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Somsen BA, Cossar PJ, Arkin MR, Brunsveld L, Ottmann C. 14-3-3 Protein-Protein Interactions: From Mechanistic Understanding to Their Small-Molecule Stabilization. Chembiochem 2024; 25:e202400214. [PMID: 38738787 DOI: 10.1002/cbic.202400214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/14/2024]
Abstract
Protein-protein interactions (PPIs) are of utmost importance for maintenance of cellular homeostasis. Herein, a central role can be found for 14-3-3 proteins. These hub-proteins are known to bind hundreds of interaction partners, thereby regulating their activity, localization, and/or stabilization. Due to their ability to bind a large variety of client proteins, studies of 14-3-3 protein complexes flourished over the last decades, aiming to gain greater molecular understanding of these complexes and their role in health and disease. Because of their crucial role within the cell, 14-3-3 protein complexes are recognized as highly interesting therapeutic targets, encouraging the discovery of small molecule modulators of these PPIs. We discuss various examples of 14-3-3-mediated regulation of its binding partners on a mechanistic level, highlighting the versatile and multi-functional role of 14-3-3 within the cell. Furthermore, an overview is given on the development of stabilizers of 14-3-3 protein complexes, from initially used natural products to fragment-based approaches. These studies show the potential of 14-3-3 PPI stabilizers as novel agents in drug discovery and as tool compounds to gain greater molecular understanding of the role of 14-3-3-based protein regulation.
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Affiliation(s)
- Bente A Somsen
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
| | - Peter J Cossar
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California, 94143, United States
| | - Luc Brunsveld
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
| | - Christian Ottmann
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
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2
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Low ZY, Yip AJW, Chan AML, Choo WS. 14-3-3 Family of Proteins: Biological Implications, Molecular Interactions, and Potential Intervention in Cancer, Virus and Neurodegeneration Disorders. J Cell Biochem 2024; 125:e30624. [PMID: 38946063 DOI: 10.1002/jcb.30624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
The 14-3-3 family of proteins are highly conserved acidic eukaryotic proteins (25-32 kDa) abundantly present in the body. Through numerous binding partners, the 14-3-3 is responsible for many essential cellular pathways, such as cell cycle regulation and gene transcription control. Hence, its dysregulation has been linked to the onset of critical illnesses such as cancers, neurodegenerative diseases and viral infections. Interestingly, explorative studies have revealed an inverse correlation of 14-3-3 protein in cancer and neurodegenerative diseases, and the direct manipulation of 14-3-3 by virus to enhance infection capacity has dramatically extended its significance. Of these, COVID-19 has been linked to the 14-3-3 proteins by the interference of the SARS-CoV-2 nucleocapsid (N) protein during virion assembly. Given its predisposition towards multiple essential host signalling pathways, it is vital to understand the holistic interactions between the 14-3-3 protein to unravel its potential therapeutic unit in the future. As such, the general structure and properties of the 14-3-3 family of proteins, as well as their known biological functions and implications in cancer, neurodegeneration, and viruses, were covered in this review. Furthermore, the potential therapeutic target of 14-3-3 proteins in the associated diseases was discussed.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Alvin Man Lung Chan
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | - Wee Sim Choo
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
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3
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Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. Phosphorylation Code of Human Nucleophosmin Includes Four Cryptic Sites for Hierarchical Binding of 14-3-3 Proteins. J Mol Biol 2024; 436:168592. [PMID: 38702038 DOI: 10.1016/j.jmb.2024.168592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phosphosites in NPM1 reside within signal sequences, this work suggests a mechanism of NPM1 regulation by which NPM1 phosphorylation can promote 14-3-3 binding to affect NPM1 shuttling between cell compartments. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.
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Affiliation(s)
- Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina V Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Richard B Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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4
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Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
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Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
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5
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Crha R, Kozeleková A, Hofrová A, Iľkovičová L, Gašparik N, Kadeřávek P, Hritz J. Hiding in plain sight: Complex interaction patterns between Tau and 14-3-3ζ protein variants. Int J Biol Macromol 2024; 266:130802. [PMID: 38492709 DOI: 10.1016/j.ijbiomac.2024.130802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 03/18/2024]
Abstract
Tau protein is an intrinsically disordered protein that plays a key role in Alzheimer's disease (AD). In brains of AD patients, Tau occurs abnormally phosphorylated and aggregated in neurofibrillary tangles (NFTs). Together with Tau, 14-3-3 proteins - abundant cytosolic dimeric proteins - were found colocalized in the NFTs. However, so far, the molecular mechanism of the process leading to pathological changes in Tau structure as well as the direct involvement of 14-3-3 proteins are not well understood. Here, we aimed to reveal the effects of phosphorylation by protein kinase A (PKA) on Tau structural preferences and provide better insight into the interaction between Tau and 14-3-3 proteins. We also addressed the impact of monomerization-inducing phosphorylation of 14-3-3 at S58 on the binding to Tau protein. Using multidimensional nuclear magnetic resonance spectroscopy (NMR), chemical cross-linking analyzed by mass spectrometry (MS) and PAGE, we unveiled differences in their binding affinity, stoichiometry, and interfaces with single-residue resolution. We revealed that the interaction between 14-3-3 and Tau proteins is mediated not only via the 14-3-3 amphipathic binding grooves, but also via less specific interactions with 14-3-3 protein surface and, in the case of monomeric 14-3-3, also partially via the exposed dimeric interface. In addition, the hyperphosphorylation of Tau changes its affinity to 14-3-3 proteins. In conclusion, we propose quite complex interaction mode between the Tau and 14-3-3 proteins.
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Affiliation(s)
- Radek Crha
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Aneta Kozeleková
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Alena Hofrová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lucia Iľkovičová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Norbert Gašparik
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Kadeřávek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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6
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Rrustemi T, Meyer K, Roske Y, Uyar B, Akalin A, Imami K, Ishihama Y, Daumke O, Selbach M. Pathogenic mutations of human phosphorylation sites affect protein-protein interactions. Nat Commun 2024; 15:3146. [PMID: 38605029 PMCID: PMC11009412 DOI: 10.1038/s41467-024-46794-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employ peptide-based interaction proteomics to investigate 36 disease-associated mutations affecting phosphorylation sites. Our results unveil significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We find that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments reveal the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering insights into potential molecular mechanisms underlying pathogenesis.
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Affiliation(s)
| | - Katrina Meyer
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 63, 14195, Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Bora Uyar
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Altuna Akalin
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Kanagawa, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Oliver Daumke
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany.
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7
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Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. Phosphorylation code of human nucleophosmin includes four cryptic sites for hierarchical binding of 14-3-3 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580064. [PMID: 38405961 PMCID: PMC10888825 DOI: 10.1101/2024.02.13.580064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phospho-sites in NPM1 reside within signal sequences, this work highlights a key mechanism of NPM1 regulation by which NPM1 phosphorylation promotes 14-3-3 binding to control nucleocytoplasmic shuttling. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.
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Affiliation(s)
- Anna A. Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina V. Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Richard B. Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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8
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Scheible N, Henning PM, McCubbin AG. Calmodulin-Domain Protein Kinase PiCDPK1 Interacts with the 14-3-3-like Protein NtGF14 to Modulate Pollen Tube Growth. PLANTS (BASEL, SWITZERLAND) 2024; 13:451. [PMID: 38337984 PMCID: PMC10857193 DOI: 10.3390/plants13030451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
Calcium-mediated signaling pathways are known to play important roles in the polar growth of pollen tubes. The calcium-dependent protein kinase, PiCDPK1, has been shown to be involved in regulating this process through interaction with a guanine dissociation inhibitor, PiRhoGDI1. To more fully understand the role of PiCDPK1 in pollen tube extension, we designed a pull-down study to identify additional substrates of this kinase. These experiments identified 123 putative interactors. Two of the identified proteins were predicted to directly interact with PiCDPK1, and this possibility was investigated in planta. The first, NtGF14, a 14-3-3-like protein, did not produce a noticeable phenotype when overexpressed in pollen alone but partially rescued the spherical tube phenotype caused by PiCDPK1 over-expression when co-over-expressed with the kinase. The second, NtREN1, a GTPase activating protein (GAP), severely inhibited pollen tube germination when over-expressed, and its co-over-expression with PiCDPK1 did not substantially affect this phenotype. These results suggest a novel in vivo interaction between NtGF14 and PiCDPK1 but do not support the direct interaction between PiCDPK1 and NtREN1. We demonstrate the utility of the methodology used to identify potential protein interactions while confirming the necessity of additional studies to confirm their validity. Finally, additional support was found for intersection between PiCDPK1 and RopGTPase pathways to control polar growth at the pollen tube tip.
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Affiliation(s)
| | | | - Andrew G. McCubbin
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA; (N.S.); (P.M.H.)
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Fan R, Zhou J, Xu Y, Gao L, Yu Z, Zang Y. Serum 14‑3‑3η levels are increased and associated with a higher risk of osteoporosis in patients with rheumatoid arthritis: A meta‑analysis. Exp Ther Med 2024; 27:76. [PMID: 38264428 PMCID: PMC10804358 DOI: 10.3892/etm.2023.12364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/22/2023] [Indexed: 01/25/2024] Open
Abstract
14-3-3η can regulate the cell cycle, immunity, inflammation and the secretion of matrix metalloproteinases, while it may also be involved in the development of rheumatoid arthritis (RA) and promote bone injury. Therefore, the present meta-analysis focused on the dysregulated serum levels of 14-3-3η and its association with osteoporosis in patients with RA. Studies comparing the serum levels of 14-3-3η between patients with RA and healthy controls (HCs) or patients with RA with different bone mineral densities were retrieved from the EMBASE, Web of Science, PubMed and Cochrane databases. A total of 14 studies comprising 2,164 patients with RA and 1,136 HCs were included and analysed. Pooled analyses showed that the serum levels of 14-3-3η were enhanced in patients with RA compared with HCs [standardized mean difference (SMD): 1.34; 95% confidence interval (CI): 1.01-1.66; P<0.001]. In addition, the serum levels of 14-3-3η were also significantly higher in patients with RA with osteoporosis and osteopenia compared with those with normal bone mass (SMD: 1.96; 95% CI: 0.01-3.92; P=0.049 and SMD: 0.80; 95% CI: 0.09-1.52; P=0.028, respectively). Begg's and Egger's tests demonstrated that the publication bias for each evaluated indicator was low (all P>0.05). However, sensitivity analyses revealed that the findings were not very robust, which may be due to the omission of several individual studies. Overall, the present meta-analysis suggested that the serum levels of 14-3-3η were elevated and were associated with a higher risk of osteoporosis in patients with RA, thus supporting its potency as a circulating biomarker in the management of RA.
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Affiliation(s)
- Ran Fan
- Department of Rheumatology and Immunology, The Suqian Clinical College of Xuzhou Medical University, Suqian, Jiangsu 223800, P.R. China
- Department of Rheumatology and Immunology, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Jun Zhou
- Department of Rheumatology and Immunology, The Suqian Clinical College of Xuzhou Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Yan Xu
- Department of Rheumatology and Immunology, The Suqian Clinical College of Xuzhou Medical University, Suqian, Jiangsu 223800, P.R. China
- Department of Rheumatology and Immunology, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Ling Gao
- Department of Rheumatology and Immunology, The Suqian Clinical College of Xuzhou Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Zhe Yu
- Department of Rheumatology and Immunology, The Suqian Clinical College of Xuzhou Medical University, Suqian, Jiangsu 223800, P.R. China
| | - Yinshan Zang
- Department of Rheumatology and Immunology, The Suqian Clinical College of Xuzhou Medical University, Suqian, Jiangsu 223800, P.R. China
- Department of Rheumatology and Immunology, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian, Jiangsu 223800, P.R. China
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10
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Son SM, Park SJ, Breusegem SY, Larrieu D, Rubinsztein DC. p300 nucleocytoplasmic shuttling underlies mTORC1 hyperactivation in Hutchinson-Gilford progeria syndrome. Nat Cell Biol 2024; 26:235-249. [PMID: 38267537 PMCID: PMC10866696 DOI: 10.1038/s41556-023-01338-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/14/2023] [Indexed: 01/26/2024]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth, metabolism and autophagy. Multiple pathways modulate mTORC1 in response to nutrients. Here we describe that nucleus-cytoplasmic shuttling of p300/EP300 regulates mTORC1 activity in response to amino acid or glucose levels. Depletion of these nutrients causes cytoplasm-to-nucleus relocalization of p300 that decreases acetylation of the mTORC1 component raptor, thereby reducing mTORC1 activity and activating autophagy. This is mediated by AMP-activated protein kinase-dependent phosphorylation of p300 at serine 89. Nutrient addition to starved cells results in protein phosphatase 2A-dependent dephosphorylation of nuclear p300, enabling its CRM1-dependent export to the cytoplasm to mediate mTORC1 reactivation. p300 shuttling regulates mTORC1 in most cell types and occurs in response to altered nutrients in diverse mouse tissues. Interestingly, p300 cytoplasm-nucleus shuttling is altered in cells from patients with Hutchinson-Gilford progeria syndrome. p300 mislocalization by the disease-causing protein, progerin, activates mTORC1 and inhibits autophagy, phenotypes that are normalized by modulating p300 shuttling. These results reveal how nutrients regulate mTORC1, a cytoplasmic complex, by shuttling its positive regulator p300 in and out of the nucleus, and how this pathway is misregulated in Hutchinson-Gilford progeria syndrome, causing mTORC1 hyperactivation and defective autophagy.
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Affiliation(s)
- Sung Min Son
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - So Jung Park
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Sophia Y Breusegem
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Delphine Larrieu
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - David C Rubinsztein
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
- UK Dementia Research Institute, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
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11
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Ward JA, Romartinez-Alonso B, Kay DF, Bellamy-Carter J, Thurairajah B, Basran J, Kwon H, Leney AC, Macip S, Roversi P, Muskett FW, Doveston RG. Characterizing the protein-protein interaction between MDM2 and 14-3-3σ; proof of concept for small molecule stabilization. J Biol Chem 2024; 300:105651. [PMID: 38237679 PMCID: PMC10864208 DOI: 10.1016/j.jbc.2024.105651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 02/10/2024] Open
Abstract
Mouse Double Minute 2 (MDM2) is a key negative regulator of the tumor suppressor protein p53. MDM2 overexpression occurs in many types of cancer and results in the suppression of WT p53. The 14-3-3 family of adaptor proteins are known to bind MDM2 and the 14-3-3σ isoform controls MDM2 cellular localization and stability to inhibit its activity. Therefore, small molecule stabilization of the 14-3-3σ/MDM2 protein-protein interaction (PPI) is a potential therapeutic strategy for the treatment of cancer. Here, we provide a detailed biophysical and structural characterization of the phosphorylation-dependent interaction between 14-3-3σ and peptides that mimic the 14-3-3 binding motifs within MDM2. The data show that di-phosphorylation of MDM2 at S166 and S186 is essential for high affinity 14-3-3 binding and that the binary complex formed involves one MDM2 di-phosphorylated peptide bound to a dimer of 14-3-3σ. However, the two phosphorylation sites do not simultaneously interact so as to bridge the 14-3-3 dimer in a 'multivalent' fashion. Instead, the two phosphorylated MDM2 motifs 'rock' between the two binding grooves of the dimer, which is unusual in the context of 14-3-3 proteins. In addition, we show that the 14-3-3σ-MDM2 interaction is amenable to small molecule stabilization. The natural product fusicoccin A forms a ternary complex with a 14-3-3σ dimer and an MDM2 di-phosphorylated peptide resulting in the stabilization of the 14-3-3σ/MDM2 PPI. This work serves as a proof-of-concept of the drugability of the 14-3-3/MDM2 PPI and paves the way toward the development of more selective and efficacious small molecule stabilizers.
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Affiliation(s)
- Jake A Ward
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; Mechanisms of Cancer and Aging Laboratory, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Beatriz Romartinez-Alonso
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Danielle F Kay
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - Bethany Thurairajah
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; School of Chemistry, University of Leicester, Leicester, UK
| | - Jaswir Basran
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Hanna Kwon
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Aneika C Leney
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Salvador Macip
- Mechanisms of Cancer and Aging Laboratory, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK; FoodLab, Faculty of Health Sciences, Universitat Oberta de Catalunya, Barcelona, Spain; Josep Carreras Leukaemia Research Institute, Ctra de Can Ruti, Camí de les Escoles, s/n, Badalona, Barcelona, Spain
| | - Pietro Roversi
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; Institute of Agricultural Biology and Biotechnology, C.N.R., Unit of Milan, Milano, Italy
| | - Frederick W Muskett
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Richard G Doveston
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, UK; School of Chemistry, University of Leicester, Leicester, UK.
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12
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Wu Q, Centorrino F, Guillory X, Wolter M, Ottmann C, Cossar PJ, Brunsveld L. Discovery of 14-3-3 PPI Stabilizers by Extension of an Amidine-Substituted Thiophene Fragment. Chembiochem 2024; 25:e202300636. [PMID: 37902676 DOI: 10.1002/cbic.202300636] [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: 09/17/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 10/31/2023]
Abstract
Protein-protein interaction (PPI) modulation is a promising approach in drug discovery with the potential to expand the 'druggable' proteome and develop new therapeutic strategies. While there have been significant advancements in methodologies for developing PPI inhibitors, there is a relative scarcity of literature describing the 'bottom-up' development of PPI stabilizers (Molecular Glues). The hub protein 14-3-3 and its interactome provide an excellent platform for exploring conceptual approaches to PPI modulation, including evolution of chemical matter for Molecular Glues. In this study, we employed a fragment extension strategy to discover stabilizers for the complex of 14-3-3 protein and an Estrogen Receptor alpha-derived peptide (ERα). A focused library of analogues derived from an amidine-substituted thiophene fragment enhanced the affinity of the 14-3-3/ERα complex up to 6.2-fold. Structure-activity relationship (SAR) analysis underscored the importance of the newly added, aromatic side chain with a certain degree of rigidity. X-ray structural analysis revealed a unique intermolecular π-π stacking binding mode of the most active analogues, resulting in the simultaneous binding of two molecules to the PPI binding pocket. Notably, analogue 11 displayed selective stabilization of the 14-3-3/ERα complex.
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Affiliation(s)
- Qi Wu
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Federica Centorrino
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
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13
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Jentoft IMA, Bäuerlein FJB, Welp LM, Cooper BH, Petrovic A, So C, Penir SM, Politi AZ, Horokhovskyi Y, Takala I, Eckel H, Moltrecht R, Lénárt P, Cavazza T, Liepe J, Brose N, Urlaub H, Fernández-Busnadiego R, Schuh M. Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices. Cell 2023; 186:5308-5327.e25. [PMID: 37922900 DOI: 10.1016/j.cell.2023.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/01/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023]
Abstract
Mammalian oocytes are filled with poorly understood structures called cytoplasmic lattices. First discovered in the 1960s and speculated to correspond to mammalian yolk, ribosomal arrays, or intermediate filaments, their function has remained enigmatic to date. Here, we show that cytoplasmic lattices are sites where oocytes store essential proteins for early embryonic development. Using super-resolution light microscopy and cryoelectron tomography, we show that cytoplasmic lattices are composed of filaments with a high surface area, which contain PADI6 and subcortical maternal complex proteins. The lattices associate with many proteins critical for embryonic development, including proteins that control epigenetic reprogramming of the preimplantation embryo. Loss of cytoplasmic lattices by knocking out PADI6 or the subcortical maternal complex prevents the accumulation of these proteins and results in early embryonic arrest. Our work suggests that cytoplasmic lattices enrich maternally provided proteins to prevent their premature degradation and cellular activity, thereby enabling early mammalian development.
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Affiliation(s)
- Ida M A Jentoft
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Felix J B Bäuerlein
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Benjamin H Cooper
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
| | - Arsen Petrovic
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Chun So
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Sarah Mae Penir
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Antonio Z Politi
- Facility for Light Microscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Yehor Horokhovskyi
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Iina Takala
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Heike Eckel
- Kinderwunschzentrum Göttingen, 37081 Göttingen, Germany
| | | | - Peter Lénárt
- Facility for Light Microscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Tommaso Cavazza
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Juliane Liepe
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Nils Brose
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
| | - Henning Urlaub
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany; Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Rubén Fernández-Busnadiego
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Faculty of Physics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany.
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14
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Williams JPC, Walport LJ. PADI6: What we know about the elusive fifth member of the peptidyl arginine deiminase family. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220242. [PMID: 37778376 PMCID: PMC10542454 DOI: 10.1098/rstb.2022.0242] [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: 01/31/2023] [Accepted: 03/05/2023] [Indexed: 10/03/2023] Open
Abstract
Peptidyl arginine deiminase 6 (PADI6) is a maternal factor that is vital for early embryonic development. Deletion and mutations of its encoding gene in female mice or women lead to early embryonic developmental arrest, female infertility, maternal imprinting defects and hyperproliferation of the trophoblast. PADI6 is the fifth and least well-characterized member of the peptidyl arginine deiminases (PADIs), which catalyse the post-translational conversion of arginine to citrulline. It is less conserved than the other PADIs, and currently has no reported catalytic activity. While there are many suggested functions of PADI6 in the early mouse embryo, including in embryonic genome activation, cytoplasmic lattice formation, maternal mRNA and ribosome regulation, and organelle distribution, the molecular mechanisms of its function remain unknown. In this review, we discuss what is known about the function of PADI6 and highlight key outstanding questions that must be answered if we are to understand the crucial role it plays in early embryo development and female fertility. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
| | - Louise J. Walport
- Imperial College of Science Technology and Medicine, London, W12 0BZ, UK
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15
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Zhang R, Feng W, Qian S, Li S, Wang F. Regulation of Rim4 distribution, function, and stability during meiosis by PKA, Cdc14, and 14-3-3 proteins. Cell Rep 2023; 42:113052. [PMID: 37659077 PMCID: PMC10591911 DOI: 10.1016/j.celrep.2023.113052] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 09/04/2023] Open
Abstract
Meiotic gene expression in budding yeast is tightly controlled by RNA-binding proteins (RBPs), with the meiosis-specific RBP Rim4 playing a key role in sequestering mid-late meiotic transcripts to prevent premature translation. However, the mechanisms governing assembly and disassembly of the Rim4-mRNA complex, critical for Rim4's function and stability, remain poorly understood. In this study, we unveil regulation of the Rim4 ribonucleoprotein (RNP) complex by the yeast 14-3-3 proteins Bmh1 and Bmh2. These proteins form a Rim4-Bmh1-Bmh2 heterotrimeric complex that expels mRNAs from Rim4 binding. We identify four Bmh1/2 binding sites (BBSs) on Rim4, with two residing within the RNA recognition motifs (RRMs). Phosphorylation and dephosphorylation of serine/threonine (S/T) residues at these BBSs by PKA kinase and Cdc14 phosphatase activities primarily control formation of Rim4-Bmh1/2, regulating Rim4's subcellular distribution, function, and stability. These findings shed light on the intricate post-transcriptional regulatory mechanisms governing meiotic gene expression.
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Affiliation(s)
- Rudian Zhang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenzhi Feng
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Suhong Qian
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shunjin Li
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Fei Wang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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16
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Visser EJ, Jaishankar P, Sijbesma E, Pennings MAM, Vandenboorn EMF, Guillory X, Neitz RJ, Morrow J, Dutta S, Renslo AR, Brunsveld L, Arkin MR, Ottmann C. From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions through Fragment Linking. Angew Chem Int Ed Engl 2023; 62:e202308004. [PMID: 37455289 DOI: 10.1002/anie.202308004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Small-molecule stabilization of protein-protein interactions (PPIs) is a promising strategy in chemical biology and drug discovery. However, the systematic discovery of PPI stabilizers remains a largely unmet challenge. Herein we report a fragment-linking approach targeting the interface of 14-3-3 and a peptide derived from the estrogen receptor alpha (ERα) protein. Two classes of fragments-a covalent and a noncovalent fragment-were co-crystallized and subsequently linked, resulting in a noncovalent hybrid molecule in which the original fragment interactions were largely conserved. Supported by 20 crystal structures, this initial hybrid molecule was further optimized, resulting in selective, 25-fold stabilization of the 14-3-3/ERα interaction. The high-resolution structures of both the single fragments, their co-crystal structures and those of the linked fragments document a feasible strategy to develop orthosteric PPI stabilizers by linking to an initial tethered fragment.
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Affiliation(s)
- Emira J Visser
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Marloes A M Pennings
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Edmee M F Vandenboorn
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - R Jeffrey Neitz
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - John Morrow
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Shubhankar Dutta
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
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17
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Shimohata A, Rai D, Akagi T, Usui S, Ogiwara I, Kaneda M. The intracellular C-terminal domain of mGluR6 contains ER retention motifs. Mol Cell Neurosci 2023; 126:103875. [PMID: 37352898 DOI: 10.1016/j.mcn.2023.103875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023] Open
Abstract
Metabotropic glutamate receptor 6 (mGluR6) predominantly localizes to the postsynaptic sites of retinal ON-bipolar cells, at which it recognizes glutamate released from photoreceptors. The C-terminal domain (CTD) of mGluR6 contains a cluster of basic amino acids resembling motifs for endoplasmic reticulum (ER) retention. We herein investigated whether these basic residues are involved in regulating the subcellular localization of mGluR6 in 293T cells expressing mGluR6 CTD mutants using immunocytochemistry, immunoprecipitation, and flow cytometry. We showed that full-length mGluR6 localized to the ER and cell surface, whereas mGluR6 mutants with 15- and 20-amino acid deletions from the C terminus localized to the ER, but were deficient at the cell surface. We also demonstrated that the cell surface deficiency of mGluR6 mutants was rescued by introducing an alanine substitution at basic residues within the CTD. The surface-deficient mGluR6 mutant still did not localize to the cell surface and was retained in the ER when co-expressed with surface-expressible constructs, including full-length mGluR6, even though surface-deficient and surface-expressible constructs formed heteromeric complexes. The co-expression of the surface-deficient mGluR6 mutant reduced the surface levels of surface-expressible constructs. These results indicate that basic residues in the mGluR6 CTD served as ER retention signals. We suggest that exposed ER retention motifs in the aberrant assembly containing truncated or misfolded mGluR6 prevent these protein complexes from being transported to the cell surface.
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Affiliation(s)
- Atsushi Shimohata
- Department of Physiology, Nippon Medical School, Tokyo 113-8602, Japan
| | - Dilip Rai
- Department of Physiology, Nippon Medical School, Tokyo 113-8602, Japan
| | - Takumi Akagi
- Department of Physiology, Nippon Medical School, Tokyo 113-8602, Japan
| | - Sumiko Usui
- Department of Physiology, Nippon Medical School, Tokyo 113-8602, Japan
| | - Ikuo Ogiwara
- Department of Physiology, Nippon Medical School, Tokyo 113-8602, Japan.
| | - Makoto Kaneda
- Department of Physiology, Nippon Medical School, Tokyo 113-8602, Japan
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18
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Safi A, Smagghe W, Gonçalves A, Wang Q, Xu K, Fernandez AI, Cappe B, Riquet FB, Mylle E, Eeckhout D, De Winne N, Van De Slijke E, Persyn F, Persiau G, Van Damme D, Geelen D, De Jaeger G, Beeckman T, Van Leene J, Vanneste S. Phase separation-based visualization of protein-protein interactions and kinase activities in plants. THE PLANT CELL 2023; 35:3280-3302. [PMID: 37378595 PMCID: PMC10473206 DOI: 10.1093/plcell/koad188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/23/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
Protein activities depend heavily on protein complex formation and dynamic posttranslational modifications, such as phosphorylation. The dynamic nature of protein complex formation and posttranslational modifications is notoriously difficult to monitor in planta at cellular resolution, often requiring extensive optimization. Here, we generated and exploited the SYnthetic Multivalency in PLants (SYMPL)-vector set to assay protein-protein interactions (PPIs) (separation of phases-based protein interaction reporter) and kinase activities (separation of phases-based activity reporter of kinase) in planta, based on phase separation. This technology enabled easy detection of inducible, binary and ternary PPIs among cytoplasmic and nuclear proteins in plant cells via a robust image-based readout. Moreover, we applied the SYMPL toolbox to develop an in vivo reporter for SNF1-related kinase 1 activity, allowing us to visualize tissue-specific, dynamic SnRK1 activity in stable transgenic Arabidopsis (Arabidopsis thaliana) plants. The SYMPL cloning toolbox provides a means to explore PPIs, phosphorylation, and other posttranslational modifications with unprecedented ease and sensitivity.
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Affiliation(s)
- Alaeddine Safi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Wouter Smagghe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Amanda Gonçalves
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- VIB, Bioimaging Core, B-9052 Ghent, Belgium
| | - Qing Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ke Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ana Ibis Fernandez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Benjamin Cappe
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
| | - Franck B Riquet
- Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Freya Persyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Danny Geelen
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
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19
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Andrews DDT, Vlok M, Akbari Bani D, Hay BN, Mohamud Y, Foster LJ, Luo H, Overall CM, Jan E. Cleavage of 14-3-3ε by the enteroviral 3C protease dampens RIG-I-mediated antiviral signaling. J Virol 2023; 97:e0060423. [PMID: 37555661 PMCID: PMC10506458 DOI: 10.1128/jvi.00604-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/13/2023] [Indexed: 08/10/2023] Open
Abstract
Viruses have evolved diverse strategies to evade the host innate immune response and promote infection. The retinoic acid-inducible gene I (RIG-I)-like receptors RIG-I and MDA5 are antiviral factors that sense viral RNA and trigger downstream signal via mitochondrial antiviral-signaling protein (MAVS) to activate type I interferon expression. 14-3-3ε is a key component of the RIG-I translocon complex that interacts with MAVS at the mitochondrial membrane; however, the exact role of 14-3-3ε in this pathway is not well understood. In this study, we demonstrate that 14-3-3ε is a direct substrate of both the poliovirus and coxsackievirus B3 (CVB3) 3C proteases (3Cpro) and that it is cleaved at Q236↓G237, resulting in the generation of N- and C-terminal fragments of 27.0 and 2.1 kDa, respectively. While the exogenous expression of wild-type 14-3-3ε enhances IFNB mRNA production during poly(I:C) stimulation, expression of the truncated N-terminal fragment does not. The N-terminal 14-3-3ε fragment does not interact with RIG-I in co-immunoprecipitation assays, nor can it facilitate RIG-I translocation to the mitochondria. Probing the intrinsically disordered C-terminal region identifies key residues responsible for the interaction between 14-3-3ε and RIG-I. Finally, overexpression of the N-terminal fragment promotes CVB3 infection in mammalian cells. The strategic enterovirus 3Cpro-mediated cleavage of 14-3-3ε antagonizes RIG-I signaling by disrupting critical interactions within the RIG-I translocon complex, thus contributing to evasion of the host antiviral response. IMPORTANCE Host antiviral factors work to sense virus infection through various mechanisms, including a complex signaling pathway known as the retinoic acid-inducible gene I (RIG-I)-like receptor pathway. This pathway drives the production of antiviral molecules known as interferons, which are necessary to establish an antiviral state in the cellular environment. Key to this antiviral signaling pathway is the small chaperone protein 14-3-3ε, which facilitates the delivery of a viral sensor protein, RIG-I, to the mitochondria. In this study, we show that the enteroviral 3C protease cleaves 14-3-3ε during infection, rendering it incapable of facilitating this antiviral response. We also find that the resulting N-terminal cleavage fragment dampens RIG-I signaling and promotes virus infection. Our findings reveal a novel viral strategy that restricts the antiviral host response and provides insights into the mechanisms underlying 14-3-3ε function in RIG-I antiviral signaling.
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Affiliation(s)
- Daniel D. T. Andrews
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marli Vlok
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dorssa Akbari Bani
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Brenna N. Hay
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yasir Mohamud
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Honglin Luo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher M. Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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20
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Liu C, Zhang H, Li T, Jiang Z, Yuan Y, Chen X. Fusobacterium nucleatum Promotes Megakaryocyte Maturation in Patients with Gastric Cancer via Inducing the Production of Extracellular Vesicles Containing 14-3-3ε. Infect Immun 2023; 91:e0010223. [PMID: 37404144 PMCID: PMC10429653 DOI: 10.1128/iai.00102-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/11/2023] [Indexed: 07/06/2023] Open
Abstract
Fusobacterium nucleatum colonization contributes to the occurrence of portal vein thrombosis in patients with gastric cancer (GC). However, the underlying mechanism by which F. nucleatum promotes thrombosis remains unclear. In this study, we recruited a total of 91 patients with GC and examined the presence of F. nucleatum in tumor and adjacent non-tumor tissues by fluorescence in situ hybridization and quantitative PCR. Neutrophil extracellular traps (NETs) were detected by immunohistochemistry. Extracellular vesicles (EVs) were extracted from the peripheral blood and proteins in the EVs were identified by mass spectrometry (MS). HL-60 cells differentiated into neutrophils were used to package engineered EVs to imitate the EVs released from NETs. Hematopoietic progenitor cells (HPCs) and K562 cells were used for megakaryocyte (MK) in vitro differentiation and maturation to examine the function of EVs. We observed that F. nucleatum-positive patients had increased NET and platelet counts. EVs from F. nucleatum-positive patients could promote the differentiation and maturation of MKs and had upregulated 14-3-3 proteins, especially 14-3-3ε. 14-3-3ε upregulation promoted MK differentiation and maturation in vitro. HPCs and K562 cells could receive 14-3-3ε from the EVs, which interacted with GP1BA and 14-3-3ζ to trigger PI3K-Akt signaling. In conclusion, we identified for the first time that F. nucleatum infection promotes NET formation, which releases EVs containing 14-3-3ε. These EVs could deliver 14-3-3ε to HPCs and promote their differentiation into MKs via activation of PI3K-Akt signaling.
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Affiliation(s)
- Chang Liu
- Department of Critical Care Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
- Department of Cardiovascular Medicine, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - He Zhang
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Tiepeng Li
- Department of Immunology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Zhiqiang Jiang
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Yiqiang Yuan
- Department of Cardiovascular Medicine, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
- Department of Cardiovascular Medicine, The 7th People’s Hospital of Zhengzhou, Henan Cardiovascular Hospital Affiliated to Southern Medical University/The Second School of Clinical Medicine, Southern Medical University, Zhengzhou, Henan, China
- Department of Cardiovascular Medicine, Henan Provincial Chest Hospital, Zhengzhou, Henan, China
| | - Xiaobing Chen
- Department of Gastrointestinal Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
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21
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Tanaka K, Hatano Y, Ohkanda J. Isoform-Selective Fluorescent Labeling of 14-3-3σ by Acrylamide-Containing Fusicoccins. Chemistry 2023; 29:e202301059. [PMID: 37170712 DOI: 10.1002/chem.202301059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023]
Abstract
The 14-3-3 family of proteins is central to the regulation of signaling pathways driven by serine/threonine kinases. In humans, 14-3-3 consists of seven highly conserved isoforms, yet the function of each isoform remains to be fully elucidated. Synthetic agents capable of isoform-specific fluorescent labeling of 14-3-3 would provide a useful tool for studying in depth the biological roles of isoforms. In this study, the 14-3-3σ isoform was evaluated, which possesses a unique Cys38, and a natural product-based fluorescent labeling agent was designed by introducing an acrylamide group and a fluorescent dye to fusicoccin (FC). In vitro evaluation demonstrated that 12-hydroxy 1 and 2 exhibit 14-3-3σ selective labeling activity over 14-3-3ζ in the presence of a mode-3 phospholigand. Furthermore, 2 was shown to label 14-3-3σ in cell lysate in the presence of a C-terminal mode-3 phosphopeptide derived from ERα, with no apparent nonspecific labeling. These results indicate that 2 is capable of selective fluorescent detection of 14-3-3σ upon binding to mode-3 phospholigand under biologically relevant conditions.
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Affiliation(s)
- Kenta Tanaka
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
| | - Yoshiya Hatano
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
| | - Junko Ohkanda
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
- Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
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22
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Andlovic B, Heilmann G, Ninck S, Andrei SA, Centorrino F, Higuchi Y, Kato N, Brunsveld L, Arkin M, Menninger S, Choidas A, Wolf A, Klebl B, Kaschani F, Kaiser M, Eickhoff J, Ottmann C. IFNα primes cancer cells for Fusicoccin-induced cell death via 14-3-3 PPI stabilization. Cell Chem Biol 2023; 30:573-590.e6. [PMID: 37130519 DOI: 10.1016/j.chembiol.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/02/2023] [Accepted: 04/06/2023] [Indexed: 05/04/2023]
Abstract
The natural product family of the fusicoccanes (FCs) has been shown to display anti-cancer activity, especially when combined with established therapeutic agents. FCs stabilize 14-3-3 protein-protein interactions (PPIs). Here, we tested combinations of a small library of FCs with interferon α (IFNα) on different cancer cell lines and report a proteomics approach to identify the specific 14-3-3 PPIs that are induced by IFNα and stabilized by FCs in OVCAR-3 cells. Among the identified 14-3-3 target proteins are THEMIS2, receptor interacting protein kinase 2 (RIPK2), EIF2AK2, and several members of the LDB1 complex. Biophysical and structural biology studies confirm these 14-3-3 PPIs as physical targets of FC stabilization, and transcriptome as well as pathway analyses suggest possible explanations for the observed synergistic effect of IFNα/FC treatment on cancer cells. This study elucidates the polypharmacological effects of FCs in cancer cells and identifies potential targets from the vast interactome of 14-3-3s for therapeutic intervention in oncology.
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Affiliation(s)
- Blaž Andlovic
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, the Netherlands; Lead Discovery Center GmbH, 44227 Dortmund, Germany
| | - Geronimo Heilmann
- Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Sabrina Ninck
- Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Sebastian A Andrei
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, the Netherlands
| | - Federica Centorrino
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, the Netherlands
| | - Yusuke Higuchi
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Ibaraki, Japan
| | - Nobuo Kato
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Ibaraki, Japan
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, the Netherlands
| | - Michelle Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Axel Choidas
- Lead Discovery Center GmbH, 44227 Dortmund, Germany
| | | | - Bert Klebl
- Lead Discovery Center GmbH, 44227 Dortmund, Germany
| | - Farnusch Kaschani
- Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Markus Kaiser
- Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Jan Eickhoff
- Lead Discovery Center GmbH, 44227 Dortmund, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, the Netherlands.
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23
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Rohrer L, Spohr C, Beha C, Griffin R, Braun S, Halbach S, Brummer T. Analysis of RAS and drug induced homo- and heterodimerization of RAF and KSR1 proteins in living cells using split Nanoluc luciferase. Cell Commun Signal 2023; 21:136. [PMID: 37316874 DOI: 10.1186/s12964-023-01146-9] [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: 11/11/2022] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The dimerization of RAF kinases represents a key event in their activation cycle and in RAS/ERK pathway activation. Genetic, biochemical and structural approaches provided key insights into this process defining RAF signaling output and the clinical efficacy of RAF inhibitors (RAFi). However, methods reporting the dynamics of RAF dimerization in living cells and in real time are still in their infancy. Recently, split luciferase systems have been developed for the detection of protein-protein-interactions (PPIs), incl. proof-of-concept studies demonstrating the heterodimerization of the BRAF and RAF1 isoforms. Due to their small size, the Nanoluc luciferase moieties LgBiT and SmBiT, which reconstitute a light emitting holoenzyme upon fusion partner promoted interaction, appear as well-suited to study RAF dimerization. Here, we provide an extensive analysis of the suitability of the Nanoluc system to study the homo- and heterodimerization of BRAF, RAF1 and the related KSR1 pseudokinase. We show that KRASG12V promotes the homo- and heterodimerization of BRAF, while considerable KSR1 homo- and KSR1/BRAF heterodimerization already occurs in the absence of this active GTPase and requires a salt bridge between the CC-SAM domain of KSR1 and the BRAF-specific region. We demonstrate that loss-of-function mutations impairing key steps of the RAF activation cycle can be used as calibrators to gauge the dynamics of heterodimerization. This approach identified the RAS-binding domains and the C-terminal 14-3-3 binding motifs as particularly critical for the reconstitution of RAF mediated LgBiT/SmBiT reconstitution, while the dimer interface was less important for dimerization but essential for downstream signaling. We show for the first time that BRAFV600E, the most common BRAF oncoprotein whose dimerization status is controversially portrayed in the literature, forms homodimers in living cells more efficiently than its wildtype counterpart. Of note, Nanoluc activity reconstituted by BRAFV600E homodimers is highly sensitive to the paradox-breaking RAFi PLX8394, indicating a dynamic and specific PPI. We report the effects of eleven ERK pathway inhibitors on RAF dimerization, incl. third-generation compounds that are less-defined in terms of their dimer promoting abilities. We identify Naporafenib as a potent and long-lasting dimerizer and show that the split Nanoluc approach discriminates between type I, I1/2 and II RAFi. Video Abstract.
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Affiliation(s)
- Lino Rohrer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Corinna Spohr
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Carina Beha
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Ricarda Griffin
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany.
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany.
- Center for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, 79104, Germany.
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24
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Kouchi Z, Kojima M. A Structural Network Analysis of Neuronal ArhGAP21/23 Interactors by Computational Modeling. ACS OMEGA 2023; 8:19249-19264. [PMID: 37305272 PMCID: PMC10249030 DOI: 10.1021/acsomega.2c08054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/05/2023] [Indexed: 06/13/2023]
Abstract
RhoGTPase-activating proteins (RhoGAPs) play multiple roles in neuronal development; however, details of their substrate recognition system remain elusive. ArhGAP21 and ArhGAP23 are RhoGAPs that contain N-terminal PDZ and pleckstrin homology domains. In the present study, the RhoGAP domain of these ArhGAPs was computationally modeled by template-based methods and the AlphaFold2 software program, and their intrinsic RhoGTPase recognition mechanism was analyzed from the domain structures using the protein docking programs HADDOCK and HDOCK. ArhGAP21 was predicted to preferentially catalyze Cdc42, RhoA, RhoB, RhoC, and RhoG and to downregulate RhoD and Tc10 activities. Regarding ArhGAP23, RhoA and Cdc42 were deduced to be its substrates, whereas RhoD downregulation was predicted to be less efficient. The PDZ domains of ArhGAP21/23 possess the FTLRXXXVY sequence, and similar globular folding consists of antiparalleled β-sheets and two α-helices that are conserved with PDZ domains of MAST-family proteins. A peptide docking analysis revealed the specific interaction of the ArhGAP23 PDZ domain with the PTEN C-terminus. The pleckstrin homology domain structure of ArhGAP23 was also predicted, and the functional selectivity for the interactors regulated by the folding and disordered domains in ArhGAP21 and ArhGAP23 was examined by an in silico analysis. An interaction analysis of these RhoGAPs revealed the existence of mammalian ArhGAP21/23-specific type I and type III Arf- and RhoGTPase-regulated signaling. Multiple recognition systems of RhoGTPase substrates and selective Arf-dependent localization of ArhGAP21/23 may form the basis of the functional core signaling necessary for synaptic homeostasis and axon/dendritic transport regulated by RhoGAP localization and activities.
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Affiliation(s)
- Zen Kouchi
- Department
of Genetics, Institute for Developmental
Research, Aichi Developmental Disability Center, 713-8 Kamiya-cho, Kasugai-city 480-0392 Aichi, Japan
| | - Masaki Kojima
- Laboratory
of Bioinformatics, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji 192-0392, Japan
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25
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Adavi B S, Pandesha PH, B J, Jha SK, Chinnusamy V, Sathee L. Nitrate supply regulates tissue calcium abundance and transcript level of Calcineurin B-like (CBL) gene family in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107724. [PMID: 37172401 DOI: 10.1016/j.plaphy.2023.107724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/14/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Calcium ion (Ca2+) is the most ubiquitous signalling molecule and is sensed by different classes of Ca2+ sensor proteins. Recent evidences underscore the role of calcium signalling in plant response to nitrogen/nitrate supply. Recently we found that under nitrate deficiency, a short-term supply of calcium could improve the plant biomass, nitrate assimilation, anthocyanin accumulation and expression of nitrate uptake and signalling genes. Long-term calcium supply, on the other hand, was not beneficial. Calcineurin B-like (CBL) proteins are one of the vital plant Ca2+ sensory protein family which is essential for stress perception and signaling. To understand the dynamics of CBL-mediated stress signalling in bread wheat, we identified CBL genes in bread wheat (Triticum aestivum) and its progenitors, namely Triticum dicoccoides, Triticum urartu and Aegilops tauschii with the aid of newly available whole-genome sequence. The expression of different CBLs and the changes in root Ca2+ localization in response to nitrate provision or deficiency were analysed. Expression of the CBLs were studied in two bread wheat genotypes with comparatively higher (B.T. Schomburgk, BTS) and lower (Gluyas early, GE) nitrate responsiveness and nitrogen use efficiency. High N promoted the expression of CBLs in seedling leaves while in roots the expression was promoted by N deficiency. At the 5 days after anthesis stage, nitrate starvation downregulated the expression of CBLs while nitrate supply enhanced the expression. At anthesis stage, expression of CBL6 was significantly promoted by HN in panicles of both the genotypes, the highest expression was recorded in BTS. Expression of CBL6 was significantly upregulated by short term nitrate treatment also suggesting its role in Primary nitrate response (PNR) in wheat. There was a significant down regulation of CBL6 expression post nitrate starvation, making it a probable regulator of nitrogen starvation response (NSR) as well. In seedling roots, the tissue localization of Ca2+ was increased both by high and low nitrate treatments, albeit at different magnitudes. Our results suggest that calcium signalling might be a major signalling pathway governing nitrogen responsiveness and CBL6 might be playing pivotal role in NSR and PNR in wheat.
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Affiliation(s)
- Sandeep Adavi B
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pratheek H Pandesha
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jagadhesan B
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra K Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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26
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Li Z, Huang X, Li M, Chen YE, Wang Z, Liu L. A ubiquitination-mediated degradation system to target 14-3-3-binding phosphoproteins. Heliyon 2023; 9:e16318. [PMID: 37251884 PMCID: PMC10213371 DOI: 10.1016/j.heliyon.2023.e16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
The phosphorylation of 14-3-3 binding motif is involved in many cellular processes. A strategy that enables targeted degradation of 14-3-3-binding phosphoproteins (14-3-3-BPPs) for studying their functions is highly desirable for basic research. Here, we report a phosphorylation-induced, ubiquitin-proteasome-system-mediated targeted protein degradation (TPD) strategy that allows specific degradation of 14-3-3-BPPs. Specifically, by ligating a modified von Hippel-Lindau E3-ligase with an engineered 14-3-3 bait, we generated a protein chimera referred to as Targeted Degradation of 14-3-3-binding PhosphoProtein (TDPP). TDPP can serve as a universal degrader for 14-3-3-BPPs based on the specific recognition of the phosphorylation in 14-3-3 binding motifs. TDPP shows high efficiency and specificity to a difopein-EGFP reporter, general and specific 14-3-3-BPPs. TDPP can also be applied for the validation of 14-3-3-BPPs. These results strongly support TDPP as a powerful tool for 14-3-3 related research.
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Affiliation(s)
- Zhaokai Li
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Emergency Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xiaoqiang Huang
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mohan Li
- Department of Geriatrics, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing 100730, China
| | - Y. Eugene Chen
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhong Wang
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Liu Liu
- Department of Cardiac Surgery, Cardiovascular Center, University of Michigan, Ann Arbor, MI 48109, USA
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27
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Martignago D, da Silveira Falavigna V, Lombardi A, Gao H, Korwin Kurkowski P, Galbiati M, Tonelli C, Coupland G, Conti L. The bZIP transcription factor AREB3 mediates FT signalling and floral transition at the Arabidopsis shoot apical meristem. PLoS Genet 2023; 19:e1010766. [PMID: 37186640 PMCID: PMC10212096 DOI: 10.1371/journal.pgen.1010766] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/25/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
The floral transition occurs at the shoot apical meristem (SAM) in response to favourable external and internal signals. Among these signals, variations in daylength (photoperiod) act as robust seasonal cues to activate flowering. In Arabidopsis, long-day photoperiods stimulate production in the leaf vasculature of a systemic florigenic signal that is translocated to the SAM. According to the current model, FLOWERING LOCUS T (FT), the main Arabidopsis florigen, causes transcriptional reprogramming at the SAM, so that lateral primordia eventually acquire floral identity. FT functions as a transcriptional coregulator with the bZIP transcription factor FD, which binds DNA at specific promoters. FD can also interact with TERMINAL FLOWER 1 (TFL1), a protein related to FT that acts as a floral repressor. Thus, the balance between FT-TFL1 at the SAM influences the expression levels of floral genes targeted by FD. Here, we show that the FD-related bZIP transcription factor AREB3, which was previously studied in the context of phytohormone abscisic acid signalling, is expressed at the SAM in a spatio-temporal pattern that strongly overlaps with FD and contributes to FT signalling. Mutant analyses demonstrate that AREB3 relays FT signals redundantly with FD, and the presence of a conserved carboxy-terminal SAP motif is required for downstream signalling. AREB3 shows unique and common patterns of expression with FD, and AREB3 expression levels are negatively regulated by FD thus forming a compensatory feedback loop. Mutations in another bZIP, FDP, further aggravate the late flowering phenotypes of fd areb3 mutants. Therefore, multiple florigen-interacting bZIP transcription factors have redundant functions in flowering at the SAM.
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Affiliation(s)
- Damiano Martignago
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | | | | | - He Gao
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Massimo Galbiati
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Chiara Tonelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Lucio Conti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
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28
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Bennison SA, Blazejewski SM, Liu X, Hacohen-Kleiman G, Sragovich S, Zoidou S, Touloumi O, Grigoriadis N, Gozes I, Toyo-Oka K. The cytoplasmic localization of ADNP through 14-3-3 promotes sex-dependent neuronal morphogenesis, cortical connectivity, and calcium signaling. Mol Psychiatry 2023; 28:1946-1959. [PMID: 36631597 DOI: 10.1038/s41380-022-01939-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023]
Abstract
Defective neuritogenesis is a contributing pathogenic mechanism underlying a variety of neurodevelopmental disorders. Single gene mutations in activity-dependent neuroprotective protein (ADNP) are the most frequent among autism spectrum disorders (ASDs) leading to the ADNP syndrome. Previous studies showed that during neuritogenesis, Adnp localizes to the cytoplasm/neurites, and Adnp knockdown inhibits neuritogenesis in culture. Here, we hypothesized that Adnp is localized in the cytoplasm during neurite formation and that this process is mediated by 14-3-3. Indeed, applying the 14-3-3 inhibitor, difopein, blocked Adnp cytoplasmic localization. Furthermore, co-immunoprecipitations showed that Adnp bound 14-3-3 proteins and proteomic analysis identified several potential phosphorylation-dependent Adnp/14-3-3 binding sites. We further discovered that knockdown of Adnp using in utero electroporation of mouse layer 2/3 pyramidal neurons in the somatosensory cortex led to previously unreported changes in neurite formation beginning at P0. Defects were sustained throughout development, the most notable included increased basal dendrite number and axon length. Paralleling the observed morphological aberrations, ex vivo calcium imaging revealed that Adnp deficient neurons had greater and more frequent spontaneous calcium influx in female mice. GRAPHIC, a novel synaptic tracing technology substantiated this finding, revealing increased interhemispheric connectivity between female Adnp deficient layer 2/3 pyramidal neurons. We conclude that Adnp is localized to the cytoplasm by 14-3-3 proteins, where it regulates neurite formation, maturation, and functional cortical connectivity significantly building on our current understanding of Adnp function and the etiology of ADNP syndrome.
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Affiliation(s)
- Sarah A Bennison
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Sara M Blazejewski
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Xiaonan Liu
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Gal Hacohen-Kleiman
- The Elton Laboratory for Neuroendocrinology; Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Shlomo Sragovich
- The Elton Laboratory for Neuroendocrinology; Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sofia Zoidou
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Olga Touloumi
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Grigoriadis
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Illana Gozes
- The Elton Laboratory for Neuroendocrinology; Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Kazuhito Toyo-Oka
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, 19129, USA.
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29
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Zhu P, Stanisheuski S, Franklin R, Vogel A, Vesely CH, Reardon P, Sluchanko NN, Beckman JS, Karplus PA, Mehl RA, Cooley RB. Autonomous Synthesis of Functional, Permanently Phosphorylated Proteins for Defining the Interactome of Monomeric 14-3-3ζ. ACS CENTRAL SCIENCE 2023; 9:816-835. [PMID: 37122473 PMCID: PMC10141581 DOI: 10.1021/acscentsci.3c00191] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Indexed: 05/03/2023]
Abstract
14-3-3 proteins are dimeric hubs that bind hundreds of phosphorylated "clients" to regulate their function. Installing stable, functional mimics of phosphorylated amino acids into proteins offers a powerful strategy to study 14-3-3 function in cellular-like environments, but a previous genetic code expansion (GCE) system to translationally install nonhydrolyzable phosphoserine (nhpSer), with the γ-oxygen replaced with CH2, site-specifically into proteins has seen limited usage. Here, we achieve a 40-fold improvement in this system by engineering into Escherichia coli a six-step biosynthetic pathway that produces nhpSer from phosphoenolpyruvate. Using this autonomous "PermaPhos" expression system, we produce three biologically relevant proteins with nhpSer and confirm that nhpSer mimics the effects of phosphoserine for activating GSK3β phosphorylation of the SARS-CoV-2 nucleocapsid protein, promoting 14-3-3/client complexation, and monomerizing 14-3-3 dimers. Then, to understand the biological function of these phosphorylated 14-3-3ζ monomers (containing nhpSer at Ser58), we isolate its interactome from HEK293T lysates and compare it with that of wild-type 14-3-3ζ. These data identify two new subsets of 14-3-3 client proteins: (i) those that selectively bind dimeric 14-3-3ζ and (ii) those that selectively bind monomeric 14-3-3ζ. We discover that monomeric-but not dimeric-14-3-3ζ interacts with cereblon, an E3 ubiquitin-ligase adaptor protein of pharmacological interest.
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Affiliation(s)
- Phillip Zhu
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Stanislau Stanisheuski
- Department
of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Rachel Franklin
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Amber Vogel
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Cat Hoang Vesely
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Patrick Reardon
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Nikolai N. Sluchanko
- A.N.
Bach Institute of Biochemistry, Federal Research Center of Biotechnology
of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Joseph S. Beckman
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- e-MSion
Inc., 2121 NE Jack London
St., Corvallis, Oregon 97330, United States
| | - P. Andrew Karplus
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Ryan A. Mehl
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Richard B. Cooley
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
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30
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Wang N, Shi Y, Jiang Q, Li H, Fan W, Feng Y, Li L, Liu B, Lin F, Jing W, Zhang W, Shen L. A 14-3-3 protein positively regulates rice salt tolerance by stabilizing phospholipase C1. PLANT, CELL & ENVIRONMENT 2023; 46:1232-1248. [PMID: 36539986 DOI: 10.1111/pce.14520] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/06/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
The phosphatidylinositol-specific phospholipase Cs (PI-PLCs) catalyze the hydrolysis of phosphatidylinositols, which play crucial roles in signaling transduction during plant development and stress response. However, the regulation of PI-PLC is still poorly understood. A previous study showed that a rice PI-PLC, OsPLC1, was essential to rice salt tolerance. Here, we identified a 14-3-3 protein, OsGF14b, as an interaction partner of OsPLC1. Similar to OsPLC1, OsGF14b also positively regulates rice salt tolerance, and their interaction can be promoted by NaCl stress. OsGF14b also positively regulated the hydrolysis activity of OsPLC1, and is essential to NaCl-induced activation of rice PI-PLCs. We further discovered that OsPLC1 was degraded via ubiquitin-proteasome pathway, and OsGF14b could inhibit the ubiquitination of OsPLC1 to protect OsPLC1 from degradation. Under salt stress, the OsPLC1 protein level in osgf14b was lower than the corresponding value of WT, whereas overexpression of OsGF14b results in a significant increase of OsPLC1 stability. Taken together, we propose that OsGF14b can interact with OsPLC1 and promote its activity and stability, thereby improving rice salt tolerance. This study provides novel insights into the important roles of 14-3-3 proteins in regulating protein stability and function in response to salt stress.
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Affiliation(s)
- Ningna Wang
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yiyuan Shi
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qun Jiang
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Huan Li
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wenxia Fan
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yu Feng
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Li Li
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Bin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Feng Lin
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wen Jing
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wenhua Zhang
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Like Shen
- Department of Plant Biology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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31
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Segal D, Maier S, Mastromarco GJ, Qian WW, Nabeel-Shah S, Lee H, Moore G, Lacoste J, Larsen B, Lin ZY, Selvabaskaran A, Liu K, Smibert C, Zhang Z, Greenblatt J, Peng J, Lee HO, Gingras AC, Taipale M. A central chaperone-like role for 14-3-3 proteins in human cells. Mol Cell 2023; 83:974-993.e15. [PMID: 36931259 DOI: 10.1016/j.molcel.2023.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 03/18/2023]
Abstract
14-3-3 proteins are highly conserved regulatory proteins that interact with hundreds of structurally diverse clients and act as central hubs of signaling networks. However, how 14-3-3 paralogs differ in specificity and how they regulate client protein function are not known for most clients. Here, we map the interactomes of all human 14-3-3 paralogs and systematically characterize the effect of disrupting these interactions on client localization. The loss of 14-3-3 binding leads to the coalescence of a large fraction of clients into discrete foci in a client-specific manner, suggesting a central chaperone-like function for 14-3-3 proteins. Congruently, the engraftment of 14-3-3 binding motifs to nonclients can suppress their aggregation or phase separation. Finally, we show that 14-3-3s negatively regulate the localization of the RNA-binding protein SAMD4A to cytoplasmic granules and inhibit its activity as a translational repressor. Our work suggests that 14-3-3s have a more prominent role as chaperone-like molecules than previously thought.
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Affiliation(s)
- Dmitri Segal
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Stefan Maier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | | | - Wesley Wei Qian
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hyunmin Lee
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Gaelen Moore
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jessica Lacoste
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Abeeshan Selvabaskaran
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Karen Liu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Craig Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada.
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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32
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Zhu P, Nguyen KT, Estelle AB, Sluchanko NN, Mehl RA, Cooley RB. Genetic encoding of 3-nitro-tyrosine reveals the impacts of 14-3-3 nitration on client binding and dephosphorylation. Protein Sci 2023; 32:e4574. [PMID: 36691781 PMCID: PMC9926477 DOI: 10.1002/pro.4574] [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: 11/10/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023]
Abstract
14-3-3 proteins are central hub regulators of hundreds of phosphorylated "client" proteins. They are subject to over 60 post-translational modifications (PTMs), yet little is known how these PTMs alter 14-3-3 function and its ability to regulate downstream signaling pathways. An often neglected, but well-documented 14-3-3 PTM found under physiological and immune-stimulatory conditions is the conversion of tyrosine to 3-nitro-tyrosine at several Tyr sites, two of which are located at sites considered important for 14-3-3 function: Y130 (β-isoform numbering) is located in the primary phospho-client peptide-binding groove, while Y213 is found on a secondary binding site that engages with clients for full 14-3-3/client complex formation and client regulation. By genetically encoding 3-nitro-tyrosine, we sought to understand if nitration at Y130 and Y213 effectively modulated 14-3-3 structure, function, and client complexation. The 1.5 Å resolution crystal structure of 14-3-3 nitrated at Y130 showed the nitro group altered the conformation of key residues in the primary binding site, while functional studies confirmed client proteins failed to bind this variant of 14-3-3. But, in contrast to other client-binding deficient variants, it did not localize to the nucleus. The 1.9 Å resolution structure of 14-3-3 nitrated at Y213 revealed unusual flexibility of its C-terminal α-helix resulting in domain swapping, suggesting additional structural plasticity though its relevance is not clear as this nitrated form retained its ability to bind clients. Collectively, our data suggest that nitration of 14-3-3 will alter downstream signaling systems, and if uncontrolled could result in global dysregulation of the 14-3-3 interactome.
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Affiliation(s)
- Phillip Zhu
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Kyle T. Nguyen
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Aidan B. Estelle
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of SciencesA.N. Bach Institute of BiochemistryMoscowRussia
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Richard B. Cooley
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
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33
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Tugaeva KV, Sysoev AA, Kapitonova AA, Smith JLR, Zhu P, Cooley RB, Antson AA, Sluchanko NN. Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation. J Mol Biol 2023; 435:167891. [PMID: 36427566 PMCID: PMC9683861 DOI: 10.1016/j.jmb.2022.167891] [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: 10/06/2022] [Revised: 11/06/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022]
Abstract
Phosphorylation of SARS-CoV-2 nucleoprotein recruits human cytosolic 14-3-3 proteins playing a well-recognized role in replication of many viruses. Here we use genetic code expansion to demonstrate that 14-3-3 binding is triggered by phosphorylation of SARS-CoV-2 nucleoprotein at either of two pseudo-repeats centered at Ser197 and Thr205. According to fluorescence anisotropy measurements, the pT205-motif,presentin SARS-CoV-2 but not in SARS-CoV, is preferred over the pS197-motif by all seven human 14-3-3 isoforms, which collectively display an unforeseen pT205/pS197 peptide binding selectivity hierarchy. Crystal structures demonstrate that pS197 and pT205 are mutually exclusive 14-3-3-binding sites, whereas SAXS and biochemical data obtained on the full protein-protein complex indicate that 14-3-3 binding occludes the Ser/Arg-rich region of the nucleoprotein, inhibiting its dephosphorylation. This Ser/Arg-rich region is highly prone to mutations, as exemplified by the Omicron and Delta variants, with our data suggesting that the strength of 14-3-3/nucleoprotein interaction can be linked with the replicative fitness of the virus.
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Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Phillip Zhu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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34
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Egbert CM, Warr LR, Pennington KL, Thornton MM, Vaughan AJ, Ashworth SW, Heaton MJ, English N, Torres MP, Andersen JL. The Integration of Proteome-Wide PTM Data with Protein Structural and Sequence Features Identifies Phosphorylations that Mediate 14-3-3 Interactions. J Mol Biol 2023; 435:167890. [PMID: 36402225 PMCID: PMC10099770 DOI: 10.1016/j.jmb.2022.167890] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
Abstract
14-3-3s are abundant proteins that regulate essentially all aspects of cell biology, including cell cycle, motility, metabolism, and cell death. 14-3-3s work by docking to phosphorylated Ser/Thr residues on a large network of client proteins and modulating client protein function in a variety of ways. In recent years, aided by improvements in proteomics, the discovery of 14-3-3 client proteins has far outpaced our ability to understand the biological impact of individual 14-3-3 interactions. The rate-limiting step in this process is often the identification of the individual phospho-serines/threonines that mediate 14-3-3 binding, which are difficult to distinguish from other phospho-sites by sequence alone. Furthermore, trial-and-error molecular approaches to identify these phosphorylations are costly and can take months or years to identify even a single 14-3-3 docking site phosphorylation. To help overcome this challenge, we used machine learning to analyze predictive features of 14-3-3 binding sites. We found that accounting for intrinsic protein disorder and the unbiased mass spectrometry identification rate of a given phosphorylation significantly improves the identification of 14-3-3 docking site phosphorylations across the proteome. We incorporated these features, coupled with consensus sequence prediction, into a publicly available web app, called "14-3-3 site-finder". We demonstrate the strength of this approach through its ability to identify 14-3-3 binding sites that do not conform to the loose consensus sequence of 14-3-3 docking phosphorylations, which we validate with 14-3-3 client proteins, including TNK1, CHEK1, MAPK7, and others. In addition, by using this approach, we identify a phosphorylation on A-kinase anchor protein-13 (AKAP13) at Ser2467 that dominantly controls its interaction with 14-3-3.
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Affiliation(s)
- C M Egbert
- Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - L R Warr
- Department of Statistics, Brigham Young University, Provo, UT, USA
| | - K L Pennington
- Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Department of Biological and Environmental Sciences, Longwood University, Farmville, VA, USA
| | - M M Thornton
- Department of Computer Science, Brigham Young University, Provo, UT, USA
| | - A J Vaughan
- Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - S W Ashworth
- Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - M J Heaton
- Department of Statistics, Brigham Young University, Provo, UT, USA
| | - N English
- Quantitative Bioscience Program, Georgia Institute of Technology, Atlanta, GA, USA
| | - M P Torres
- Quantitative Bioscience Program, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - J L Andersen
- Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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35
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Suhda S, Yamamoto Y, Wisesa S, Sada R, Sakisaka T. The 14-3-3γ isoform binds to and regulates the localization of endoplasmic reticulum (ER) membrane protein TMCC3 for the reticular network of the ER. J Biol Chem 2022; 299:102813. [PMID: 36549645 PMCID: PMC9860497 DOI: 10.1016/j.jbc.2022.102813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
The reticular network of the endoplasmic reticulum (ER) is formed by connecting ER tubules through three-way junctions and undergoes constant remodeling through formation and loss of the three-way junctions. Transmembrane and coiled-coil domain family 3 (TMCC3), an ER membrane protein localizing at three-way junctions, has been shown to positively regulate formation of the reticular ER network. However, elements that negatively regulate TMCC3 localization have not been characterized. In this study, we report that 14-3-3γ, a phospho-serine/phospho-threonine-binding protein involved in various signal transduction pathways, is a negative regulator of TMCC3. We demonstrate that overexpression of 14-3-3γ reduced localization of TMCC3 to three-way junctions and decreased the number of three-way junctions. TMCC3 bound to 14-3-3γ through the N terminus and had deduced 14-3-3 binding motifs. Additionally, we determined that a TMCC3 mutant substituting alanine for serine to be phosphorylated in the binding motif reduced binding to 14-3-3γ. The TMCC3 mutant was more prone than wildtype TMCC3 to localize at three-way junctions in the cells overexpressing 14-3-3γ. Furthermore, the TMCC3 mutant rescued the ER sheet expansion caused by TMCC3 knockdown less than wild-type TMCC3. Taken together, these results indicate that 14-3-3γ binding negatively regulates localization of TMCC3 to the three-way junctions for the proper reticular ER network, implying that the negative regulation of TMCC3 by 14-3-3γ would underlie remodeling of the reticular network of the ER.
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Affiliation(s)
- Saihas Suhda
- Division of Membrane Dynamics, Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Japan
| | - Yasunori Yamamoto
- Division of Membrane Dynamics, Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Japan
| | - Sindhu Wisesa
- Division of Membrane Dynamics, Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Japan
| | - Risa Sada
- Division of Membrane Dynamics, Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Japan
| | - Toshiaki Sakisaka
- Division of Membrane Dynamics, Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Japan.
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36
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Moen JM, Mohler K, Rogulina S, Shi X, Shen H, Rinehart J. Enhanced access to the human phosphoproteome with genetically encoded phosphothreonine. Nat Commun 2022; 13:7226. [PMID: 36433969 PMCID: PMC9700786 DOI: 10.1038/s41467-022-34980-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 11/15/2022] [Indexed: 11/27/2022] Open
Abstract
Protein phosphorylation is a ubiquitous post-translational modification used to regulate cellular processes and proteome architecture by modulating protein-protein interactions. The identification of phosphorylation events through proteomic surveillance has dramatically outpaced our capacity for functional assignment using traditional strategies, which often require knowledge of the upstream kinase a priori. The development of phospho-amino-acid-specific orthogonal translation systems, evolutionarily divergent aminoacyl-tRNA synthetase and tRNA pairs that enable co-translational insertion of a phospho-amino acids, has rapidly improved our ability to assess the physiological function of phosphorylation by providing kinase-independent methods of phosphoprotein production. Despite this utility, broad deployment has been hindered by technical limitations and an inability to reconstruct complex phopho-regulatory networks. Here, we address these challenges by optimizing genetically encoded phosphothreonine translation to characterize phospho-dependent kinase activation mechanisms and, subsequently, develop a multi-level protein interaction platform to directly assess the overlap of kinase and phospho-binding protein substrate networks with phosphosite-level resolution.
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Affiliation(s)
- Jack M. Moen
- grid.47100.320000000419368710Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520 USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, New Haven, CT 06516 USA
| | - Kyle Mohler
- grid.47100.320000000419368710Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520 USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, New Haven, CT 06516 USA
| | - Svetlana Rogulina
- grid.47100.320000000419368710Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520 USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, New Haven, CT 06516 USA
| | - Xiaojian Shi
- grid.47100.320000000419368710Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520 USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, New Haven, CT 06516 USA ,grid.47100.320000000419368710Wu Tsai Institute, Yale University, New Haven, CT 06520 USA
| | - Hongying Shen
- grid.47100.320000000419368710Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520 USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, New Haven, CT 06516 USA ,grid.47100.320000000419368710Wu Tsai Institute, Yale University, New Haven, CT 06520 USA
| | - Jesse Rinehart
- grid.47100.320000000419368710Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520 USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, New Haven, CT 06516 USA
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Thurairajah B, Hudson AJ, Doveston RG. Contemporary biophysical approaches for studying 14-3-3 protein-protein interactions. Front Mol Biosci 2022; 9:1043673. [PMID: 36425654 PMCID: PMC9679655 DOI: 10.3389/fmolb.2022.1043673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/24/2022] [Indexed: 06/28/2024] Open
Abstract
14-3-3 proteins are a family of regulatory hubs that function through a vast network of protein-protein interactions. Their dysfunction or dysregulation is implicated in a wide range of diseases, and thus they are attractive drug targets, especially for molecular glues that promote protein-protein interactions for therapeutic intervention. However, an incomplete understanding of the molecular mechanisms that underpin 14-3-3 function hampers progress in drug design and development. Biophysical methodologies are an essential element of the 14-3-3 analytical toolbox, but in many cases have not been fully exploited. Here, we present a contemporary review of the predominant biophysical techniques used to study 14-3-3 protein-protein interactions, with a focus on examples that address key questions and challenges in the 14-3-3 field.
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Affiliation(s)
| | | | - Richard G. Doveston
- Leicester Institute for Structural and Chemical Biology and School of Chemistry, University of Leicester, Leicester, United Kingdom
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38
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Structure-activity-relationship study of semi-synthetically modified fusicoccins on their stabilization effect for 14-3-3-phospholigand interactions. Bioorg Med Chem 2022; 73:117020. [DOI: 10.1016/j.bmc.2022.117020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022]
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High-Resolution Crystal Structure of Muscle Phosphoglycerate Mutase Provides Insight into Its Nuclear Import and Role. Int J Mol Sci 2022; 23:ijms232113198. [DOI: 10.3390/ijms232113198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Phosphoglycerate mutase (PGAM) is a glycolytic enzyme converting 3-phosphoglycerate to 2-phosphoglycerate, which in mammalian cells is expressed in two isoforms: brain (PGAM1) and muscle (PGAM2). Recently, it was shown that besides its enzymatic function, PGAM2 can be imported to the cell nucleus where it co-localizes with the nucleoli. It was suggested that it functions there to stabilize the nucleolar structure, maintain mRNA expression, and assist in the assembly of new pre-ribosomal subunits. However, the precise mechanism by which the protein translocates to the nucleus is unknown. In this study, we present the first crystal structure of PGAM2, identify the residues involved in the nuclear localization of the protein and propose that PGAM contains a “quaternary nuclear localization sequence (NLS)”, i.e., one that consists of residues from different protein chains. Additionally, we identify potential interaction partners for PGAM2 in the nucleoli and demonstrate that 14-3-3ζ/δ is indeed an interaction partner of PGAM2 in the nucleus. We also present evidence that the insulin/IGF1–PI3K–Akt–mTOR signaling pathway is responsible for the nuclear localization of PGAM2.
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Obsilova V, Obsil T. Structural insights into the functional roles of 14-3-3 proteins. Front Mol Biosci 2022; 9:1016071. [PMID: 36188227 PMCID: PMC9523730 DOI: 10.3389/fmolb.2022.1016071] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Signal transduction cascades efficiently transmit chemical and/or physical signals from the extracellular environment to intracellular compartments, thereby eliciting an appropriate cellular response. Most often, these signaling processes are mediated by specific protein-protein interactions involving hundreds of different receptors, enzymes, transcription factors, and signaling, adaptor and scaffolding proteins. Among them, 14-3-3 proteins are a family of highly conserved scaffolding molecules expressed in all eukaryotes, where they modulate the function of other proteins, primarily in a phosphorylation-dependent manner. Through these binding interactions, 14-3-3 proteins participate in key cellular processes, such as cell-cycle control, apoptosis, signal transduction, energy metabolism, and protein trafficking. To date, several hundreds of 14-3-3 binding partners have been identified, including protein kinases, phosphatases, receptors and transcription factors, which have been implicated in the onset of various diseases. As such, 14-3-3 proteins are promising targets for pharmaceutical interventions. However, despite intensive research into their protein-protein interactions, our understanding of the molecular mechanisms whereby 14-3-3 proteins regulate the functions of their binding partners remains insufficient. This review article provides an overview of the current state of the art of the molecular mechanisms whereby 14-3-3 proteins regulate their binding partners, focusing on recent structural studies of 14-3-3 protein complexes.
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Affiliation(s)
- Veronika Obsilova
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Structural Biology of Signaling Proteins, Division BIOCEV, Vestec, Czechia
- *Correspondence: Veronika Obsilova, ; Tomas Obsil,
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czechia
- *Correspondence: Veronika Obsilova, ; Tomas Obsil,
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41
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Angelotti T. Exploring the eukaryotic Yip and REEP/Yop superfamily of membrane-shaping adapter proteins (MSAPs): A cacophony or harmony of structure and function? Front Mol Biosci 2022; 9:912848. [PMID: 36060263 PMCID: PMC9437294 DOI: 10.3389/fmolb.2022.912848] [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: 04/04/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Polytopic cargo proteins are synthesized and exported along the secretory pathway from the endoplasmic reticulum (ER), through the Golgi apparatus, with eventual insertion into the plasma membrane (PM). While searching for proteins that could enhance cell surface expression of olfactory receptors, a new family of proteins termed “receptor expression-enhancing proteins” or REEPs were identified. These membrane-shaping hairpin proteins serve as adapters, interacting with intracellular transport machinery, to regulate cargo protein trafficking. However, REEPs belong to a larger family of proteins, the Yip (Ypt-interacting protein) family, conserved in yeast and higher eukaryotes. To date, eighteen mammalian Yip family members, divided into four subfamilies (Yipf, REEP, Yif, and PRAF), have been identified. Yeast research has revealed many intriguing aspects of yeast Yip function, functions that have not completely been explored with mammalian Yip family members. This review and analysis will clarify the different Yip family nomenclature that have encumbered prior comparisons between yeast, plants, and eukaryotic family members, to provide a more complete understanding of their interacting proteins, membrane topology, organelle localization, and role as regulators of cargo trafficking and localization. In addition, the biological role of membrane shaping and sensing hairpin and amphipathic helical domains of various Yip proteins and their potential cellular functions will be described. Lastly, this review will discuss the concept of Yip proteins as members of a larger superfamily of membrane-shaping adapter proteins (MSAPs), proteins that both shape membranes via membrane-sensing and hairpin insertion, and well as act as adapters for protein-protein interactions. MSAPs are defined by their localization to specific membranes, ability to alter membrane structure, interactions with other proteins via specific domains, and specific interactions/effects on cargo proteins.
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42
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Dwyer ME, Hangarter RP. Light-induced displacement of PLASTID MOVEMENT IMPAIRED1 precedes light-dependent chloroplast movements. PLANT PHYSIOLOGY 2022; 189:1866-1880. [PMID: 35477788 PMCID: PMC9237684 DOI: 10.1093/plphys/kiac193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Light-dependent chloroplast movements are an actin-dependent cellular response to changes in the light environment that help plants maximize photosynthetic potential and reduce photodamage. Over a dozen proteins are known to be required for normal chloroplast movements, but the molecular mechanisms regulating the transformation of light perception into chloroplast motility are not fully understood. Here, we show that in Arabidopsis (Arabidopsis thaliana) the actin-bundling plasma membrane-associated proteins THRUMIN1, PLASTID MOVEMENT IMPAIRED1 (PMI1), and KINESIN-LIKE PROTEIN FOR ACTIN-BASED CHLOROPLAST MOVEMENT1 (KAC1) interact through the 14-3-3 proteins KAPPA and OMEGA. We also show that the interaction of PMI1 with 14-3-3 KAPPA and OMEGA is regulated by blue light activation of the Phototropin2 photoreceptor. Live-cell confocal microscopy revealed light-induced dynamic changes in the cellular localizations of PMI1 and KAC1. In particular, PMI1 was relocated away from irradiated areas of the plasma membrane in less than a minute after blue light exposure, consistent with PMI1 playing a critical role in initiating light-dependent chloroplast movements. We present a modified conceptual model for high light-dependent chloroplast movements in which PMI1 acts as the mobile signal that initiates a coordinated sequence of changes in protein-protein and protein-plasma membrane interactions that initiate the chloroplast movement response and determine where in the cell chloroplasts are able to anchor to the plasma membrane.
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Affiliation(s)
- Matthew E Dwyer
- Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA
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43
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Soini L, Leysen S, Davis J, Ottmann C. Molecular glues to stabilise protein-protein interactions. Curr Opin Chem Biol 2022; 69:102169. [PMID: 35749929 DOI: 10.1016/j.cbpa.2022.102169] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/21/2022] [Accepted: 05/11/2022] [Indexed: 11/27/2022]
Abstract
Targeting protein-protein interactions (PPIs) has become a common approach to tackle various diseases whose pathobiology is driven by their mis-regulation in important signalling pathways. Modulating PPIs has tremendous untapped therapeutic potential and different approaches can be used to modulate PPIs. Initially, therapeutic effects were mostly sought by inhibiting PPIs. However, by gaining insight in the mode of action of certain therapeutic compounds, it became clear that stabilising (i.e. enhancing) PPIs can also be useful. The latter strategy is recently gaining a lot of attention, as stabilising physiologic, or even inducing novel interactions of a target protein with E3 ubiquitin ligases forms the basis of the targeted protein degradation (TPD) approach. An emerging additional example for drug discovery based on PPI stabilisation are the 14-3-3 proteins, a family of regulatory proteins, which engages in many protein-protein interactions, some of which might become therapeutical targets.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands; Department of Structural Biology and Biophysics, UCB Biopharma UK, Slough, UK
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Biopharma UK, Slough, UK
| | - Jeremy Davis
- Department of Chemistry, UCB Biopharma UK, Slough, UK.
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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44
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Lankford C, Houtman J, Baker SA. Identification of HCN1 as a 14-3-3 client. PLoS One 2022; 17:e0268335. [PMID: 35679272 PMCID: PMC9182292 DOI: 10.1371/journal.pone.0268335] [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: 10/10/2021] [Accepted: 04/28/2022] [Indexed: 11/19/2022] Open
Abstract
Hyperpolarization activated cyclic nucleotide-gated channel 1 (HCN1) is expressed throughout the nervous system and is critical for regulating neuronal excitability, with mutations being associated with multiple forms of epilepsy. Adaptive modulation of HCN1 has been observed, as has pathogenic dysregulation. While the mechanisms underlying this modulation remain incompletely understood, regulation of HCN1 has been shown to include phosphorylation. A candidate phosphorylation-dependent regulator of HCN1 channels is 14-3-3. We used bioinformatics to identify three potential 14-3-3 binding sites in HCN1. We confirmed that 14-3-3 could pull down HCN1 from multiple tissue sources and used HEK293 cells to detail the interaction. Two sites in the intrinsically disordered C-terminus of HCN1 were necessary and sufficient for a phosphorylation-dependent interaction with 14-3-3. The same region of HCN1 containing the 14-3-3 binding peptides is required for phosphorylation-independent protein degradation. We propose a model in which phosphorylation of mouse S810 and S867 (human S789 and S846) recruits 14-3-3 to inhibit a yet unidentified factor signaling for protein degradation, thus increasing the half-life of HCN1.
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Affiliation(s)
- Colten Lankford
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Jon Houtman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, United States of America
| | - Sheila A. Baker
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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45
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Repton C, Cullen CF, Costa MFA, Spanos C, Rappsilber J, Ohkura H. The phospho-docking protein 14-3-3 regulates microtubule-associated proteins in oocytes including the chromosomal passenger Borealin. PLoS Genet 2022; 18:e1009995. [PMID: 35666772 PMCID: PMC9203013 DOI: 10.1371/journal.pgen.1009995] [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: 12/15/2021] [Revised: 06/16/2022] [Accepted: 04/27/2022] [Indexed: 11/18/2022] Open
Abstract
Global regulation of spindle-associated proteins is crucial in oocytes due to the absence of centrosomes and their very large cytoplasmic volume, but little is known about how this is achieved beyond involvement of the Ran-importin pathway. We previously uncovered a novel regulatory mechanism in Drosophila oocytes, in which the phospho-docking protein 14-3-3 suppresses microtubule binding of Kinesin-14/Ncd away from chromosomes. Here we report systematic identification of microtubule-associated proteins regulated by 14-3-3 from Drosophila oocytes. Proteins from ovary extract were co-sedimented with microtubules in the presence or absence of a 14-3-3 inhibitor. Through quantitative mass-spectrometry, we identified proteins or complexes whose ability to bind microtubules is suppressed by 14-3-3, including the chromosomal passenger complex (CPC), the centralspindlin complex and Kinesin-14/Ncd. We showed that 14-3-3 binds to the disordered region of Borealin, and this binding is regulated differentially by two phosphorylations on Borealin. Mutations at these two phospho-sites compromised normal Borealin localisation and centromere bi-orientation in oocytes, showing that phospho-regulation of 14-3-3 binding is important for Borealin localisation and function.
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Affiliation(s)
- Charlotte Repton
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - C. Fiona Cullen
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Mariana F. A. Costa
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Christos Spanos
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Hiroyuki Ohkura
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
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Sluchanko NN. Recent advances in structural studies of 14-3-3 protein complexes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:289-324. [PMID: 35534110 DOI: 10.1016/bs.apcsb.2021.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Being phosphopeptide-binding hubs, 14-3-3 proteins coordinate multiple cellular processes in eukaryotes, including the regulation of apoptosis, cell cycle, ion channels trafficking, transcription, signal transduction, and hormone biosynthesis. Forming constitutive α-helical dimers, 14-3-3 proteins predominantly recognize specifically phosphorylated Ser/Thr sites within their partners; this generally stabilizes phosphotarget conformation and affects its activity, intracellular distribution, dephosphorylation, degradation and interactions with other proteins. Not surprisingly, 14-3-3 complexes are involved in the development of a range of diseases and are considered promising drug targets. The wide interactome of 14-3-3 proteins encompasses hundreds of different phosphoproteins, for many of which the interaction is well-documented in vitro and in vivo but lack the structural data that would help better understand underlying regulatory mechanisms and develop new drugs. Despite obtaining structural information on 14-3-3 complexes is still lagging behind the research of 14-3-3 interactions on a proteome-wide scale, recent works provided some advances, including methodological improvements and accumulation of new interesting structural data, that are discussed in this review.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russian Federation.
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47
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Navarrete M, Zhou Y. The 14-3-3 Protein Family and Schizophrenia. Front Mol Neurosci 2022; 15:857495. [PMID: 35359567 PMCID: PMC8964262 DOI: 10.3389/fnmol.2022.857495] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
Schizophrenia is a debilitating mental disorder that affects approximately 1% of the world population, yet the disorder is not very well understood. The genetics of schizophrenia is very heterogenous, making it hard to pinpoint specific alterations that may cause the disorder. However, there is growing evidence from human studies suggesting a link between alterations in the 14-3-3 family and schizophrenia. The 14-3-3 proteins are abundantly expressed in the brain and are involved in many important cellular processes. Knockout of 14-3-3 proteins in mice has been shown to cause molecular, structural, and behavioral alterations associated with schizophrenia. Thus, 14-3-3 animal models allow for further exploration of the relationship between 14-3-3 and schizophrenia as well as the study of schizophrenia pathology. This review considers evidence from both human and animal model studies that implicate the 14-3-3 family in schizophrenia. In addition, possible mechanisms by which alterations in 14-3-3 proteins may contribute to schizophrenia-like phenotypes such as dopaminergic, glutamatergic, and cytoskeletal dysregulations are discussed.
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Affiliation(s)
| | - Yi Zhou
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, United States
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48
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Kouchi Z, Kojima M. Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis. Sci Rep 2022; 12:4325. [PMID: 35279680 PMCID: PMC8918327 DOI: 10.1038/s41598-022-08147-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 03/02/2022] [Indexed: 11/21/2022] Open
Abstract
Recent investigations of neurological developmental disorders have revealed the Rho-family modulators such as Syde and its interactors as the candidate genes. Although the mammalian Syde proteins are reported to possess GTPase-accelerating activity for RhoA-family proteins, diverse species-specific substrate selectivities and binding partners have been described, presumably based on their evolutionary variance in the molecular organization. A comprehensive in silico analysis of Syde family proteins was performed to elucidate their molecular functions and neurodevelopmental networks. Predicted structural modeling of the RhoGAP domain may account for the molecular constraints to substrate specificity among Rho-family proteins. Deducing conserved binding motifs can extend the Syde interaction network and highlight diverse but Syde isoform-specific signaling pathways in neuronal homeostasis, differentiation, and synaptic plasticity from novel aspects of post-translational modification and proteolysis.
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49
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Fragment-based exploration of the 14-3-3/Amot-p130 interface. Curr Res Struct Biol 2022; 4:21-28. [PMID: 35036934 PMCID: PMC8743172 DOI: 10.1016/j.crstbi.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 02/06/2023] Open
Abstract
The modulation of protein-protein interactions (PPIs) has developed into a well-established field of drug discovery. Despite the advances achieved in the field, many PPIs are still deemed as ‘undruggable’ targets and the design of PPIs stabilizers remains a significant challenge. The application of fragment-based methods for the identification of drug leads and to evaluate the ‘tractability’ of the desired protein target has seen a remarkable development in recent years. In this study, we explore the molecular characteristics of the 14-3-3/Amot-p130 PPI and the conceptual possibility of targeting this interface using X-ray crystallography fragment-based screening. We report the first structural elucidation of the 14-3-3 binding motif of Amot-p130 and the characterization of the binding mode and affinities involved. We made use of fragments to probe the ‘ligandability’ of the 14-3-3/Amot-p130 composite binding pocket. Here we disclose initial hits with promising stabilizing activity and an early-stage selectivity toward the Amot-p130 motifs over other representatives 14-3-3 partners. Our findings highlight the potential of using fragments to characterize and explore proteins' surfaces and might provide a starting point toward the development of small molecules capable of acting as molecular glues. Phosphorylation of Ser 175 mediates binding of Amot-p130 to 14-3-3. The crystal structure of the 14-3-3σΔC/Amot-p130 peptide complex describes the interface. A fragment-based exploration of the interface assesses ‘ligandability’. Fragments binding at the 14-3-3/Amot-p130 interface display an initial stabilizing activity.
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Key Words
- 14-3-3 /protein-protein interactions stabilizers
- AIP4, Atrophin-1 interacting protein 4
- Amot, Angiomotin
- Amot-p130
- AmotL1/2, Angiomotin-like 1/2
- FBDD, Fragment-based drug discovery
- FP, Fluorescence polarization
- Fragment-based drug discovery
- Lats 1/2, Large tumor suppressor 1/2
- Ligandability
- MST, Microscale thermophoresis
- PPI, Protein-protein interaction
- PTMs, post-translational modifications
- X-ray crystallography
- YAP1, Yes-associated protein 1
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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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