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Shin S, Lee SY, Kang MG, Jang DG, Kim J, Rhee HW, Kim JS. Super-resolution proximity labeling with enhanced direct identification of biotinylation sites. Commun Biol 2024; 7:554. [PMID: 38724559 PMCID: PMC11082246 DOI: 10.1038/s42003-024-06112-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/26/2024] [Indexed: 05/12/2024] Open
Abstract
Promiscuous labeling enzymes, such as APEX2 or TurboID, are commonly used in in situ biotinylation studies of subcellular proteomes or protein-protein interactions. Although the conventional approach of enriching biotinylated proteins is widely implemented, in-depth identification of specific biotinylation sites remains challenging, and current approaches are technically demanding with low yields. A novel method to systematically identify specific biotinylation sites for LC-MS analysis followed by proximity labeling showed excellent performance compared with that of related approaches in terms of identification depth with high enrichment power. The systematic identification of biotinylation sites enabled a simpler and more efficient experimental design to identify subcellular localized proteins within membranous organelles. Applying this method to the processing body (PB), a non-membranous organelle, successfully allowed unbiased identification of PB core proteins, including novel candidates. We anticipate that our newly developed method will replace the conventional method for identifying biotinylated proteins labeled by promiscuous labeling enzymes.
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Affiliation(s)
- Sanghee Shin
- Center for RNA Research, Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
- The Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Song-Yi Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Dong-Gi Jang
- Center for RNA Research, Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hyun-Woo Rhee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea.
| | - Jong-Seo Kim
- Center for RNA Research, Institute of Basic Science, Seoul National University, Seoul, 08826, Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
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2
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Melamed Kadosh D, Beenstock J, Engelberg D, Admon A. Differential Modulation of the Phosphoproteome by the MAP Kinases Isoforms p38α and p38β. Int J Mol Sci 2023; 24:12442. [PMID: 37569817 PMCID: PMC10419006 DOI: 10.3390/ijms241512442] [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: 06/22/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
The p38 members of the mitogen-activated protein kinases (MAPKs) family mediate various cellular responses to stress conditions, inflammatory signals, and differentiation factors. They are constitutively active in chronic inflammatory diseases and some cancers. The differences between their transient effects in response to signals and the chronic effect in diseases are not known. The family is composed of four isoforms, of which p38α seems to be abnormally activated in diseases. p38α and p38β are almost identical in sequence, structure, and biochemical and pharmacological properties, and the specific unique effects of each of them, if any, have not yet been revealed. This study aimed to reveal the specific effects induced by p38α and p38β, both when transiently activated in response to stress and when chronically active. This was achieved via large-scale proteomics and phosphoproteomics analyses using stable isotope labeling of two experimental systems: one, mouse embryonic fibroblasts (MEFs) deficient in each of these p38 kinases and harboring either an empty vector or vectors expressing p38αWT, p38βWT, or intrinsically active variants of these MAPKs; second, induction of transient stress by exposure of MEFs, p38α-/-, and p38β-/- MEFs to anisomycin. Significant differences in the repertoire of the proteome and phosphoproteome between cells expressing active p38α and p38β suggest distinct roles for each kinase. Interestingly, in both cases, the constitutive activation induced adaptations of the cells to the chronic activity so that known substrates of p38 were downregulated. Within the dramatic effect of p38s on the proteome and phosphoproteome, some interesting affected phosphorylation sites were those found in cancer-associated p53 and Hspb1 (HSP27) proteins and in cytoskeleton-associated proteins. Among these, was the stronger direct phosphorylation by p38α of p53-Ser309, which was validated on the Ser315 in human p53. In summary, this study sheds new light on the differences between chronic and transient p38α and p38β signaling and on the specific targets of these two kinases.
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Affiliation(s)
| | - Jonah Beenstock
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - David Engelberg
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Arie Admon
- Faculty of Biology, Technion—Israel Institute of Technology, Haifa 3200003, Israel;
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3
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Abbasi S, Bayat L, Schild-Poulter C. Analysis of Ku70 S155 Phospho-Specific BioID2 Interactome Identifies Ku Association with TRIP12 in Response to DNA Damage. Int J Mol Sci 2023; 24:ijms24087041. [PMID: 37108203 PMCID: PMC10138931 DOI: 10.3390/ijms24087041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The Ku heterodimer, composed of subunits Ku70 and Ku80, is known for its essential role in repairing double-stranded DNA breaks via non-homologous end joining (NHEJ). We previously identified Ku70 S155 as a novel phosphorylation site within the von Willebrand A-like (vWA) domain of Ku70 and documented an altered DNA damage response in cells expressing a Ku70 S155D phosphomimetic mutant. Here, we conducted proximity-dependent biotin identification (BioID2) screening using wild-type Ku70, Ku70 S155D mutant, and Ku70 with a phosphoablative substitution (S155A) to identify Ku70 S155D-specific candidate proteins that may rely on this phosphorylation event. Using the BioID2 screen with multiple filtering approaches, we compared the protein interactor candidate lists for Ku70 S155D and S155A. TRIP12 was exclusive to the Ku70 S155D list, considered a high confidence interactor based on SAINTexpress analysis, and appeared in all three biological replicates of the Ku70 S155D-BioID2 mass spectrometry results. Using proximity ligation assays (PLA), we demonstrated a significantly increased association between Ku70 S155D-HA and TRIP12 compared to wild-type Ku70-HA cells. In addition, we were able to demonstrate a robust PLA signal between endogenous Ku70 and TRIP12 in the presence of double-stranded DNA breaks. Finally, co-immunoprecipitation analyses showed an enhanced interaction between TRIP12 and Ku70 upon treatment with ionizing radiation, suggesting a direct or indirect association in response to DNA damage. Altogether, these results suggest an association between Ku70 phospho-S155 and TRIP12.
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Affiliation(s)
- Sanna Abbasi
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 3K7, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Laila Bayat
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 3K7, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 3K7, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
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4
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Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
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5
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Dan Y, Radic N, Gay M, Fernández-Torras A, Arauz G, Vilaseca M, Aloy P, Canovas B, Nebreda A. Characterization of p38α signaling networks in cancer cells using quantitative proteomics and phosphoproteomics. Mol Cell Proteomics 2023; 22:100527. [PMID: 36894123 PMCID: PMC10105487 DOI: 10.1016/j.mcpro.2023.100527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
p38α (encoded by MAPK14) is a protein kinase that regulates cellular responses to almost all types of environmental and intracellular stresses. Upon activation, p38α phosphorylates many substrates both in the cytoplasm and nucleus, allowing this pathway to regulate a wide variety of cellular processes. While the role of p38α in the stress response has been widely investigated, its implication in cell homeostasis is less understood. To investigate the signaling networks regulated by p38α in proliferating cancer cells, we performed quantitative proteomic and phosphoproteomic analyses in breast cancer cells in which this pathway had been either genetically targeted or chemically inhibited. Our study identified with high confidence 35 proteins and 82 phosphoproteins (114 phosphosites) that are modulated by p38α, and highlighted the implication of various protein kinases, including MK2 and mTOR, in the p38α-regulated signaling networks. Moreover, functional analyses revealed an important contribution of p38α to the regulation of cell adhesion, DNA replication and RNA metabolism. Indeed, we provide experimental evidence supporting that p38α facilitates cancer cell adhesion, and showed that this p38α function is likely mediated by the modulation of the adaptor protein ArgBP2. Collectively, our results illustrate the complexity of the p38α regulated signaling networks, provide valuable information on p38α-dependent phosphorylation events in cancer cells, and document a mechanism by which p38α can regulate cell adhesion.
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Affiliation(s)
- Yuzhen Dan
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Nevenka Radic
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Adrià Fernández-Torras
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Gianluca Arauz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Begoña Canovas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - AngelR Nebreda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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6
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Poljak A, Raftery M, Polly P. Evaluating Cellular Viability by iTRAQ Proteomic Profiling. Methods Mol Biol 2023; 2644:193-209. [PMID: 37142923 DOI: 10.1007/978-1-0716-3052-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Cellular health, functionality, response to environment, and other variables affecting cell, tissue, or organ viability are reflected in the cellular proteomes and metabolomes. These "omic" profiles are in constant flux even during normal cellular functioning, to maintain cellular homeostasis, in response to small environmental changes and maintenance of optimal cell viability. However proteomic "fingerprints" can also provide insight into cellular ageing, response to disease, adjustment to environmental changes, and other variables that impact cellular viability. A variety of proteomic methods can be used to determine qualitative and quantitative proteomic change. In this chapter, we will focus on a labeling method called isobaric tags for relative and absolute quantification (iTRAQ), which is frequently used to identify and quantify proteomic expression changes in cells and tissues.
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Affiliation(s)
- Anne Poljak
- Bioanalytical Mass Spectrometry Facility (BMSF), Mark Wainwright Analytical Centre (MWAC), University of New South Wales, Sydney, NSW, Australia
| | - Mark Raftery
- Bioanalytical Mass Spectrometry Facility (BMSF), Mark Wainwright Analytical Centre (MWAC), University of New South Wales, Sydney, NSW, Australia
| | - Patsie Polly
- Department of Pathology, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.
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7
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Prikas E, Paric E, Asih PR, Stefanoska K, Stefen H, Fath T, Poljak A, Ittner A. Tau target identification reveals NSF-dependent effects on AMPA receptor trafficking and memory formation. EMBO J 2022; 41:e10242. [PMID: 35993331 PMCID: PMC9475529 DOI: 10.15252/embj.2021110242] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 07/03/2022] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Microtubule-associated protein tau is a central factor in Alzheimer's disease and other tauopathies. However, the physiological functions of tau are unclear. Here, we used proximity-labelling proteomics to chart tau interactomes in primary neurons and mouse brains in vivo. Tau interactors map onto pathways of cytoskeletal, synaptic vesicle and postsynaptic receptor regulation and show significant enrichment for Parkinson's, Alzheimer's and prion disease. We find that tau interacts with and dose-dependently reduces the activity of N-ethylmaleimide sensitive fusion protein (NSF), a vesicular ATPase essential for AMPA-type glutamate receptor (AMPAR) trafficking. Tau-deficient (tau-/- ) neurons showed mislocalised expression of NSF and enhanced synaptic AMPAR surface levels, reversible through the expression of human tau or inhibition of NSF. Consequently, enhanced AMPAR-mediated associative and object recognition memory in tau-/- mice is suppressed by both hippocampal tau and infusion with an NSF-inhibiting peptide. Pathologic mutant tau from mouse models or Alzheimer's disease significantly enhances NSF inhibition. Our results map neuronal tau interactomes and delineate a functional link of tau with NSF in plasticity-associated AMPAR-trafficking and memory.
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Affiliation(s)
- Emmanuel Prikas
- Flinders Health & Medical Research Institute, College of Medicine and Public HealthFlinders UniversityAdelaideSAAustralia
| | - Esmeralda Paric
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Prita R Asih
- Flinders Health & Medical Research Institute, College of Medicine and Public HealthFlinders UniversityAdelaideSAAustralia
| | - Kristie Stefanoska
- Flinders Health & Medical Research Institute, College of Medicine and Public HealthFlinders UniversityAdelaideSAAustralia
| | - Holly Stefen
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Thomas Fath
- Dementia Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Anne Poljak
- Mark Wainwright Analytical CentreUniversity of New South WalesSydneyNSWAustralia
| | - Arne Ittner
- Flinders Health & Medical Research Institute, College of Medicine and Public HealthFlinders UniversityAdelaideSAAustralia
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8
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Asih PR, Poljak A, Kassiou M, Ke YD, Ittner LM. Differential mitochondrial protein interaction profile between human translocator protein and its A147T polymorphism variant. PLoS One 2022; 17:e0254296. [PMID: 35522669 PMCID: PMC9075623 DOI: 10.1371/journal.pone.0254296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 04/06/2022] [Indexed: 11/19/2022] Open
Abstract
The translocator protein (TSPO) has been implicated in mitochondrial transmembrane cholesterol transport, brain inflammation, and other mitochondrial functions. It is upregulated in glial cells during neuroinflammation in Alzheimer’s disease. High affinity TSPO imaging radioligands are utilized to visualize neuroinflammation. However, this is hampered by the common A147T polymorphism which compromises ligand binding. Furthermore, this polymorphism has been linked to increased risk of neuropsychiatric disorders, and possibly reduces TSPO protein stability. Here, we used immunoprecipitation coupled to mass-spectrometry (IP-MS) to establish a mitochondrial protein binding profile of wild-type (WT) TSPO and the A147T polymorphism variant. Using mitochondria from human glial cells expressing either WT or A147T TSPO, we identified 30 WT TSPO binding partners, yet only 23 for A147T TSPO. Confirming that A147T polymorphism of the TSPO might confer loss of function, we found that one of the identified interactors of WT TSPO, 14-3-3 theta (YWHAQ), a protein involved in regulating mitochondrial membrane proteins, interacts much less with A147T TSPO. Our data presents a network of mitochondrial interactions of TSPO and its A147T polymorphism variant in human glial cells and indicate functional relevance of A147T in mitochondrial protein networks.
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Affiliation(s)
- Prita R. Asih
- Dementia Research Centre, Faculty of Health and Medical Sciences, Macquarie University, Sydney, NSW, Australia
| | - Anne Poljak
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Michael Kassiou
- School of Chemistry, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Yazi D. Ke
- Dementia Research Centre, Faculty of Health and Medical Sciences, Macquarie University, Sydney, NSW, Australia
| | - Lars M. Ittner
- Dementia Research Centre, Faculty of Health and Medical Sciences, Macquarie University, Sydney, NSW, Australia
- * E-mail:
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9
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Niinae T, Ishihama Y, Imami K. Biotinylation-based proximity labeling proteomics: Basics, applications, and technical considerations. J Biochem 2021; 170:569-576. [PMID: 34752609 DOI: 10.1093/jb/mvab123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/07/2021] [Indexed: 11/13/2022] Open
Abstract
Recent advances in biotinylation-based proximity labeling (PL) have opened up new avenues for mapping the protein composition of cellular compartments and protein complexes in living cells at high spatiotemporal resolution. In particular, PL combined with mass spectrometry-based proteomics has been successfully applied to defining protein-protein interactions, protein-nucleic acid interactions, (membraneless) organelle proteomes, and secretomes in various systems ranging from cultured cells to whole animals. In this review, we first summarize the basics and recent biological applications of PL proteomics, and then highlight recent developments in enrichment techniques for biotinylated proteins and peptides, focusing on the advantages of PL and technical considerations.
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Affiliation(s)
- Tomoya Niinae
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Koshi Imami
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,PRESTO, Japan Science and Technology Agency (JST), 5-3 Yonban-cho, Chiyoda-ku, Tokyo, 102-0075, Japan
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10
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Carrasco E, Gomez-Gutierrez P, Campos PM, Messeguer A, Perez JJ, Vega M. Structure-Activity Studies of Novel di-substituted [1,2,5]oxadiazolo[3,4-b]pyrazine Analogs Targeting the A-loop Regulatory Site of p38 MAP Kinase. Curr Med Chem 2021; 29:1640-1653. [PMID: 34931978 DOI: 10.2174/0929867328666210712165659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 11/22/2022]
Abstract
INTRODUCTION In the quest for novel allosteric inhibitors of the p38 MAP kinase, we recently described the A-loop regulatory site, identified through molecular modeling studies together with the disclosure of a small molecule hit with a moderate inhibitory profile. Starting from this structure, we subsequently identified two additional hits with simpler molecular structures from an in silico screening study, using a substructure search in the SciFinder database. After corroboration of their inhibitory profile, analysis of their structures permitted to conclude about the suitability of the [1,2,5]oxadiazolo[3,4-b]pyrazine (furazano[3,4-b]pyrazine) scaffold for the development of potent A-loop regulatory site p38 MAP kinase inhibitors. Accordingly, we report the synthesis and pharmacological evaluation of a series of di-substituted analogs with a potent inhibitory profile of p38 MAP kinase, as shown by in vitro assays of their capability to inhibit IL-1β secretion in human monocyte-derived macrophages. BACKGROUND In the quest for novel allosteric inhibitors of the p38 MAP kinase, we recently described the A-loop regulatory site, identified through molecular modeling studies together with the disclosure of a small molecule hit with a moderate inhibitory profile. OBJECTIVE To find small molecule potent inhibitors of the p38 MAP kinase A-loop regulatory site. METHODS Starting from this structure, we subsequently identified two additional hits with simpler molecular structures from an in silico screening study, using a substructure search in the SciFinder database. After corroboration of their inhibitory profile, we carried out a hit-to-lead optimization process guided by molecular modeling using a [1,2,5]oxadiazolo[3,4-b]pyrazine (furazano[3,4-b]pyrazine) scaffold. RESULTS We report the synthesis and pharmacological evaluation of a series of di-substituted analogs with a potent inhibitory profile of p38 MAP kinase, as shown by in vitro assays of their capability to inhibit IL-1β secretion in human monocyte-derived macrophages. CONCLUSIONS We describe in the present work a series of [1,2,5]oxadiazolo[3,4-b]pyrazine (furazano[3,4-b]pyrazine), potent inhibitors of IL-1β secretion in human monocyte-derived macrophages allosteric modulators of the p38 MAP kinase A-loop regulatory site.
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Affiliation(s)
- Esther Carrasco
- Allinky Biopharma, Campus de Cantoblanco, Faraday 7, 28049 Madrid, Spain
| | | | - Pedro M Campos
- Allinky Biopharma, Campus de Cantoblanco, Faraday 7, 28049 Madrid, Spain
| | - Angel Messeguer
- IQAC CSIC, Institute of Advanced Chemistry of Catalonia, Dept. Biol. Chem., Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Juan Jesus Perez
- Dept. of Chemical Engineering, Universitat Politecnica de Catalunya, 08028 Barcelona, Spain
| | - Miguel Vega
- Allinky Biopharma, Campus de Cantoblanco, Faraday 7, 28049 Madrid, Spain
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11
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Qin W, Cho KF, Cavanagh PE, Ting AY. Deciphering molecular interactions by proximity labeling. Nat Methods 2021; 18:133-143. [PMID: 33432242 PMCID: PMC10548357 DOI: 10.1038/s41592-020-01010-5] [Citation(s) in RCA: 227] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
Many biological processes are executed and regulated through the molecular interactions of proteins and nucleic acids. Proximity labeling (PL) is a technology for tagging the endogenous interaction partners of specific protein 'baits', via genetic fusion to promiscuous enzymes that catalyze the generation of diffusible reactive species in living cells. Tagged molecules that interact with baits can then be enriched and identified by mass spectrometry or nucleic acid sequencing. Here we review the development of PL technologies and highlight studies that have applied PL to the discovery and analysis of molecular interactions. In particular, we focus on the use of PL for mapping protein-protein, protein-RNA and protein-DNA interactions in living cells and organisms.
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Affiliation(s)
- Wei Qin
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kelvin F Cho
- Department of Genetics, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Peter E Cavanagh
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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12
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Kaur G, Poljak A, Ali SA, Zhong L, Raftery MJ, Sachdev P. Extending the Depth of Human Plasma Proteome Coverage Using Simple Fractionation Techniques. J Proteome Res 2021; 20:1261-1279. [PMID: 33471535 DOI: 10.1021/acs.jproteome.0c00670] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human plasma is one of the most widely used tissues in clinical analysis, and plasma-based biomarkers are used for monitoring patient health status and/or response to medical treatment to avoid unnecessary invasive biopsy. Data-driven plasma proteomics has suffered from a lack of throughput and detection sensitivity, largely due to the complexity of the plasma proteome and in particular the enormous quantitative dynamic range, estimated to be between 9 and 13 orders of magnitude between the lowest and the highest abundance protein. A major challenge is to identify workflows that can achieve depth of plasma proteome coverage while minimizing the complexity of the sample workup and maximizing the sample throughput. In this study, we have performed intensive depletion of high-abundant plasma proteins or enrichment of low-abundant proteins using the Agilent multiple affinity removal liquid chromatography (LC) column-Human 6 (Hu6), the Agilent multiple affinity removal LC column-Human 14 (Hu14), and ProteoMiner followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS PAGE) and C18 prefractionation techniques. We compared the performance of each of these fractionation approaches to identify the method that satisfies requirements for analysis of clinical samples and to include good plasma proteome coverage in combination with reasonable sample output. In this study, we report that one-dimensional (1D) gel-based prefractionation allows parallel sample processing and no loss of proteome coverage, compared with serial chromatographic separation, and significantly accelerates analysis time, particularly important for large clinical projects. Furthermore, we show that a variety of methodologies can achieve similarly high plasma proteome coverage, allowing flexibility in method selection based on project-specific needs. These considerations are important in the effort to accelerate plasma proteomics research so as to provide efficient, reliable, and accurate diagnoses, population-based health screening, clinical research studies, and other clinical work.
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Affiliation(s)
- Gurjeet Kaur
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia.,Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Anne Poljak
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia.,Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Syed Azmal Ali
- Cell Biology and Proteomics Lab, National Dairy Research Institute, Karnal, Haryana 132001, India
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Perminder Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia.,Neuropsychiatric Institute, Euroa Centre, Prince of Wales Hospital, Sydney, NSW 2052, Australia
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Guedouari H, Ould Amer Y, Pichaud N, Hebert-Chatelain E. Characterization of the interactome of c-Src within the mitochondrial matrix by proximity-dependent biotin identification. Mitochondrion 2021; 57:257-269. [PMID: 33412331 DOI: 10.1016/j.mito.2020.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/09/2020] [Accepted: 12/30/2020] [Indexed: 12/27/2022]
Abstract
C-Src kinase is localized in several subcellular compartments, including mitochondria where it is involved in the regulation of organelle functions and overall metabolism. Surprisingly, the characterization of the intramitochondrial Src interactome has never been fully determined. Using in vitro proximity-dependent biotin identification (BioID) coupled to mass spectrometry, we identified 51 candidate proteins that may interact directly or indirectly with c-Src within the mitochondrial matrix. Pathway analysis suggests that these proteins are involved in a large array of mitochondrial functions such as protein folding and import, mitochondrial organization and transport, oxidative phosphorylation, tricarboxylic acid cycle and metabolism of amino and fatty acids. Among these proteins, we identified 24 tyrosine phosphorylation sites in 17 mitochondrial proteins (AKAP1, VDAC1, VDAC2, VDAC3, LonP1, Hsp90, SLP2, PHB2, MIC60, UBA1, EF-Tu, LRPPRC, ACO2, OAT, ACAT1, ETFβ and ATP5β) as potential substrates for intramitochondrial Src using in silico prediction of tyrosine phospho-sites. Interaction of c-Src with SLP2 and ATP5β was confirmed using coimmunoprecipitation. This study suggests that the intramitochondrial Src could target several proteins and regulate different mitochondrial functions.
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Affiliation(s)
- Hala Guedouari
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Moncton, NB, Canada; University of Moncton, Dept. of Biology, Moncton, NB, Canada
| | - Yasmine Ould Amer
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Moncton, NB, Canada; University of Moncton, Dept. of Biology, Moncton, NB, Canada
| | - Nicolas Pichaud
- University of Moncton, Dept. of Chemistry and Biochemistry, Moncton, NB, Canada
| | - Etienne Hebert-Chatelain
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Moncton, NB, Canada; University of Moncton, Dept. of Biology, Moncton, NB, Canada.
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14
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Chua XY, Aballo T, Elnemer W, Tran M, Salomon A. Quantitative Interactomics of Lck-TurboID in Living Human T Cells Unveils T Cell Receptor Stimulation-Induced Proximal Lck Interactors. J Proteome Res 2020; 20:715-726. [PMID: 33185455 DOI: 10.1021/acs.jproteome.0c00616] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
While Lck has been widely recognized to play a pivotal role in the initiation of the T cell receptor (TCR) signaling pathway, an understanding of the precise regulation of Lck in T cells upon TCR activation remains elusive. Investigation of protein-protein interaction (PPI) using proximity labeling techniques such as TurboID has the potential to provide valuable molecular insights into Lck regulatory networks. By expressing Lck-TurboID in Jurkat T cells, we have uncovered a dynamic, short-range Lck protein interaction network upon 30 min of TCR stimulation. In this novel application of TurboID, we detected 27 early signaling-induced Lck-proximal interactors in living T cells, including known and novel Lck interactors, validating the discovery power of this tool. Our results revealed previously unappreciated Lck PPI which may be associated with cytoskeletal rearrangement, ubiquitination of TCR signaling proteins, activation of the mitogen-activated protein kinase cascade, coalescence of the LAT signalosome, and formation of the immunological synapse. In this study, we demonstrated for the first time in immune cells and for the kinase Lck that TurboID can be utilized to unveil PPI dynamics in living cells at a time scale consistent with early TCR signaling. Data are available via ProteomeXchange with identifier PXD020759.
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Affiliation(s)
- Xien Yu Chua
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island, United States
| | - Timothy Aballo
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States
| | - William Elnemer
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States
| | - Melanie Tran
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States
| | - Arthur Salomon
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States
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15
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Asih PR, Prikas E, Stefanoska K, Tan ARP, Ahel HI, Ittner A. Functions of p38 MAP Kinases in the Central Nervous System. Front Mol Neurosci 2020; 13:570586. [PMID: 33013322 PMCID: PMC7509416 DOI: 10.3389/fnmol.2020.570586] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/18/2020] [Indexed: 12/22/2022] Open
Abstract
Mitogen-activated protein (MAP) kinases are a central component in signaling networks in a multitude of mammalian cell types. This review covers recent advances on specific functions of p38 MAP kinases in cells of the central nervous system. Unique and specific functions of the four mammalian p38 kinases are found in all major cell types in the brain. Mechanisms of p38 activation and downstream phosphorylation substrates in these different contexts are outlined and how they contribute to functions of p38 in physiological and under disease conditions. Results in different model organisms demonstrated that p38 kinases are involved in cognitive functions, including functions related to anxiety, addiction behavior, neurotoxicity, neurodegeneration, and decision making. Finally, the role of p38 kinases in psychiatric and neurological conditions and the current progress on therapeutic inhibitors targeting p38 kinases are covered and implicate p38 kinases in a multitude of CNS-related physiological and disease states.
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Affiliation(s)
- Prita R Asih
- Dementia Research Centre, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Emmanuel Prikas
- Dementia Research Centre, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kristie Stefanoska
- Dementia Research Centre, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Amanda R P Tan
- Dementia Research Centre, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Holly I Ahel
- Dementia Research Centre, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Arne Ittner
- Dementia Research Centre, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
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16
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Germann UA, Alam JJ. P38α MAPK Signaling-A Robust Therapeutic Target for Rab5-Mediated Neurodegenerative Disease. Int J Mol Sci 2020; 21:E5485. [PMID: 32751991 PMCID: PMC7432772 DOI: 10.3390/ijms21155485] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/25/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022] Open
Abstract
Multifactorial pathologies, involving one or more aggregated protein(s) and neuroinflammation are common in major neurodegenerative diseases, such as Alzheimer's disease and dementia with Lewy bodies. This complexity of multiple pathogenic drivers is one potential explanation for the lack of success or, at best, the partial therapeutic effects, respectively, with approaches that have targeted one specific driver, e.g., amyloid-beta, in Alzheimer's disease. Since the endosome-associated protein Rab5 appears to be a convergence point for many, if not all the most prominent pathogenic drivers, it has emerged as a major therapeutic target for neurodegenerative disease. Further, since the alpha isoform of p38 mitogen-activated protein kinase (p38α) is a major regulator of Rab5 activity and its effectors, a biology that is distinct from the classical nuclear targets of p38 signaling, brain-penetrant selective p38α kinase inhibitors provide the opportunity for significant therapeutic advances in neurogenerative disease through normalizing dysregulated Rab5 activity. In this review, we provide a brief summary of the role of Rab5 in the cell and its association with neurodegenerative disease pathogenesis. We then discuss the connection between Rab5 and p38α and summarize the evidence that through modulating Rab5 activity there are therapeutic opportunities in neurodegenerative diseases for p38α kinase inhibitors.
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17
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Cores Á, Piquero M, Villacampa M, León R, Menéndez JC. NRF2 Regulation Processes as a Source of Potential Drug Targets against Neurodegenerative Diseases. Biomolecules 2020; 10:E904. [PMID: 32545924 PMCID: PMC7356958 DOI: 10.3390/biom10060904] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
NRF2 acts by controlling gene expression, being the master regulator of the Phase II antioxidant response, and also being key to the control of neuroinflammation. NRF2 activity is regulated at several levels, including protein degradation by the proteasome, transcription, and post-transcription. The purpose of this review is to offer a concise and critical overview of the main mechanisms of NRF2 regulation and their actual or potential use as targets for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Ángel Cores
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (Á.C.); (M.P.); (M.V.)
| | - Marta Piquero
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (Á.C.); (M.P.); (M.V.)
| | - Mercedes Villacampa
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (Á.C.); (M.P.); (M.V.)
| | - Rafael León
- Instituto Teófilo Hernando y Departamento de Farmacología y Terapéutica, Facultad de Medicina, Universidad Autónoma de Madrid, 28029 Madrid, Spain;
- Instituto de Investigación Sanitaria, Servicio de Farmacología Clínica, Hospital Universitario de la Princesa, 28006 Madrid, Spain
| | - J. Carlos Menéndez
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain; (Á.C.); (M.P.); (M.V.)
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18
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Prikas E, Poljak A, Ittner A. Mapping p38α mitogen-activated protein kinase signaling by proximity-dependent labeling. Protein Sci 2020; 29:1196-1210. [PMID: 32189389 DOI: 10.1002/pro.3854] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/03/2020] [Accepted: 03/16/2020] [Indexed: 12/15/2022]
Abstract
Mitogen-activated protein (MAP) kinase signaling is central to multiple cellular responses and processes. MAP kinase p38α is the best characterized member of the p38 MAP kinase family. Upstream factors and downstream targets of p38α have been identified in the past by conventional methods such as coimmunoprecipitation. However, a complete picture of its interaction partners and substrates in cells is lacking. Here, we employ a proximity-dependent labeling approach using biotinylation tagging to map the interactome of p38α in cultured 293T cells. Fusing the advanced biotin ligase BioID2 to the N-terminus of p38α, we used mass spectrometry to identify 37 biotin-labeled proteins that putatively interact with p38α. Gene ontology analysis confirms known upstream and downstream factors in the p38 MAP kinase cascade (e.g., MKK3, MAPKAPK2, TAB2, and c-jun). We furthermore identify a cluster of zinc finger (ZnF) domain-containing proteins that is significantly enriched among proximity-labeled interactors and is involved in gene transcription and DNA damage response. Fluorescence imaging and coimmunoprecipitation with overexpressed p38α in cells supports an interaction of p38α with ZnF protein XPA, a key factor in the DNA damage response, that is promoted by UV irradiation. These results define an extensive network of interactions of p38α in cells and new direct molecular targets of MAP kinase p38α in gene regulation and the DNA damage response.
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Affiliation(s)
- Emmanuel Prikas
- Dementia Research Centre, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Anne Poljak
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Arne Ittner
- Dementia Research Centre, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
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