep 2025;44:115179. [PMID: 39808525 PMCID: PMC11840829 DOI: 10.1016/j.celrep.2024.115179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 11/20/2024] [Accepted: 12/18/2024] [Indexed: 01/16/2025]  Open
12
Liu X, Dawson SL, Gygi SP, Paulo JA. Isobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.17.628765. [PMID: 39764012 PMCID: PMC11702835 DOI: 10.1101/2024.12.17.628765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2025]
13
Shin YC, Latorre-Muro P, Djurabekova A, Zdorevskyi O, Bennett CF, Burger N, Song K, Xu C, Paulo JA, Gygi SP, Sharma V, Liao M, Puigserver P. Structural basis of respiratory complex adaptation to cold temperatures. Cell 2024;187:6584-6598.e17. [PMID: 39395414 PMCID: PMC11601890 DOI: 10.1016/j.cell.2024.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 08/07/2024] [Accepted: 09/17/2024] [Indexed: 10/14/2024]
14
Zuniga NR, Frost DC, Kuhn K, Shin M, Whitehouse RL, Wei TY, He Y, Dawson SL, Pike I, Bomgarden RD, Gygi SP, Paulo JA. Achieving a 35-Plex Tandem Mass Tag Reagent Set through Deuterium Incorporation. J Proteome Res 2024;23:5153-5165. [PMID: 39380184 DOI: 10.1021/acs.jproteome.4c00668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2024]
15
Scott DC, Dharuman S, Griffith E, Chai SC, Ronnebaum J, King MT, Tangallapally R, Lee C, Gee CT, Yang L, Li Y, Loudon VC, Lee HW, Ochoada J, Miller DJ, Jayasinghe T, Paulo JA, Elledge SJ, Harper JW, Chen T, Lee RE, Schulman BA. Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2. Nat Commun 2024;15:8829. [PMID: 39396041 PMCID: PMC11470957 DOI: 10.1038/s41467-024-52966-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 09/27/2024] [Indexed: 10/14/2024]  Open
16
Bjørnstad OV, Carrasco M, Finne K, Ardawatia V, Winge I, Askeland C, Arnes JB, Knutsvik G, Kleftogiannis D, Paulo JA, Akslen LA, Vethe H. Global and single-cell proteomics view of the co-evolution between neural progenitors and breast cancer cells in a co-culture model. EBioMedicine 2024;108:105325. [PMID: 39232464 PMCID: PMC11404160 DOI: 10.1016/j.ebiom.2024.105325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 08/15/2024] [Accepted: 08/22/2024] [Indexed: 09/06/2024]  Open
17
Castro JP, Shindyapina AV, Barbieri A, Ying K, Strelkova OS, Paulo JA, Tyshkovskiy A, Meinl R, Kerepesi C, Petrashen AP, Mariotti M, Meer MV, Hu Y, Karamyshev A, Losyev G, Galhardo M, Logarinho E, Indzhykulian AA, Gygi SP, Sedivy JM, Manis JP, Gladyshev VN. Age-associated clonal B cells drive B cell lymphoma in mice. NATURE AGING 2024;4:1403-1417. [PMID: 39117982 DOI: 10.1038/s43587-024-00671-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 06/19/2024] [Indexed: 08/10/2024]
18
Gygi JS, Liu X, Levi BP, Paulo JA. Proteome-wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing. Proteomics 2024;24:e2300303. [PMID: 37882342 PMCID: PMC11045664 DOI: 10.1002/pmic.202300303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023]
19
Gu S, Maurya S, Lona A, Borrega-Roman L, Salanga C, Gonzalez DJ, Kufareva I, Handel TM. Ligand-Dependent Mechanisms of CC Chemokine Receptor 5 (CCR5) Trafficking Revealed by APEX2 Proximity Labeling Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565224. [PMID: 37961097 PMCID: PMC10635066 DOI: 10.1101/2023.11.01.565224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
20
Rahman MA, Amirkhani A, Mempin M, Ahn SB, Deva AK, Baker MS, Vickery K, Hu H. The Low-Abundance Plasma Proteome Reveals Differentially Abundant Proteins Associated with Breast Implant Capsular Contracture: A Pilot Study. Proteomes 2024;12:22. [PMID: 39189262 PMCID: PMC11348101 DOI: 10.3390/proteomes12030022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/02/2024] [Accepted: 08/04/2024] [Indexed: 08/28/2024]  Open
21
Zhang T, Liu X, Rossio V, Dawson SL, Gygi SP, Paulo JA. Enhancing Proteome Coverage by Using Strong Anion-Exchange in Tandem with Basic-pH Reversed-Phase Chromatography for Sample Multiplexing-Based Proteomics. J Proteome Res 2024;23:2870-2881. [PMID: 37962907 PMCID: PMC11090996 DOI: 10.1021/acs.jproteome.3c00492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
22
Mathisen AF, Legøy TA, Larsen U, Unger L, Abadpour S, Paulo JA, Scholz H, Ghila L, Chera S. The age-dependent regulation of pancreatic islet landscape is fueled by a HNF1a-immune signaling loop. Mech Ageing Dev 2024;220:111951. [PMID: 38825059 DOI: 10.1016/j.mad.2024.111951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/30/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024]
23
Pattamaprapanont P, Cooney EM, MacDonald TL, Paulo JA, Pan H, Dreyfuss JM, Lessard SJ. Matrisome proteomics reveals novel mediators of muscle remodeling with aerobic exercise training. Matrix Biol Plus 2024;23:100159. [PMID: 39220302 PMCID: PMC11363848 DOI: 10.1016/j.mbplus.2024.100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]  Open
24
Babina AM, Kirsebom LA, Andersson DI. Suppression of the Escherichia coli rnpA49 conditionally lethal phenotype by different compensatory mutations. RNA (NEW YORK, N.Y.) 2024;30:977-991. [PMID: 38688559 PMCID: PMC11251521 DOI: 10.1261/rna.079909.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
25
Sinha NK, McKenney C, Yeow ZY, Li JJ, Nam KH, Yaron-Barir TM, Johnson JL, Huntsman EM, Cantley LC, Ordureau A, Regot S, Green R. The ribotoxic stress response drives UV-mediated cell death. Cell 2024;187:3652-3670.e40. [PMID: 38843833 PMCID: PMC11246228 DOI: 10.1016/j.cell.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 03/03/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024]
26
Arunachalam E, Keber FC, Law RC, Kumar CK, Shen Y, Park JO, Wühr M, Needleman DJ. Robustness of mitochondrial biogenesis and respiration explain aerobic glycolysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.601975. [PMID: 39005310 PMCID: PMC11245115 DOI: 10.1101/2024.07.04.601975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
27
Laverty DJ, Gupta SK, Bradshaw GA, Hunter AS, Carlson BL, Calmo NM, Chen J, Tian S, Sarkaria JN, Nagel ZD. ATM inhibition exploits checkpoint defects and ATM-dependent double strand break repair in TP53-mutant glioblastoma. Nat Commun 2024;15:5294. [PMID: 38906885 PMCID: PMC11192742 DOI: 10.1038/s41467-024-49316-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/28/2024] [Indexed: 06/23/2024]  Open
28
König LE, Rodriguez S, Hug C, Daneshvari S, Chung A, Bradshaw GA, Sahin A, Zhou G, Eisert RJ, Piccioni F, Das S, Kalocsay M, Sokolov A, Sorger P, Root DE, Albers MW. TYK2 as a novel therapeutic target in Alzheimer's Disease with TDP-43 inclusions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.595773. [PMID: 38895380 PMCID: PMC11185596 DOI: 10.1101/2024.06.04.595773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
29
Yi SA, Sepic S, Schulman BA, Ordureau A, An H. mTORC1-CTLH E3 ligase regulates the degradation of HMG-CoA synthase 1 through the Pro/N-degron pathway. Mol Cell 2024;84:2166-2184.e9. [PMID: 38788716 PMCID: PMC11186538 DOI: 10.1016/j.molcel.2024.04.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/15/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024]
30
Mitchell W, Goeminne LJE, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. eLife 2024;12:RP90579. [PMID: 38517750 PMCID: PMC10959535 DOI: 10.7554/elife.90579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]  Open
31
Brennan PJ, Saunders RE, Spanou M, Serafini M, Sun L, Heger GP, Konopacka A, Beveridge RD, Gordon L, Bunally SB, Saudemont A, Benowitz AB, Martinez-Fleites C, Queisser MA, An H, Deane CM, Hann MM, Brayshaw LL, Conway SJ. Orthogonal IMiD-Degron Pairs Induce Selective Protein Degradation in Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585309. [PMID: 38559242 PMCID: PMC10979945 DOI: 10.1101/2024.03.15.585309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
32
Hoyer MJ, Capitanio C, Smith IR, Paoli JC, Bieber A, Jiang Y, Paulo JA, Gonzalez-Lozano MA, Baumeister W, Wilfling F, Schulman BA, Harper JW. Combinatorial selective ER-phagy remodels the ER during neurogenesis. Nat Cell Biol 2024;26:378-392. [PMID: 38429475 PMCID: PMC10940164 DOI: 10.1038/s41556-024-01356-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/11/2024] [Indexed: 03/03/2024]
33
Paul S, Sarraf SA, Nam KH, Zavar L, DeFoor N, Biswas SR, Fritsch LE, Yaron TM, Johnson JL, Huntsman EM, Cantley LC, Ordureau A, Pickrell AM. NAK-associated protein 1/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis. J Cell Biol 2024;223:e202303082. [PMID: 38059900 PMCID: PMC10702366 DOI: 10.1083/jcb.202303082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 10/03/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]  Open
34
O'Brien JJ, Raj A, Gaun A, Waite A, Li W, Hendrickson DG, Olsson N, McAllister FE. A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments. Nat Methods 2024;21:290-300. [PMID: 38110636 DOI: 10.1038/s41592-023-02120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/31/2023] [Indexed: 12/20/2023]
35
Ahlstedt BA, Ganji R, Mukkavalli S, Paulo JA, Gygi SP, Raman M. UBXN1 maintains ER proteostasis and represses UPR activation by modulating translation. EMBO Rep 2024;25:672-703. [PMID: 38177917 PMCID: PMC10897191 DOI: 10.1038/s44319-023-00027-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024]  Open
36
Watts ME, Giadone RM, Ordureau A, Holton KM, Harper JW, Rubin LL. Analyzing the ER stress response in ALS patient derived motor neurons identifies druggable neuroprotective targets. Front Cell Neurosci 2024;17:1327361. [PMID: 38314348 PMCID: PMC10834640 DOI: 10.3389/fncel.2023.1327361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/15/2023] [Indexed: 02/06/2024]  Open
37
Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. Cell Rep 2023;42:113478. [PMID: 37991919 PMCID: PMC10785701 DOI: 10.1016/j.celrep.2023.113478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/13/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]  Open
38
Ledvin L, Gassaway BM, Tawil J, Urso O, Pizzo D, Welsh KA, Bolhuis DL, Fisher D, Bonni A, Gygi SP, Brown NG, Ferguson CJ. The anaphase-promoting complex controls a ubiquitination-phosphoprotein axis in chromatin during neurodevelopment. Dev Cell 2023;58:2666-2683.e9. [PMID: 37875116 PMCID: PMC10872926 DOI: 10.1016/j.devcel.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/26/2023]
39
Mitchell W, Goeminne LJ, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.546730. [PMID: 37425825 PMCID: PMC10327104 DOI: 10.1101/2023.06.30.546730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
40
Hoyer MJ, Capitanio C, Smith IR, Paoli JC, Bieber A, Jiang Y, Paulo JA, Gonzalez-Lozano MA, Baumeister W, Wilfling F, Schulman BA, Harper JW. Combinatorial selective ER-phagy remodels the ER during neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546565. [PMID: 37425907 PMCID: PMC10326971 DOI: 10.1101/2023.06.26.546565] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
41
Nguyen V, Xue P, Li Y, Zhao H, Lu T. Controlling circuitry underlies the growth optimization of Saccharomyces cerevisiae. Metab Eng 2023;80:173-183. [PMID: 37739159 PMCID: PMC11089650 DOI: 10.1016/j.ymben.2023.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
42
Adhikary U, Paulo JA, Godes M, Roychoudhury S, Prew MS, Ben-Nun Y, Yu EW, Budhraja A, Opferman JT, Chowdhury D, Gygi SP, Walensky LD. Targeting MCL-1 triggers DNA damage and an anti-proliferative response independent from apoptosis induction. Cell Rep 2023;42:113176. [PMID: 37773750 PMCID: PMC10787359 DOI: 10.1016/j.celrep.2023.113176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 07/13/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023]  Open
43
Gourisankar S, Wenderski W, Paulo JA, Kim SH, Roepke K, Ellis C, Gygi SP, Crabtree GR. Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562244. [PMID: 37873481 PMCID: PMC10592824 DOI: 10.1101/2023.10.13.562244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
44
Rossio V, Liu X, Paulo JA. Comparative Proteomic Analysis of Two Commonly Used Laboratory Yeast Strains: W303 and BY4742. Proteomes 2023;11:30. [PMID: 37873872 PMCID: PMC10594481 DOI: 10.3390/proteomes11040030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]  Open
45
Mathisen AF, Abadpour S, Legøy TA, Paulo JA, Ghila L, Scholz H, Chera S. Global proteomics reveals insulin abundance as a marker of human islet homeostasis alterations. Acta Physiol (Oxf) 2023;239:e14037. [PMID: 37621186 PMCID: PMC10592125 DOI: 10.1111/apha.14037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
46
Rossio V, Paulo JA. Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae Cells Harvested with Different Strategies. Proteomes 2023;11:28. [PMID: 37873870 PMCID: PMC10594529 DOI: 10.3390/proteomes11040028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023]  Open
47
Knöringer K, Groh C, Krämer L, Stein KC, Hansen KG, Zimmermann J, Morgan B, Herrmann JM, Frydman J, Boos F. The unfolded protein response of the endoplasmic reticulum supports mitochondrial biogenesis by buffering nonimported proteins. Mol Biol Cell 2023;34:ar95. [PMID: 37379206 PMCID: PMC10551703 DOI: 10.1091/mbc.e23-05-0205] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023]  Open
48
Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555625. [PMID: 37693555 PMCID: PMC10491142 DOI: 10.1101/2023.08.31.555625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
49
Jordan VN, Ordureau A, An H. Identifying E3 Ligase Substrates With Quantitative Degradation Proteomics. Chembiochem 2023;24:e202300108. [PMID: 37166757 PMCID: PMC10548883 DOI: 10.1002/cbic.202300108] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/12/2023]
50
Weith M, Großbach J, Clement‐Ziza M, Gillet L, Rodríguez‐López M, Marguerat S, Workman CT, Picotti P, Bähler J, Aebersold R, Beyer A. Genetic effects on molecular network states explain complex traits. Mol Syst Biol 2023;19:e11493. [PMID: 37485750 PMCID: PMC10407735 DOI: 10.15252/msb.202211493] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023]  Open
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