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Szulc NA, Stefaniak F, Piechota M, Soszyńska A, Piórkowska G, Cappannini A, Bujnicki J, Maniaci C, Pokrzywa W. DEGRONOPEDIA: a web server for proteome-wide inspection of degrons. Nucleic Acids Res 2024; 52:W221-W232. [PMID: 38567734 PMCID: PMC11223883 DOI: 10.1093/nar/gkae238] [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: 02/02/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 07/06/2024] Open
Abstract
E3 ubiquitin ligases recognize substrates through their short linear motifs termed degrons. While degron-signaling has been a subject of extensive study, resources for its systematic screening are limited. To bridge this gap, we developed DEGRONOPEDIA, a web server that searches for degrons and maps them to nearby residues that can undergo ubiquitination and disordered regions, which may act as protein unfolding seeds. Along with an evolutionary assessment of degron conservation, the server also reports on post-translational modifications and mutations that may modulate degron availability. Acknowledging the prevalence of degrons at protein termini, DEGRONOPEDIA incorporates machine learning to assess N-/C-terminal stability, supplemented by simulations of proteolysis to identify degrons in newly formed termini. An experimental validation of a predicted C-terminal destabilizing motif, coupled with the confirmation of a post-proteolytic degron in another case, exemplifies its practical application. DEGRONOPEDIA can be freely accessed at degronopedia.com.
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Affiliation(s)
- Natalia A Szulc
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Małgorzata Piechota
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Anna Soszyńska
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Gabriela Piórkowska
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Andrea Cappannini
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Chiara Maniaci
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
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2
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Cochran JD, Leathers TA, Maldosevic E, Siejda KW, Vitello J, Lee H, Bradley LA, Young A, Jomaa A, Wolf MJ. Cell cycle specific, differentially tagged ribosomal proteins to measure phase specific transcriptomes from asynchronously cycling cells. Sci Rep 2024; 14:1623. [PMID: 38238470 PMCID: PMC10796924 DOI: 10.1038/s41598-024-52085-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 01/13/2024] [Indexed: 01/22/2024] Open
Abstract
Asynchronously cycling cells pose a challenge to the accurate characterization of phase-specific gene expression. Current strategies, including RNAseq, survey the steady state gene expression across the cell cycle and are inherently limited by their inability to resolve dynamic gene regulatory networks. Single cell RNAseq (scRNAseq) can identify different cell cycle transcriptomes if enough cycling cells are present, however some cells are not amenable to scRNAseq. Therefore, we merged two powerful strategies, the CDT1 and GMNN degrons used in Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) cell cycle sensors and the ribosomal protein epitope tagging used in RiboTrap/Tag technologies to isolate cell cycle phase-specific mRNA for sequencing. The resulting cell cycle dependent, tagged ribosomal proteins (ccTaggedRP) were differentially expressed during the cell cycle, had similar subcellular locations as endogenous ribosomal proteins, incorporated into ribosomes and polysomes, and facilitated the recovery of cell cycle phase-specific RNA for sequencing. ccTaggedRP has broad applications to investigate phase-specific gene expression in complex cell populations.
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Affiliation(s)
- Jesse D Cochran
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, USA
| | - Tess A Leathers
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, USA
| | - Emir Maldosevic
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Klara W Siejda
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Julian Vitello
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Haesol Lee
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Leigh A Bradley
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Alex Young
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Ahmad Jomaa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Matthew J Wolf
- Department of Medicine, University of Virginia, Charlottesville, VA, USA.
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA.
- Division of Cardiology, University of Virginia, Medical Research Building 5 (MR5), Room G213, 415 Lane Road, Charlottesville, VA, 22908, USA.
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3
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Scalia P, Williams SJ. Over-expression by degradation rescue of RTKs via cancer-secreted autocrine growth factors: a Phospho-degron-driven actionable layer of post-translational regulation?. Front Oncol 2023; 13:1278402. [PMID: 37823054 PMCID: PMC10562641 DOI: 10.3389/fonc.2023.1278402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
Recently published work provide the first known evidence of a malignancy-associated regulatory mechanism, functionally connecting a phospho-regulated degron domain embedded in a receptor tyrosine kinase (RTK), with its ectopic expression in cancer, conditional to a specific autocrine growth factor signal. Mechanistically, the growth factor-triggered phosphorylation inhibits the degron domain present in the regulated RTK, blocking access to a specific degradation complex. This ultimately rescues the RTK from rapid ubiquitin-proteasome-system-mediated degradation and, most importantly, causes its cellular overexpression. This mechanism, which has been here assigned the new functional name "Over-Expression by Degradation Rescue" (OEDR), provides an additional layer and potentially preferential tool for the control of RTKs expression in cancer, in addition to other mechanisms acting at the transcriptional and messenger transcript stabilization levels. We propose this newly defined phosphorylation/ubiquitination switch-dependent signal to bear wider unexploited relevance in cell biology and human pathophysiology. The recently identified mechanism underlying an OEDR-regulated RTK is discussed herein in the context of physiological endocrine circuits and cancer.
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Affiliation(s)
- Pierluigi Scalia
- Istituto Somatogene per la Oncologia Personalizzata e la Ricerca Onco-Genomica (ISOPROG)-Somatolink Expert-Patients For Patients (EPFP) Research Network, Philadelphia, PA, United States
- Istituto Somatogene per la Oncologia Personalizzata e la Ricerca Onco-Genomica (ISOPROG)-Somatolink Expert-Patients For Patients (EPFP) Research Network, Caltanissetta, Italy
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Stephen J. Williams
- Istituto Somatogene per la Oncologia Personalizzata e la Ricerca Onco-Genomica (ISOPROG)-Somatolink Expert-Patients For Patients (EPFP) Research Network, Philadelphia, PA, United States
- Istituto Somatogene per la Oncologia Personalizzata e la Ricerca Onco-Genomica (ISOPROG)-Somatolink Expert-Patients For Patients (EPFP) Research Network, Caltanissetta, Italy
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States
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4
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Thrash HL, Pendergast AM. Multi-Functional Regulation by YAP/TAZ Signaling Networks in Tumor Progression and Metastasis. Cancers (Basel) 2023; 15:4701. [PMID: 37835395 PMCID: PMC10572014 DOI: 10.3390/cancers15194701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
The Hippo pathway transcriptional co-activators, YES-associated protein (YAP) and Transcriptional Co-Activator with PDZ Binding Motif (TAZ), have both been linked to tumor progression and metastasis. These two proteins possess overlapping and distinct functions, and their activities lead to the expression of genes involved in multiple cellular processes, including cell proliferation, survival, and migration. The dysregulation of YAP/TAZ-dependent cellular processes can result in altered tumor growth and metastasis. In addition to their well-documented roles in the regulation of cancer cell growth, survival, migration, and invasion, the YAP/TAZ-dependent signaling pathways have been more recently implicated in cellular processes that promote metastasis and therapy resistance in several solid tumor types. This review highlights the role of YAP/TAZ signaling networks in the regulation of tumor cell plasticity mediated by hybrid and reversible epithelial-mesenchymal transition (EMT) states, and the promotion of cancer stem cell/progenitor phenotypes. Mechanistically, YAP and TAZ regulate these cellular processes by targeting transcriptional networks. In this review, we detail recently uncovered mechanisms whereby YAP and TAZ mediate tumor growth, metastasis, and therapy resistance, and discuss new therapeutic strategies to target YAP/TAZ function in various solid tumor types. Understanding the distinct and overlapping roles of YAP and TAZ in multiple cellular processes that promote tumor progression to metastasis is expected to enable the identification of effective therapies to treat solid tumors through the hyper-activation of YAP and TAZ.
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Affiliation(s)
| | - Ann Marie Pendergast
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
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Abdelbaki A, Ascanelli C, Okoye CN, Akman HB, Janson G, Min M, Marcozzi C, Hagting A, Grant R, De Luca M, Asteriti IA, Guarguaglini G, Paiardini A, Lindon C. Revisiting degron motifs in human AURKA required for its targeting by APC/C FZR1. Life Sci Alliance 2023; 6:6/2/e202201372. [PMID: 36450448 PMCID: PMC9713472 DOI: 10.26508/lsa.202201372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022] Open
Abstract
Mitotic kinase Aurora A (AURKA) diverges from other kinases in its multiple active conformations that may explain its interphase roles and the limited efficacy of drugs targeting the kinase pocket. Regulation of AURKA activity by the cell is critically dependent on destruction mediated by the anaphase-promoting complex (APC/CFZR1) during mitotic exit and G1 phase and requires an atypical N-terminal degron in AURKA called the "A-box" in addition to a reported canonical D-box degron in the C-terminus. Here, we find that the reported C-terminal D-box of AURKA does not act as a degron and instead mediates essential structural features of the protein. In living cells, the N-terminal intrinsically disordered region of AURKA containing the A-box is sufficient to confer FZR1-dependent mitotic degradation. Both in silico and in cellulo assays predict the QRVL short linear interacting motif of the A-box to be a phospho-regulated D-box. We propose that degradation of full-length AURKA also depends on an intact C-terminal domain because of critical conformational parameters permissive for both activity and mitotic degradation of AURKA.
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Affiliation(s)
- Ahmed Abdelbaki
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | | | - Cynthia N Okoye
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - H Begum Akman
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Giacomo Janson
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Mingwei Min
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Chiara Marcozzi
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Anja Hagting
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Rhys Grant
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Maria De Luca
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Italia Anna Asteriti
- Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Sapienza University of Rome, Rome, Italy
| | - Giulia Guarguaglini
- Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Sapienza University of Rome, Rome, Italy
| | | | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge, UK
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6
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Li W, Salovska B, Fornasiero EF, Liu Y. Toward a hypothesis-free understanding of how phosphorylation dynamically impacts protein turnover. Proteomics 2023; 23:e2100387. [PMID: 36422574 PMCID: PMC10964180 DOI: 10.1002/pmic.202100387] [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] [Received: 10/13/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
The turnover measurement of proteins and proteoforms has been largely facilitated by workflows coupling metabolic labeling with mass spectrometry (MS), including dynamic stable isotope labeling by amino acids in cell culture (dynamic SILAC) or pulsed SILAC (pSILAC). Very recent studies including ours have integrated themeasurement of post-translational modifications (PTMs) at the proteome level (i.e., phosphoproteomics) with pSILAC experiments in steady state systems, exploring the link between PTMs and turnover at the proteome-scale. An open question in the field is how to exactly interpret these complex datasets in a biological perspective. Here, we present a novel pSILAC phosphoproteomic dataset which was obtained during a dynamic process of cell starvation using data-independent acquisition MS (DIA-MS). To provide an unbiased "hypothesis-free" analysis framework, we developed a strategy to interrogate how phosphorylation dynamically impacts protein turnover across the time series data. With this strategy, we discovered a complex relationship between phosphorylation and protein turnover that was previously underexplored. Our results further revealed a link between phosphorylation stoichiometry with the turnover of phosphorylated peptidoforms. Moreover, our results suggested that phosphoproteomic turnover diversity cannot directly explain the abundance regulation of phosphorylation during cell starvation, underscoring the importance of future studies addressing PTM site-resolved protein turnover.
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Affiliation(s)
- Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Eugenio F. Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
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7
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Comparative Ubiquitination Proteomics Revealed the Salt Tolerance Mechanism in Sugar Beet Monomeric Additional Line M14. Int J Mol Sci 2022; 23:ijms232416088. [PMID: 36555729 PMCID: PMC9782053 DOI: 10.3390/ijms232416088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Post-translational modifications (PTMs) are important molecular processes that regulate organismal responses to different stresses. Ubiquitination modification is not only involved in human health but also plays crucial roles in plant growth, development, and responses to environmental stresses. In this study, we investigated the ubiquitination proteome changes in the salt-tolerant sugar beet monomeric additional line M14 under salt stress treatments. Based on the expression of the key genes of the ubiquitination system and the ubiquitination-modified proteins before and after salt stress, 30 min of 200 mM NaCl treatment and 6 h of 400 mM NaCl treatment were selected as time points. Through label-free proteomics, 4711 and 3607 proteins were identified in plants treated with 200 mM NaCl and 400 mM NaCl, respectively. Among them, 611 and 380 proteins were ubiquitinated, with 1085 and 625 ubiquitination sites, in the two salt stress conditions, respectively. A quantitative analysis revealed that 70 ubiquitinated proteins increased and 47 ubiquitinated proteins decreased. At the total protein level, 42 were induced and 20 were repressed with 200 mM NaCl, while 28 were induced and 27 were repressed with 400 mM NaCl. Gene ontology, KEGG pathway, protein interaction, and PTM crosstalk analyses were performed using the differentially ubiquitinated proteins. The differentially ubiquitinated proteins were mainly involved in cellular transcription and translation processes, signal transduction, metabolic pathways, and the ubiquitin/26S proteasome pathway. The uncovered ubiquitinated proteins constitute an important resource of the plant stress ubiquitinome, and they provide a theoretical basis for the marker-based molecular breeding of crops for enhanced stress tolerance.
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8
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Leite AC, Martins TS, Campos A, Costa V, Pereira C. Phosphoregulation of the ATP synthase beta subunit stimulates mitochondrial activity for G2/M progression. Adv Biol Regul 2022; 85:100905. [PMID: 36030696 DOI: 10.1016/j.jbior.2022.100905] [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: 07/03/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022]
Abstract
Mitochondrial ATP synthase is a multifunctional enzyme complex involved in ATP production. We previously reported that the ATP synthase catalytic beta subunit (Atp2p in yeast) is regulated by the 2A-like protein phosphatase Sit4p, which targets Atp2p at T124/T317 impacting on ATP synthase levels and mitochondrial respiration. Here we report that Atp2-T124/T317 is also potentially regulated by Cdc5p, a polo-like mitotic kinase. Since both Cdc5p and Sit4p have established roles in cell cycle regulation, we investigated whether Atp2-T124/T317 phosphorylation was cell cycle-related. We present evidence that Atp2p levels and phosphorylation vary during cell cycle progression, with an increase at G2/M phase. Atp2-T124/T317 phosphorylation stimulates mitochondrial membrane potential, respiration and ATP levels at G2/M phase, indicating that dynamic Atp2p phosphorylation contributes to mitochondrial activity at this specific cell cycle phase. Preventing Atp2p phosphorylation delays G2/M to G1 transition, suggesting that enhanced bioenergetics at G2/M may help meet the energetic demands of cell cycle progression. However, mimicking constitutive T124/T317 phosphorylation or overexpressing Atp2p leads to mitochondrial DNA instability, indicating that reversible Atp2p phosphorylation is critical for homeostasis. These results indicate that transient phosphorylation of Atp2p, a protein at the core of the ATP production machinery, impacts on mitochondrial bioenergetics and supports cell cycle progression at G2/M.
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Affiliation(s)
- Ana Cláudia Leite
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Telma Silva Martins
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Ana Campos
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal
| | - Vítor Costa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Clara Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal.
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9
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Hsu KL, Yen HCS, Yeang CH. Cooperative stability renders protein complex formation more robust and controllable. Sci Rep 2022; 12:10490. [PMID: 35729235 PMCID: PMC9213465 DOI: 10.1038/s41598-022-14362-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/06/2022] [Indexed: 11/19/2022] Open
Abstract
Protein complexes are the fundamental units of many biological functions. Despite their many advantages, one major adverse impact of protein complexes is accumulations of unassembled subunits that may disrupt other processes or exert cytotoxic effects. Synthesis of excess subunits can be inhibited via negative feedback control or they can be degraded more efficiently than assembled subunits, with this latter being termed cooperative stability. Whereas controlled synthesis of complex subunits has been investigated extensively, how cooperative stability acts in complex formation remains largely unexplored. To fill this knowledge gap, we have built quantitative models of heteromeric complexes with or without cooperative stability and compared their behaviours in the presence of synthesis rate variations. A system displaying cooperative stability is robust against synthesis rate variations as it retains high dimer/monomer ratios across a broad range of parameter configurations. Moreover, cooperative stability can alleviate the constraint of limited supply of a given subunit and makes complex abundance more responsive to unilateral upregulation of another subunit. We also conducted an in silico experiment to comprehensively characterize and compare four types of circuits that incorporate combinations of negative feedback control and cooperative stability in terms of eight systems characteristics pertaining to optimality, robustness and controllability. Intriguingly, though individual circuits prevailed for distinct characteristics, the system with cooperative stability alone achieved the most balanced performance across all characteristics. Our study provides theoretical justification for the contribution of cooperative stability to natural biological systems and represents a guideline for designing synthetic complex formation systems with desirable characteristics.
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Affiliation(s)
- Kuan-Lun Hsu
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Taipei, Taiwan
| | - Hsueh-Chi S Yen
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Taipei, Taiwan
| | - Chen-Hsiang Yeang
- Institute of Statistical Science, Academia Sinica, 128 Academia Road, Section 2, Taipei, Taiwan.
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10
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Guharoy M, Lazar T, Macossay-Castillo M, Tompa P. Degron masking outlines degronons, co-degrading functional modules in the proteome. Commun Biol 2022; 5:445. [PMID: 35545699 PMCID: PMC9095673 DOI: 10.1038/s42003-022-03391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/22/2022] [Indexed: 11/28/2022] Open
Abstract
Effective organization of proteins into functional modules (networks, pathways) requires systems-level coordination between transcription, translation and degradation. Whereas the cooperation between transcription and translation was extensively studied, the cooperative degradation regulation of protein complexes and pathways has not been systematically assessed. Here we comprehensively analyzed degron masking, a major mechanism by which cellular systems coordinate degron recognition and protein degradation. For over 200 substrates with characterized degrons (E3 ligase targeting motifs, ubiquitination sites and disordered proteasomal entry sequences), we demonstrate that degrons extensively overlap with protein-protein interaction sites. Analysis of binding site information and protein abundance comparisons show that regulatory partners effectively outcompete E3 ligases, masking degrons from the ubiquitination machinery. Protein abundance variations between normal and cancer cells highlight the dynamics of degron masking components. Finally, integrative analysis of gene co-expression, half-life correlations and functional relationships between interacting proteins point towards higher-order, co-regulated degradation modules (‘degronons’) in the proteome. Systematic bioinformatics analysis of cooperative degradation of protein complexes indicates that degrons extensively overlap with protein-protein interaction sites, hiding degrons from ubiquitination machinery and suggesting the existence of co-degrading functional modules in the proteome.
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Affiliation(s)
- Mainak Guharoy
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium. .,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium. .,VIB Bioinformatics Core, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium.
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Mauricio Macossay-Castillo
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium. .,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, 1117, Budapest, Hungary.
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11
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Strini EJ, Bertolino LT, San Martin JAB, Souza HAO, Pessotti F, Pinoti VF, Ferreira PB, De Paoli HC, Lubini G, Del-Bem LE, Quiapim AC, Mondin M, Araujo APU, Eloy NB, Barberis M, Goldman MHS. Stigma/Style Cell-Cycle Inhibitor 1, a Regulator of Cell Proliferation, Interacts With a Specific 14-3-3 Protein and Is Degraded During Cell Division. FRONTIERS IN PLANT SCIENCE 2022; 13:857745. [PMID: 35444668 PMCID: PMC9013909 DOI: 10.3389/fpls.2022.857745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The final shape and size of plant organs are determined by a network of genes that modulate cell proliferation and expansion. Among those, SCI1 (Stigma/style Cell-cycle Inhibitor 1) functions by inhibiting cell proliferation during pistil development. Alterations in SCI1 expression levels can lead to remarkable stigma/style size changes. Recently, we demonstrated that SCI1 starts to be expressed at the specification of the Nicotiana tabacum floral meristem and is expressed at all floral meristematic cells. To elucidate how SCI1 regulates cell proliferation, we screened a stigma/style cDNA library through the yeast two-hybrid (Y2H) system, using SCI1 as bait. Among the interaction partners, we identified the 14-3-3D protein of the Non-Epsilon group. The interaction between SCI1 and 14-3-3D was confirmed by pulldown and co-immunoprecipitation experiments. 14-3-3D forms homo- and heterodimers in the cytoplasm of plant cells and interacts with SCI1 in the nucleus, as demonstrated by Bimolecular Fluorescence Complementation (BiFC). Analyses of SCI1-GFP fluorescence through the cell-cycle progression revealed its presence in the nucleoli during interphase and prophase. At metaphase, SCI1-GFP fluorescence faded and was no longer detected at anaphase, reappearing at telophase. Upon treatment with the 26S proteasome inhibitor MG132, SCI1-GFP was stabilized during cell division. Site-directed mutagenesis of seven serines into alanines in the predicted 14-3-3 binding sites on the SCI1 sequence prevented its degradation during mitosis. Our results demonstrate that SCI1 degradation at the beginning of metaphase is dependent on the phosphorylation of serine residues and on the action of the 26S proteasome. We concluded that SCI1 stability/degradation is cell-cycle regulated, consistent with its role in fine-tuning cell proliferation.
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Affiliation(s)
- Edward J. Strini
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Lígia T. Bertolino
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Juca A. B. San Martin
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Hebréia A. O. Souza
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Francine Pessotti
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Vitor F. Pinoti
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Pedro B. Ferreira
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Henrique C. De Paoli
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Greice Lubini
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz-Eduardo Del-Bem
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Andréa C. Quiapim
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Mateus Mondin
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, Piracicaba, Brazil
| | - Ana Paula U. Araujo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Nubia B. Eloy
- Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, Piracicaba, Brazil
| | - Matteo Barberis
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Maria Helena S. Goldman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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12
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Rusilowicz-Jones EV, Urbé S, Clague MJ. Protein degradation on the global scale. Mol Cell 2022; 82:1414-1423. [PMID: 35305310 DOI: 10.1016/j.molcel.2022.02.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/01/2022] [Accepted: 02/17/2022] [Indexed: 12/15/2022]
Abstract
Protein degradation occurs through proteasomal, endosomal, and lysosomal pathways. Technological advancements have allowed for the determination of protein copy numbers and turnover rates on a global scale, which has provided an overview of trends and rules governing protein degradation. Sharper chemical and gene-editing tools have enabled the specific perturbation of each degradation pathway, whose effects on protein dynamics can now be comprehensively analyzed. We review major studies and innovation in this field and discuss the interdependence between the major pathways of protein degradation.
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Affiliation(s)
- Emma V Rusilowicz-Jones
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Sylvie Urbé
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Michael J Clague
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
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13
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Kliche J, Ivarsson Y. Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs. Biochem J 2022; 479:1-22. [PMID: 34989786 PMCID: PMC8786283 DOI: 10.1042/bcj20200714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
Cellular function is based on protein-protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications, such as phosphorylation, that create and break motif binding sites or tune the affinity of the interactions. In addition, motif-based interactions are involved in targeting serine/threonine kinases and phosphatases to their substrate and contribute to the specificity of the enzymatic actions regulating which sites are phosphorylated. Here, we review how SLiM-based interactions assist in determining the specificity of serine/threonine kinases and phosphatases, and how phosphorylation, in turn, affects motif-based interactions. We provide examples of SLiM-based interactions that are turned on/off, or are tuned by serine/threonine phosphorylation and exemplify how this affects SLiM-based protein complex formation.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
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14
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Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling. Nat Commun 2022; 13:165. [PMID: 35013197 PMCID: PMC8748498 DOI: 10.1038/s41467-021-27639-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 12/02/2021] [Indexed: 12/21/2022] Open
Abstract
Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labeling and mass spectrometry to measure the turnover of >120,000 peptidoforms including >33,000 phosphorylated, acetylated, and ubiquitinated peptides for >9,000 native proteins. This site-resolved protein turnover (SPOT) profiling discloses global and site-specific differences in turnover associated with the presence or absence of PTMs. While causal relationships may not always be immediately apparent, we speculate that PTMs with diverging turnover may distinguish states of differential protein stability, structure, localization, enzymatic activity, or protein-protein interactions. We show examples of how the turnover data may give insights into unknown functions of PTMs and provide a freely accessible online tool that allows interrogation and visualisation of all turnover data. The SPOT methodology is applicable to many cell types and modifications, offering the potential to prioritize PTMs for future functional investigations. Post-translational modifications (PTMs) can regulate cellular protein function but their global impact on protein turnover is largely unknown. Here, the authors develop proteomic workflows to profile PTM-resolved protein turnover and analyze the effects of phosphorylation, acetylation and ubiquitination.
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15
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Smol T, Frénois F, Manouvrier-Hanu S, Petit F, Ghoumid J. Performance of meta-predictors for the classification of MED13L missense variations, implication of raw parameters. Eur J Med Genet 2021; 65:104398. [PMID: 34798324 DOI: 10.1016/j.ejmg.2021.104398] [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: 06/23/2021] [Revised: 09/14/2021] [Accepted: 11/13/2021] [Indexed: 11/26/2022]
Abstract
MED13L syndrome is a rare congenital disorder comprising moderate intellectual disability, hypotonia and facial dysmorphism. Whole exome or genome sequencing in patients with non-specific neurodevelopmental disorders leads to identification of an increasing number of MED13L missense variations of unknown signification. The aim of our study was to identify relevant annotation parameters enhancing discrimination between candidate pathogenic or neutral missense variations, and to assess the performance of seven meta-predictor algorithms: BayesDel, CADD, DANN, FATHMM-XF, M-CAP, MISTIC and REVEL for the classification of MED13L missense variants. Significant differences were identified for five parameters: global conservation through verPhyloP and verPhCons scores; physico-chemical difference between amino acids estimated by Grantham scores; conservation of residues between MED13L and MED13 protein; proximity to phosphorylation sites for pathogenic variations. Among the seven selected in-silico tools, BayesDel, REVEL, and MISTIC provided the most interesting performances to discriminate pathogenic from neutral missense variations. Individual gene parameter studies with MED13L have provided expertise on elements of annotation improving meta-predictor choices. The in-silico approach allows us to make valuable hypotheses to predict the involvement of these amino acids in MED13L pathogenic missense variations.
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Affiliation(s)
- Thomas Smol
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Institut de Génétique Médicale, F-59000, Lille, France
| | - Frédéric Frénois
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France
| | - Sylvie Manouvrier-Hanu
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France
| | - Florence Petit
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France
| | - Jamal Ghoumid
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France.
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16
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Chen JS, Jones CM, Igarashi MG, Ren L, Johnson AE, Gould KL. Localization of the ubiquitin ligase Dma1 to the fission yeast contractile ring is modulated by phosphorylation. FEBS Lett 2021; 595:2781-2792. [PMID: 34674264 PMCID: PMC8721890 DOI: 10.1002/1873-3468.14211] [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: 09/06/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/06/2022]
Abstract
The timing of cytokinesis relative to other mitotic events in the fission yeast Schizosaccharomyces pombe is controlled by the septation initiation network (SIN). During a mitotic checkpoint, the SIN is inhibited by the E3 ubiquitin ligase Dma1 to prevent chromosome mis-segregation. Dma1 dynamically localizes to spindle pole bodies (SPBs) and the contractile ring (CR) during mitosis, though its role at the CR is unknown. Here, we examined whether Dma1 phosphorylation affects its localization or function. We found that preventing Dma1 phosphorylation by substituting the six phosphosites with alanines diminished its CR localization but did not affect its mitotic checkpoint function. These studies reinforce the conclusion that Dma1 localization to the SPB is key to its role in the mitotic checkpoint.
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Affiliation(s)
- Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240
| | | | - Maya G. Igarashi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240
| | | | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240
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17
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Correa Marrero M, Barrio-Hernandez I. Toward Understanding the Biochemical Determinants of Protein Degradation Rates. ACS OMEGA 2021; 6:5091-5100. [PMID: 33681549 PMCID: PMC7931188 DOI: 10.1021/acsomega.0c05318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Protein degradation is a key component of the regulation of gene expression and is at the center of several pathogenic processes. Proteins are regularly degraded, but there is large variation in their lifetimes, and the kinetics of protein degradation are not well understood. Many different factors can influence protein degradation rates, painting a highly complex picture. This has been partially unravelled in recent years thanks to invaluable advances in proteomics techniques. In this Mini-Review, we give a global vision of the determinants of protein degradation rates with the backdrop of the current understanding of proteolytic systems to give a contemporary view of the field.
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Affiliation(s)
- Miguel Correa Marrero
- European
Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10
1SD, United Kingdom
| | - Inigo Barrio-Hernandez
- European
Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10
1SD, United Kingdom
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18
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Alquezar C, Arya S, Kao AW. Tau Post-translational Modifications: Dynamic Transformers of Tau Function, Degradation, and Aggregation. Front Neurol 2021; 11:595532. [PMID: 33488497 PMCID: PMC7817643 DOI: 10.3389/fneur.2020.595532] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Post-translational modifications (PTMs) on tau have long been recognized as affecting protein function and contributing to neurodegeneration. The explosion of information on potential and observed PTMs on tau provides an opportunity to better understand these modifications in the context of tau homeostasis, which becomes perturbed with aging and disease. Prevailing views regard tau as a protein that undergoes abnormal phosphorylation prior to its accumulation into the toxic aggregates implicated in Alzheimer's disease (AD) and other tauopathies. However, the phosphorylation of tau may, in fact, represent part of the normal but interrupted function and catabolism of the protein. In addition to phosphorylation, tau undergoes another forms of post-translational modification including (but not limited to), acetylation, ubiquitination, glycation, glycosylation, SUMOylation, methylation, oxidation, and nitration. A holistic appreciation of how these PTMs regulate tau during health and are potentially hijacked in disease remains elusive. Recent studies have reinforced the idea that PTMs play a critical role in tau localization, protein-protein interactions, maintenance of levels, and modifying aggregate structure. These studies also provide tantalizing clues into the possibility that neurons actively choose how tau is post-translationally modified, in potentially competitive and combinatorial ways, to achieve broad, cellular programs commensurate with the distinctive environmental conditions found during development, aging, stress, and disease. Here, we review tau PTMs and describe what is currently known about their functional impacts. In addition, we classify these PTMs from the perspectives of protein localization, electrostatics, and stability, which all contribute to normal tau function and homeostasis. Finally, we assess the potential impact of tau PTMs on tau solubility and aggregation. Tau occupies an undoubtedly important position in the biology of neurodegenerative diseases. This review aims to provide an integrated perspective of how post-translational modifications actively, purposefully, and dynamically remodel tau function, clearance, and aggregation. In doing so, we hope to enable a more comprehensive understanding of tau PTMs that will positively impact future studies.
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Affiliation(s)
- Carolina Alquezar
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States
| | - Shruti Arya
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States
| | - Aimee W Kao
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States
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19
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Separovich RJ, Wong MWM, Chapman TR, Slavich E, Hamey JJ, Wilkins MR. Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential. J Biol Chem 2021; 296:100192. [PMID: 33334889 PMCID: PMC7948420 DOI: 10.1074/jbc.ra120.015995] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/06/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022] Open
Abstract
Histone methylation is central to the regulation of eukaryotic transcription. In Saccharomyces cerevisiae, it is controlled by a system of four methyltransferases (Set1p, Set2p, Set5p, and Dot1p) and four demethylases (Jhd1p, Jhd2p, Rph1p, and Gis1p). While the histone targets for these enzymes are well characterized, the connection of the enzymes with the intracellular signaling network and thus their regulation is poorly understood; this also applies to all other eukaryotes. Here we report the detailed characterization of the eight S. cerevisiae enzymes and show that they carry a total of 75 phosphorylation sites, 92 acetylation sites, and two ubiquitination sites. All enzymes are subject to phosphorylation, although demethylases Jhd1p and Jhd2p contained one and five sites respectively, whereas other enzymes carried 14 to 36 sites. Phosphorylation was absent or underrepresented on catalytic and other domains but strongly enriched for regions of disorder on methyltransferases, suggesting a role in the modulation of protein-protein interactions. Through mutagenesis studies, we show that phosphosites within the acidic and disordered N-terminus of Set2p affect H3K36 methylation levels in vivo, illustrating the functional importance of such sites. While most kinases upstream of the yeast histone methylation enzymes remain unknown, we model the possible connections between the cellular signaling network and the histone-based gene regulatory system and propose an integrated regulatory structure. Our results provide a foundation for future, detailed exploration of the role of specific kinases and phosphosites in the regulation of histone methylation.
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Affiliation(s)
- Ryan J Separovich
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mandy W M Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Tyler R Chapman
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Eve Slavich
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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20
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Abstract
The ubiquitin–proteasome system (UPS) is responsible for the rapid targeting of proteins for degradation at 26S proteasomes and requires the orchestrated action of E1, E2 and E3 enzymes in a well-defined cascade. F-box proteins (FBPs) are substrate-recruiting subunits of Skp1-cullin1-FBP (SCF)-type E3 ubiquitin ligases that determine which proteins are ubiquitinated. To date, around 70 FBPs have been identified in humans and can be subdivided into distinct families, based on the protein-recruiting domains they possess. The FBXL subfamily is defined by the presence of multiple leucine-rich repeat (LRR) protein-binding domains. But how the 22 FBPs of the FBXL family achieve their individual specificities, despite having highly similar structural domains to recruit their substrates, is not clear. Here, we review and explore the FBXL family members in detail highlighting their structural and functional similarities and differences and how they engage their substrates through their LRRs to adopt unique interactomes.
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Affiliation(s)
- Bethany Mason
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
| | - Heike Laman
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
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21
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Wu C, Ba Q, Lu D, Li W, Salovska B, Hou P, Mueller T, Rosenberger G, Gao E, Di Y, Zhou H, Fornasiero EF, Liu Y. Global and Site-Specific Effect of Phosphorylation on Protein Turnover. Dev Cell 2020; 56:111-124.e6. [PMID: 33238149 DOI: 10.1016/j.devcel.2020.10.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/05/2020] [Accepted: 10/30/2020] [Indexed: 02/02/2023]
Abstract
To date, the effects of specific modification types and sites on protein lifetime have not been systematically illustrated. Here, we describe a proteomic method, DeltaSILAC, to quantitatively assess the impact of site-specific phosphorylation on the turnover of thousands of proteins in live cells. Based on the accurate and reproducible mass spectrometry-based method, a pulse labeling approach using stable isotope-labeled amino acids in cells (pSILAC), phosphoproteomics, and a unique peptide-level matching strategy, our DeltaSILAC profiling revealed a global, unexpected delaying effect of many phosphosites on protein turnover. We further found that phosphorylated sites accelerating protein turnover are functionally selected for cell fitness, enriched in Cyclin-dependent kinase substrates, and evolutionarily conserved, whereas the glutamic acids surrounding phosphosites significantly delay protein turnover. Our method represents a generalizable approach and provides a rich resource for prioritizing the effects of phosphorylation sites on protein lifetime in the context of cell signaling and disease biology.
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Affiliation(s)
- Chongde Wu
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qian Ba
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Dayun Lu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pingfu Hou
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Torsten Mueller
- German Cancer Research Center, DKFZ, 69120 Heidelberg, Germany
| | | | - Erli Gao
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yi Di
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
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22
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Manohar S, Yu Q, Gygi SP, King RW. The Insulin Receptor Adaptor IRS2 is an APC/C Substrate That Promotes Cell Cycle Protein Expression and a Robust Spindle Assembly Checkpoint. Mol Cell Proteomics 2020; 19:1450-1467. [PMID: 32554797 PMCID: PMC8143631 DOI: 10.1074/mcp.ra120.002069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/01/2020] [Indexed: 01/21/2023] Open
Abstract
Insulin receptor substrate 2 (IRS2) is an essential adaptor that mediates signaling downstream of the insulin receptor and other receptor tyrosine kinases. Transduction through IRS2-dependent pathways is important for coordinating metabolic homeostasis, and dysregulation of IRS2 causes systemic insulin signaling defects. Despite the importance of maintaining proper IRS2 abundance, little is known about what factors mediate its protein stability. We conducted an unbiased proteomic screen to uncover novel substrates of the Anaphase Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that controls the abundance of key cell cycle regulators. We found that IRS2 levels are regulated by APC/C activity and that IRS2 is a direct APC/C target in G1 Consistent with the APC/C's role in degrading cell cycle regulators, quantitative proteomic analysis of IRS2-null cells revealed a deficiency in proteins involved in cell cycle progression. We further show that cells lacking IRS2 display a weakened spindle assembly checkpoint in cells treated with microtubule inhibitors. Together, these findings reveal a new pathway for IRS2 turnover and indicate that IRS2 is a component of the cell cycle control system in addition to acting as an essential metabolic regulator.
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Affiliation(s)
- Sandhya Manohar
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Randall W King
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
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23
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Chua NK, Coates HW, Brown AJ. Squalene monooxygenase: a journey to the heart of cholesterol synthesis. Prog Lipid Res 2020; 79:101033. [DOI: 10.1016/j.plipres.2020.101033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
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24
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Butler VJ, Salazar DA, Soriano-Castell D, Alves-Ferreira M, Dennissen FJA, Vohra M, Oses-Prieto JA, Li KH, Wang AL, Jing B, Li B, Groisman A, Gutierrez E, Mooney S, Burlingame AL, Ashrafi K, Mandelkow EM, Encalada SE, Kao AW. Tau/MAPT disease-associated variant A152T alters tau function and toxicity via impaired retrograde axonal transport. Hum Mol Genet 2020; 28:1498-1514. [PMID: 30590647 PMCID: PMC6489414 DOI: 10.1093/hmg/ddy442] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/19/2018] [Accepted: 12/17/2018] [Indexed: 12/17/2022] Open
Abstract
Mutations in the microtubule-associated protein tau (MAPT) underlie multiple neurodegenerative disorders, yet the pathophysiological mechanisms are unclear. A novel variant in MAPT resulting in an alanine to threonine substitution at position 152 (A152T tau) has recently been described as a significant risk factor for both frontotemporal lobar degeneration and Alzheimer’s disease. Here we use complementary computational, biochemical, molecular, genetic and imaging approaches in Caenorhabditis elegans and mouse models to interrogate the effects of the A152T variant on tau function. In silico analysis suggests that a threonine at position 152 of tau confers a new phosphorylation site. This finding is borne out by mass spectrometric survey of A152T tau phosphorylation in C. elegans and mouse. Optical pulse-chase experiments of Dendra2-tau demonstrate that A152T tau and phosphomimetic A152E tau exhibit increased diffusion kinetics and the ability to traverse across the axon initial segment more efficiently than wild-type (WT) tau. A C. elegans model of tauopathy reveals that A152T and A152E tau confer patterns of developmental toxicity distinct from WT tau, likely due to differential effects on retrograde axonal transport. These data support a role for phosphorylation of the variant threonine in A152T tau toxicity and suggest a mechanism involving impaired retrograde axonal transport contributing to human neurodegenerative disease.
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Affiliation(s)
- Victoria J Butler
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Dominique A Salazar
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - David Soriano-Castell
- Departments of Molecular Medicine and Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Miguel Alves-Ferreira
- Departments of Molecular Medicine and Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Frank J A Dennissen
- German Center for Neurodegenerative Diseases (DZNE), Ludwig-Erhard-Allee 2, Bonn, Germany.,MPI for Neurological Research, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg, Germany.,The Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, Bonn, Germany
| | - Mihir Vohra
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Austin L Wang
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Beibei Jing
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Biao Li
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Alex Groisman
- Department of Physics, University of California San Diego, La Jolla, CA, USA
| | - Edgar Gutierrez
- Department of Physics, University of California San Diego, La Jolla, CA, USA
| | - Sean Mooney
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Kaveh Ashrafi
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Eva-Maria Mandelkow
- German Center for Neurodegenerative Diseases (DZNE), Ludwig-Erhard-Allee 2, Bonn, Germany.,MPI for Neurological Research, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg, Germany.,The Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, Bonn, Germany
| | - Sandra E Encalada
- Departments of Molecular Medicine and Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Aimee W Kao
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
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25
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Wang X, Rusin A, Walkey CJ, Lin JJ, Johnson DL. The RNA polymerase III repressor MAF1 is regulated by ubiquitin-dependent proteasome degradation and modulates cancer drug resistance and apoptosis. J Biol Chem 2019; 294:19255-19268. [PMID: 31645432 DOI: 10.1074/jbc.ra119.008849] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/01/2019] [Indexed: 01/03/2023] Open
Abstract
MAF1 homolog, negative regulator of RNA polymerase III (MAF1) is a key repressor of RNA polymerase (pol) III-dependent transcription and functions as a tumor suppressor. Its expression is frequently down-regulated in primary human hepatocellular carcinomas (HCCs). However, this reduction in MAF1 protein levels does not correlate with its transcript levels, indicating that MAF1 is regulated post-transcriptionally. Here, we demonstrate that MAF1 is a labile protein whose levels are regulated through the ubiquitin-dependent proteasome pathway. We found that MAF1 ubiquitination is enhanced upon mTOR complex 1 (TORC1)-mediated phosphorylation at Ser-75. Moreover, we observed that the E3 ubiquitin ligase cullin 2 (CUL2) critically regulates MAF1 ubiquitination and controls its stability and subsequent RNA pol III-dependent transcription. Analysis of the phenotypic consequences of modulating either CUL2 or MAF1 protein expression revealed changes in actin cytoskeleton reorganization and altered sensitivity to doxorubicin-induced apoptosis. Repression of RNA pol III-dependent transcription by chemical inhibition or knockdown of BRF1 RNA pol III transcription initiation factor subunit (BRF1) enhanced HCC cell sensitivity to doxorubicin, suggesting that MAF1 regulates doxorubicin resistance in HCC by controlling RNA pol III-dependent transcription. Together, our results identify the ubiquitin proteasome pathway and CUL2 as important regulators of MAF1 levels. They suggest that decreases in MAF1 protein underlie chemoresistance in HCC and perhaps other cancers and point to an important role for MAF1 and RNA pol III-mediated transcription in chemosensitivity and apoptosis.
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Affiliation(s)
- Xianlong Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Aleksandra Rusin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Christopher J Walkey
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | | | - Deborah L Johnson
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
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26
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Ehm PAH, Lange F, Hentschel C, Jepsen A, Glück M, Nelson N, Bettin B, de Bruyn Kops C, Kirchmair J, Nalaskowski M, Jücker M. Analysis of the FLVR motif of SHIP1 and its importance for the protein stability of SH2 containing signaling proteins. Cell Signal 2019; 63:109380. [PMID: 31377397 DOI: 10.1016/j.cellsig.2019.109380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022]
Abstract
Binding of proteins with SH2 domains to tyrosine-phosphorylated signaling proteins is a key mechanism for transmission of biological signals within the cell. Characterization of dysregulated proteins in cell signaling pathways is important for the development of therapeutic approaches. The AKT pathway is a frequently upregulated pathway in most cancer cells and the SH2-containing inositol 5-phosphatase SHIP1 is a negative regulator of the AKT pathway. In this study we investigated different mutations of the conserved FLVR motif of the SH2 domain and putative phosphorylation sites of SHIP1 which are located in close proximity to its FLVR motif. We demonstrate that patient-derived SHIP1-FLVR motif mutations e.g. F28L, and L29F possess reduced protein expression and increased phospho-AKT-S473 levels in comparison to SHIP1 wildtype. The estimated half-life of SHIP1-F28L protein was reduced from 23.2 h to 0.89 h in TF-1 cells and from 4.7 h to 0.6 h in Jurkat cells. These data indicate that the phenylalanine residue at position 28 of SHIP1 is important for its stability. Replacement of F28 with other aromatic residues like tyrosine and tryptophan preserves protein stability while replacement with non-aromatic amino acids like leucine, isoleucine, valine or alanine severely affects the stability of SHIP1. In consequence, a SHIP1-mutant with an aromatic amino acid at position 28 i.e. F28W can rescue the inhibitory function of wild type SHIP1, whereas SHIP1-mutants with non-aromatic amino acids i.e. F28V do not inhibit cell growth anymore. A detailed structural analysis revealed that F28 forms hydrophobic surface contacts in particular with W5, I83, L97 and P100 which can be maintained by tyrosine and tryptophan residues, but not by non-aromatic residues at position 28. In line with this model of mutation-induced instability of SHIP1-F28L, treatment of cells with proteasomal inhibitor MG132 was able to rescue expression of SHIP1-F28L. In addition, mutation of putative phosphorylation sites S27 and S33 adjacent to the FLVR motif of SHIP1 have an influence on its protein stability. These results further support a functional role of SHIP1 as tumor suppressor protein and indicate a regulation of protein expression of SH2 domain containing proteins via the FLVR motif.
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Affiliation(s)
- Patrick A H Ehm
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Fabiola Lange
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Carolin Hentschel
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Anneke Jepsen
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Madeleine Glück
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Nina Nelson
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Bettina Bettin
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Christina de Bruyn Kops
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, 20146 Hamburg, Germany
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, 20146 Hamburg, Germany; Department of Chemistry, University of Bergen, N-5020 Bergen, Norway; Computational Biology Unit (CBU), University of Bergen, N-5020 Bergen, Norway
| | - Marcus Nalaskowski
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Manfred Jücker
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany.
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27
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Abstract
The quantitative model of cyclin-dependent kinase (CDK) function states that cyclins temporally order cell cycle events at different CDK activity levels, or thresholds. The model lacks a mechanistic explanation, as it is not understood how different thresholds are encoded into substrates. We show that a multisite phosphorylation code governs the phosphorylation of CDK targets and that phosphorylation clusters act as timing tags that trigger specific events at different CDK thresholds. Using phospho-degradable CDK threshold sensors with rationally encoded phosphorylation patterns, we were able to predictably program thresholds over the entire range of the Saccharomyces cerevisiae cell cycle. We defined three levels of CDK multisite phosphorylation encoding: (i) Ser-Thr swapping in phosphorylation sites, (ii) patterning of phosphorylation sites, and (iii) cyclin-specific docking combined with modulation of CDK activity. Thus, CDK can signal via hundreds of differentially encoded targets at precise times to provide a temporally ordered phosphorylation pattern required for cell division.
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28
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Hu Q, Li C, Wang S, Li Y, Wen B, Zhang Y, Liang K, Yao J, Ye Y, Hsiao H, Nguyen TK, Park PK, Egranov SD, Hawke DH, Marks JR, Han L, Hung MC, Zhang B, Lin C, Yang L. LncRNAs-directed PTEN enzymatic switch governs epithelial-mesenchymal transition. Cell Res 2019; 29:286-304. [PMID: 30631154 PMCID: PMC6461864 DOI: 10.1038/s41422-018-0134-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023] Open
Abstract
Despite the structural conservation of PTEN with dual-specificity phosphatases, there have been no reports regarding the regulatory mechanisms that underlie this potential dual-phosphatase activity. Here, we report that K27-linked polyubiquitination of PTEN at lysines 66 and 80 switches its phosphoinositide/protein tyrosine phosphatase activity to protein serine/threonine phosphatase activity. Mechanistically, high glucose, TGF-β, CTGF, SHH, and IL-6 induce the expression of a long non-coding RNA, GAEA (Glucose Aroused for EMT Activation), which associates with an RNA-binding E3 ligase, MEX3C, and enhances its enzymatic activity, leading to the K27-linked polyubiquitination of PTEN. The MEX3C-catalyzed PTENK27-polyUb activates its protein serine/threonine phosphatase activity and inhibits its phosphatidylinositol/protein tyrosine phosphatase activity. With this altered enzymatic activity, PTENK27-polyUb dephosphorylates the phosphoserine/threonine residues of TWIST1, SNAI1, and YAP1, leading to accumulation of these master regulators of EMT. Animals with genetic inhibition of PTENK27-polyUb, by a single nucleotide mutation generated using CRISPR/Cas9 (PtenK80R/K80R), exhibit inhibition of EMT markers during mammary gland morphogenesis in pregnancy/lactation and during cutaneous wound healing processes. Our findings illustrate an unexpected paradigm in which the lncRNA-dependent switch in PTEN protein serine/threonine phosphatase activity is important for physiological homeostasis and disease development.
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Affiliation(s)
- Qingsong Hu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chunlai Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shouyu Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, China
| | - Yajuan Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bo Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yanyan Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Institute of Immunology, Third Military Medical University, 400038, Chongqing, China
| | - Ke Liang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGroven Medical School, Houston, TX, 77030, USA
| | - Heidi Hsiao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Tina K Nguyen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Peter K Park
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sergey D Egranov
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David H Hawke
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jeffrey R Marks
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGroven Medical School, Houston, TX, 77030, USA
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Program in Cancer Biology, Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Program in Cancer Biology, Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Program in Cancer Biology, Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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29
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Tay AP, Liang A, Wilkins MR, Pang CNI. Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle. ACTA ACUST UNITED AC 2019; 66:e71. [PMID: 30653846 DOI: 10.1002/cpbi.71] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Post-translational modifications (PTMs) of proteins act as key regulators of protein activity, including the regulation of protein-protein interactions (PPIs). However, exploring functional links between PTMs and PPIs can be difficult. PTMOracle is a Cytoscape app that facilitates the co-visualization and co-analysis of PTMs in the context of PPI networks. PTMOracle also allows extensive data to be integrated and co-analyzed, allowing the role of domains, motifs, and disordered regions to be considered. Here, we describe several PTMOracle protocols investigating complex PTM-associated relationships and their role in PPIs. This is assisted by OraclePainter for coloring proteins by the modifications present and visualizing these in the context of networks, by OracleTools for cross-matching PTMs with sequence feature for all nodes in the network, and by OracleResults for exploring specific proteins and visualizing their PTMs in the context of protein sequences. This unit aims to demonstrate how PTMOracle can be used to systematically explore network visualizations and generate testable hypotheses regarding the functional role of PTMs in PPIs, and how the results can be analyzed to better understand the regulatory role of PTMs in PPIs. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Aidan P Tay
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Angelita Liang
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Chi Nam Ignatius Pang
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
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30
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Vu LD, Gevaert K, De Smet I. Protein Language: Post-Translational Modifications Talking to Each Other. TRENDS IN PLANT SCIENCE 2018; 23:1068-1080. [PMID: 30279071 DOI: 10.1016/j.tplants.2018.09.004] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/31/2018] [Accepted: 09/10/2018] [Indexed: 05/21/2023]
Abstract
Post-translational modifications (PTMs) are at the heart of many cellular signaling events. Apart from a single regulatory PTM, there are also PTMs that function in orchestrated manners. Such PTM crosstalk usually serves as a fine-tuning mechanism to adjust cellular responses to the slightest changes in the environment. While PTM crosstalk has been studied in depth in various species; in plants, this field is just emerging. In this review, we discuss recent studies on crosstalk between three of the most common protein PTMs in plant cells, being phosphorylation, ubiquitination, and sumoylation, and we highlight the diverse underlying mechanisms as well as signaling outputs of such crosstalk.
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Affiliation(s)
- Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium; These authors contributed equally. https://twitter.com/KrisGevaert_VIB
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium; These authors contributed equally.
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31
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Laarse SAM, Leney AC, Heck AJR. Crosstalk between phosphorylation and O‐Glc
NA
cylation: friend or foe. FEBS J 2018; 285:3152-3167. [DOI: 10.1111/febs.14491] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/27/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Saar A. M. Laarse
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
| | - Aneika C. Leney
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University The Netherlands
- Netherlands Proteomics Centre Utrecht The Netherlands
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32
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Zecha J, Meng C, Zolg DP, Samaras P, Wilhelm M, Kuster B. Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics. Mol Cell Proteomics 2018; 17:974-992. [PMID: 29414762 PMCID: PMC5930408 DOI: 10.1074/mcp.ra118.000583] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/31/2018] [Indexed: 11/06/2022] Open
Abstract
The coordination of protein synthesis and degradation regulating protein abundance is a fundamental process in cellular homeostasis. Today, mass spectrometry-based technologies allow determination of endogenous protein turnover on a proteome-wide scale. However, standard dynamic SILAC (Stable Isotope Labeling in Cell Culture) approaches can suffer from missing data across pulse time-points limiting the accuracy of such analysis. This issue is of particular relevance when studying protein stability at the level of proteoforms because often only single peptides distinguish between different protein products of the same gene. To address this shortcoming, we evaluated the merits of combining dynamic SILAC and tandem mass tag (TMT)-labeling of ten pulse time-points in a single experiment. Although the comparison to the standard dynamic SILAC method showed a high concordance of protein turnover rates, the pulsed SILAC-TMT approach yielded more comprehensive data (6000 proteins on average) without missing values. Replicate analysis further established that the same reproducibility of turnover rate determination can be obtained for peptides and proteins facilitating proteoform resolved investigation of protein stability. We provide several examples of differentially turned over splice variants and show that post-translational modifications can affect cellular protein half-lives. For example, N-terminally processed peptides exhibited both faster and slower turnover behavior compared with other peptides of the same protein. In addition, the suspected proteolytic processing of the fusion protein FAU was substantiated by measuring vastly different stabilities of the cleavage products. Furthermore, differential peptide turnover suggested a previously unknown mechanism of activity regulation by post-translational destabilization of cathepsin D as well as the DNA helicase BLM. Finally, our comprehensive data set facilitated a detailed evaluation of the impact of protein properties and functions on protein stability in steady-state cells and uncovered that the high turnover of respiratory chain complex I proteins might be explained by oxidative stress.
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Affiliation(s)
- Jana Zecha
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- §German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- ¶German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Chen Meng
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Daniel Paul Zolg
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Patroklos Samaras
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Bernhard Kuster
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany;
- §German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- ¶German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- ‖Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, 85354 Freising, Germany
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33
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Tamara S, Scheltema RA, Heck AJR, Leney AC. Phosphate Transfer in Activated Protein Complexes Reveals Interaction Sites. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Aneika C. Leney
- Biomolecular Mass Spectrometry and Proteomics; Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
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34
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Tamara S, Scheltema RA, Heck AJR, Leney AC. Phosphate Transfer in Activated Protein Complexes Reveals Interaction Sites. Angew Chem Int Ed Engl 2017; 56:13641-13644. [PMID: 28869719 DOI: 10.1002/anie.201706749] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/17/2017] [Indexed: 01/10/2023]
Abstract
For many proteins, phosphorylation regulates their interaction with other biomolecules. Herein, we describe an unexpected phenomenon whereby phosphate groups are transferred non-enzymatically from one interaction partner to the other within a binding interface upon activation in the gas phase. Providing that a high affinity exists between the donor and acceptor sites, this phosphate transfer is very efficient and the phosphate groups only ligate to sites in proximity to the binding region. Consequently, such phosphate-transfer reactions may define with high precision the binding site between a phosphoprotein and its binding partner, as well as reveal that the binding site in this system is retained in the phase transfer from solution to the gas phase.
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Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Aneika C Leney
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Tay AP, Pang CNI, Winter DL, Wilkins MR. PTMOracle: A Cytoscape App for Covisualizing and Coanalyzing Post-Translational Modifications in Protein Interaction Networks. J Proteome Res 2017; 16:1988-2003. [PMID: 28349685 DOI: 10.1021/acs.jproteome.6b01052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Post-translational modifications of proteins (PTMs) act as key regulators of protein activity and of protein-protein interactions (PPIs). To date, it has been difficult to comprehensively explore functional links between PTMs and PPIs. To address this, we developed PTMOracle, a Cytoscape app for coanalyzing PTMs within PPI networks. PTMOracle also allows extensive data to be integrated and coanalyzed with PPI networks, allowing the role of domains, motifs, and disordered regions to be considered. For proteins of interest, or a whole proteome, PTMOracle can generate network visualizations to reveal complex PTM-associated relationships. This is assisted by OraclePainter for coloring proteins by modifications, OracleTools for network analytics, and OracleResults for exploring tabulated findings. To illustrate the use of PTMOracle, we investigate PTM-associated relationships and their role in PPIs in four case studies. In the yeast interactome and its rich set of PTMs, we construct and explore histone-associated and domain-domain interaction networks and show how integrative approaches can predict kinases involved in phosphodegrons. In the human interactome, a phosphotyrosine-associated network is analyzed but highlights the sparse nature of human PPI networks and lack of PTM-associated data. PTMOracle is open source and available at the Cytoscape app store: http://apps.cytoscape.org/apps/ptmoracle .
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Affiliation(s)
- Aidan P Tay
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Chi Nam Ignatius Pang
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Daniel L Winter
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
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Zhang Z, Hou SQ, He J, Gu T, Yin Y, Shen WH. PTEN regulates PLK1 and controls chromosomal stability during cell division. Cell Cycle 2016; 15:2476-85. [PMID: 27398835 PMCID: PMC5026806 DOI: 10.1080/15384101.2016.1203493] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/12/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022] Open
Abstract
PTEN functions as a guardian of the genome through multiple mechanisms. We have previously established that PTEN maintains the structural integrity of chromosomes. In this report, we demonstrate a fundamental role of PTEN in controlling chromosome inheritance to prevent gross genomic alterations. Disruption of PTEN or depletion of PTEN protein phosphatase activity causes abnormal chromosome content, manifested by enlarged or polyploid nuclei. We further identify polo-like kinase 1 (PLK1) as a substrate of PTEN phosphatase. PTEN can physically associate with PLK1 and reduce PLK1 phosphorylation in a phosphatase-dependent manner. We show that PTEN deficiency leads to PLK1 phosphorylation and that a phospho-mimicking PLK1 mutant causes polyploidy, imitating functional deficiency of PTEN phosphatase. Inhibition of PLK1 activity or overexpression of a non-phosphorylatable PLK1 mutant reduces the polyploid cell population. These data reveal a new mechanism by which PTEN controls genomic stability during cell division.
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Affiliation(s)
- Zhong Zhang
- Department of Radiation Oncology, Weill Medical Medicine, Cornell University, New York, NY, USA
| | - Sheng-Qi Hou
- Department of Radiation Oncology, Weill Medical Medicine, Cornell University, New York, NY, USA
| | - Jinxue He
- Department of Radiation Oncology, Weill Medical Medicine, Cornell University, New York, NY, USA
| | - Tingting Gu
- Department of Radiation Oncology, Weill Medical Medicine, Cornell University, New York, NY, USA
| | - Yuxin Yin
- Department of Radiation Oncology, Weill Medical Medicine, Cornell University, New York, NY, USA
- Present address: Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Wen H. Shen
- Department of Radiation Oncology, Weill Medical Medicine, Cornell University, New York, NY, USA
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Doughty TW, Arsenault HE, Benanti JA. Levels of Ycg1 Limit Condensin Function during the Cell Cycle. PLoS Genet 2016; 12:e1006216. [PMID: 27463097 PMCID: PMC4963108 DOI: 10.1371/journal.pgen.1006216] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 07/05/2016] [Indexed: 11/19/2022] Open
Abstract
During mitosis chromosomes are condensed to facilitate their segregation, through a process mediated by the condensin complex. Although several factors that promote maximal condensin activity during mitosis have been identified, the mechanisms that downregulate condensin activity during interphase are largely unknown. Here, we demonstrate that Ycg1, the Cap-G subunit of budding yeast condensin, is cell cycle-regulated with levels peaking in mitosis and decreasing as cells enter G1 phase. This cyclical expression pattern is established by a combination of cell cycle-regulated transcription and constitutive degradation. Interestingly, overexpression of YCG1 and mutations that stabilize Ycg1 each result in delayed cell-cycle entry and an overall proliferation defect. Overexpression of no other condensin subunit impacts the cell cycle, suggesting that Ycg1 is limiting for condensin complex formation. Consistent with this possibility, we find that levels of intact condensin complex are reduced in G1 phase compared to mitosis, and that increased Ycg1 expression leads to increases in both levels of condensin complex and binding to chromatin in G1. Together, these results demonstrate that Ycg1 levels limit condensin function in interphase cells, and suggest that the association of condensin with chromosomes must be reduced following mitosis to enable efficient progression through the cell cycle.
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Affiliation(s)
- Tyler W. Doughty
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Heather E. Arsenault
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jennifer A. Benanti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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Lee HJ, Kim MY, Park HS. Phosphorylation-dependent regulation of Notch1 signaling: the fulcrum of Notch1 signaling. BMB Rep 2016; 48:431-7. [PMID: 26058398 PMCID: PMC4576950 DOI: 10.5483/bmbrep.2015.48.8.107] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Indexed: 11/20/2022] Open
Abstract
Notch signaling plays a pivotal role in cell fate determination, cellular development, cellular self-renewal, tumor progression, and has been linked to developmental disorders and carcinogenesis. Notch1 is activated through interactions with the ligands of neighboring cells, and acts as a transcriptional activator in the nucleus. The Notch1 intracellular domain (Notch1-IC) regulates the expression of target genes related to tumor development and progression. The Notch1 protein undergoes modification after translation by posttranslational modification enzymes. Phosphorylation modification is critical for enzymatic activation, complex formation, degradation, and subcellular localization. According to the nuclear cycle, Notch1-IC is degraded by E3 ligase, FBW7 in the nucleus via phosphorylation-dependent degradation. Here, we summarize the Notch signaling pathway, and resolve to understand the role of phosphorylation in the regulation of Notch signaling as well as to understand its relation to cancer.
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Affiliation(s)
- Hye-Jin Lee
- Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Mi-Yeon Kim
- Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Hee-Sae Park
- Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
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Schinke J, Kolog Gulko M, Christmann M, Valerius O, Stumpf SK, Stirz M, Braus GH. The DenA/DEN1 Interacting Phosphatase DipA Controls Septa Positioning and Phosphorylation-Dependent Stability of Cytoplasmatic DenA/DEN1 during Fungal Development. PLoS Genet 2016; 12:e1005949. [PMID: 27010942 PMCID: PMC4806917 DOI: 10.1371/journal.pgen.1005949] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/01/2016] [Indexed: 11/18/2022] Open
Abstract
DenA/DEN1 and the COP9 signalosome (CSN) represent two deneddylases which remove the ubiquitin-like Nedd8 from modified target proteins and are required for distinct fungal developmental programmes. The cellular DenA/DEN1 population is divided into a nuclear and a cytoplasmatic subpopulation which is especially enriched at septa. DenA/DEN1 stability control mechanisms are different for the two cellular subpopulations and depend on different physical interacting proteins and the C-terminal DenA/DEN1 phosphorylation pattern. Nuclear DenA/DEN1 is destabilized during fungal development by five of the eight CSN subunits which target nuclear DenA/DEN1 for degradation. DenA/DEN1 becomes stabilized as a phosphoprotein at S243/S245 during vegetative growth, which is necessary to support further asexual development. After the initial phase of development, the newly identified cytoplasmatic DenA/DEN1 interacting phosphatase DipA and an additional developmental specific C-terminal phosphorylation site at serine S253 destabilize DenA/DEN1. Outside of the nucleus, DipA is co-transported with DenA/DEN1 in the cytoplasm between septa and nuclei. Deletion of dipA resulted in increased DenA/DEN1 stability in a strain which is unresponsive to illumination. The mutant strain is dysregulated in cytokinesis and impaired in asexual development. Our results suggest a dual phosphorylation-dependent DenA/DEN1 stability control with stabilizing and destabilizing modifications and physical interaction partner proteins which function as control points in the nucleus and the cytoplasm.
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Affiliation(s)
- Josua Schinke
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Miriam Kolog Gulko
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Martin Christmann
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Sina Kristin Stumpf
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Margarita Stirz
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
- * E-mail:
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Abstract
Protein phosphatase 2A (PP2A) plays a critical multi-faceted role in the regulation of the cell cycle. It is known to dephosphorylate over 300 substrates involved in the cell cycle, regulating almost all major pathways and cell cycle checkpoints. PP2A is involved in such diverse processes by the formation of structurally distinct families of holoenzymes, which are regulated spatially and temporally by specific regulators. Here, we review the involvement of PP2A in the regulation of three cell signaling pathways: wnt, mTOR and MAP kinase, as well as the G1→S transition, DNA synthesis and mitotic initiation. These processes are all crucial for proper cell survival and proliferation and are often deregulated in cancer and other diseases.
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Affiliation(s)
- Nathan Wlodarchak
- a McArdle Laboratory for Cancer Research, University of Wisconsin-Madison , Madison , WI , USA
| | - Yongna Xing
- a McArdle Laboratory for Cancer Research, University of Wisconsin-Madison , Madison , WI , USA
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Guharoy M, Bhowmick P, Tompa P. Design Principles Involving Protein Disorder Facilitate Specific Substrate Selection and Degradation by the Ubiquitin-Proteasome System. J Biol Chem 2016; 291:6723-31. [PMID: 26851277 DOI: 10.1074/jbc.r115.692665] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) regulates diverse cellular pathways by the timely removal (or processing) of proteins. Here we review the role of structural disorder and conformational flexibility in the different aspects of degradation. First, we discuss post-translational modifications within disordered regions that regulate E3 ligase localization, conformation, and enzymatic activity, and also the role of flexible linkers in mediating ubiquitin transfer and reaction processivity. Next we review well studied substrates and discuss that substrate elements (degrons) recognized by E3 ligases are highly disordered: short linear motifs recognized by many E3s constitute an important class of degrons, and these are almost always present in disordered regions. Substrate lysines targeted for ubiquitination are also often located in neighboring regions of the E3 docking motifs and are therefore part of the disordered segment. Finally, biochemical experiments and predictions show that initiation of degradation at the 26S proteasome requires a partially unfolded region to facilitate substrate entry into the proteasomal core.
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Affiliation(s)
- Mainak Guharoy
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and
| | - Pallab Bhowmick
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and
| | - Peter Tompa
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and the Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, 1117 Budapest, Hungary
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Herhaus L, Dikic I. Expanding the ubiquitin code through post-translational modification. EMBO Rep 2015; 16:1071-83. [PMID: 26268526 PMCID: PMC4576978 DOI: 10.15252/embr.201540891] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/23/2015] [Accepted: 07/27/2015] [Indexed: 12/14/2022] Open
Abstract
Ubiquitylation is among the most prevalent post-translational modifications (PTMs) and regulates numerous cellular functions. Interestingly, ubiquitin (Ub) can be itself modified by other PTMs, including acetylation and phosphorylation. Acetylation of Ub on K6 and K48 represses the formation and elongation of Ub chains. Phosphorylation of Ub happens on multiple sites, S57 and S65 being the most frequently modified in yeast and mammalian cells, respectively. In mammals, the PINK1 kinase activates ubiquitin ligase Parkin by phosphorylating S65 of Ub and of the Parkin Ubl domain, which in turn promotes the amplification of autophagy signals necessary for the removal of damaged mitochondria. Similarly, TBK1 phosphorylates the autophagy receptors OPTN and p62 to initiate feedback and feedforward programs for Ub-dependent removal of protein aggregates, mitochondria and pathogens (such as Salmonella and Mycobacterium tuberculosis). The impact of PINK1-mediated phosphorylation of Ub and TBK1-dependent phosphorylation of autophagy receptors (OPTN and p62) has been recently linked to the development of Parkinson's disease and amyotrophic lateral sclerosis, respectively. Hence, the post-translational modification of Ub and its receptors can efficiently expand the Ub code and modulate its functions in health and disease.
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Affiliation(s)
- Lina Herhaus
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany
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KHATTAR VINAYAK, THOTTASSERY JAIDEEPV. Cks1 proteasomal turnover is a predominant mode of regulation in breast cancer cells: Role of key tyrosines and lysines. Int J Oncol 2014; 46:395-406. [DOI: 10.3892/ijo.2014.2728] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/01/2014] [Indexed: 11/06/2022] Open
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