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Sun X, Zhou D, Sun Y, Zhao Y, Deng Y, Pang X, Liu Q, Zhou Z. Oxidative stress reprograms the transcriptional coactivator Yki to suppress cell proliferation. Cell Rep 2024; 43:114584. [PMID: 39106181 DOI: 10.1016/j.celrep.2024.114584] [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: 12/12/2023] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 08/09/2024] Open
Abstract
The transcriptional coactivator Yorkie (Yki) regulates organ size by promoting cell proliferation. It is unclear how cells control Yki activity when exposed to harmful stimuli such as oxidative stress. In this study, we show that oxidative stress inhibits the binding of Yki to Scalloped (Sd) but promotes the interaction of Yki with another transcription factor, forkhead box O (Foxo), ultimately leading to a halt in cell proliferation. Mechanistically, Foxo normally exhibits a low binding affinity for Yki, allowing Yki to form a complex with Sd and activate proliferative genes. Under oxidative stress, Usp7 deubiquitinates Foxo to promote its interaction with Yki, thereby activating the expression of proliferation suppressors. Finally, we show that Yki is essential for Drosophila survival under oxidative stress. In summary, these findings suggest that oxidative stress reprograms Yki from a proliferation-promoting factor to a proliferation suppressor, forming a self-protective mechanism.
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Affiliation(s)
- Xiaohan Sun
- Key Laboratory of Biodiversity Conservation and Bioresource Utilization of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, China
| | - Dafa Zhou
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Yuanfei Sun
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Yunhe Zhao
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Yanran Deng
- Key Laboratory of Biodiversity Conservation and Bioresource Utilization of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Xiaolin Pang
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Qingxin Liu
- College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Zizhang Zhou
- Key Laboratory of Biodiversity Conservation and Bioresource Utilization of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.
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2
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Wu X, Hu Z, Zhang Y, Li M, Liao N, Dong J, Wang B, Wu J, Wu X, Wang Y, Wang J, Lu Z, Yang Y, Sun Y, Dong W, Zhang M, Li G. Differential selection of yield and quality traits has shaped genomic signatures of cowpea domestication and improvement. Nat Genet 2024; 56:992-1005. [PMID: 38649710 DOI: 10.1038/s41588-024-01722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
Cowpeas (tropical legumes) are important in ensuring food and nutritional security in developing countries, especially in sub-Saharan Africa. Herein, we report two high-quality genome assemblies of grain and vegetable cowpeas and we re-sequenced 344 accessions to characterize the genomic variations landscape. We identified 39 loci for ten important agronomic traits and more than 541 potential loci that underwent selection during cowpea domestication and improvement. In particular, the synchronous selections of the pod-shattering loci and their neighboring stress-relevant loci probably led to the enhancement of pod-shattering resistance and the compromise of stress resistance during the domestication from grain to vegetable cowpeas. Moreover, differential selections on multiple loci associated with pod length, grain number per pod, seed weight, pod and seed soluble sugars, and seed crude proteins shaped the yield and quality diversity in cowpeas. Our findings provide genomic insights into cowpea domestication and improvement footprints, enabling further genome-informed cultivar improvement of cowpeas.
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Affiliation(s)
- Xinyi Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Zhongyuan Hu
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Yan Zhang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Mao Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Nanqiao Liao
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Junyang Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Baogen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Xiaohua Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Ying Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Jian Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Zhongfu Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Yi Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Yuyan Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Wenqi Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Mingfang Zhang
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China.
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, P. R. China.
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou, P. R. China.
| | - Guojing Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.
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3
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Sciandra F, Desiderio C, Vincenzoni F, Viscuso S, Bozzi M, Hübner W, Jimenez-Gutierrez GE, Cisneros B, Brancaccio A. Analysis of the GFP-labelled β-dystroglycan interactome in HEK-293 transfected cells reveals novel intracellular networks. Biochem Biophys Res Commun 2024; 703:149656. [PMID: 38364681 DOI: 10.1016/j.bbrc.2024.149656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024]
Abstract
Dystroglycan (DG) is a cell adhesion complex that is widely expressed in tissues. It is composed by two subunits, α-DG, a highly glycosylated protein that interacts with several extracellular matrix proteins, and transmembrane β-DG whose, cytodomain binds to the actin cytoskeleton. Glycosylation of α-DG is crucial for functioning as a receptor for its multiple extracellular binding partners. Perturbation of α-DG glycosylation is the central event in the pathogenesis of severe pathologies such as muscular dystrophy and cancer. β-DG acts as a scaffold for several cytoskeletal and nuclear proteins and very little is known about the fine regulation of some of these intracellular interactions and how they are perturbed in diseases. To start filling this gap by identifying uncharacterized intracellular networks preferentially associated with β-DG, HEK-293 cells were transiently transfected with a plasmid carrying the β-DG subunit with GFP fused at its C-terminus. With this strategy, we aimed at forcing β-DG to occupy multiple intracellular locations instead of sitting tightly at its canonical plasma membrane milieu, where it is commonly found in association with α-DG. Immunoprecipitation by anti-GFP antibodies followed by shotgun proteomic analysis led to the identification of an interactome formed by 313 exclusive protein matches for β-DG binding. A series of already known β-DG interactors have been found, including ezrin and emerin, whilst significant new matches, which include potential novel β-DG interactors and their related networks, were identified in diverse subcellular compartments, such as cytoskeleton, endoplasmic reticulum/Golgi, mitochondria, nuclear membrane and the nucleus itself. Of particular interest amongst the novel identified matches, Lamina-Associated Polypeptide-1B (LAP1B), an inner nuclear membrane protein, whose mutations are known to cause nuclear envelopathies characterized by muscular dystrophy, was found to interact with β-DG in HEK-293 cells. This evidence was confirmed by immunoprecipitation, Western blotting and immunofluorescence experiments. We also found by immunofluorescence experiments that LAP1B looses its nuclear envelope localization in C2C12 DG-knock-out cells, suggesting that LAP1B requires β-DG for a proper nuclear localization. These results expand the role of β-DG as a nuclear scaffolding protein and provide novel evidence of a possible link between dystroglycanopathies and nuclear envelopathies displaying with muscular dystrophy.
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Affiliation(s)
- Francesca Sciandra
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR), Largo F. Vito, 00168, Roma, Italy
| | - Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR), Largo F. Vito, 00168, Roma, Italy
| | - Federica Vincenzoni
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie, Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Roma, Italy; Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Simona Viscuso
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie, Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Roma, Italy
| | - Manuela Bozzi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR), Largo F. Vito, 00168, Roma, Italy; Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie, Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Roma, Italy
| | - Wolfgang Hübner
- Biomolecular Photonics, University of Bielefeld, 33615, Bielefeld, Germany
| | | | - Bulmaro Cisneros
- Departamento de Genética y Biología Molecular, CINVESTAV Zacatenco IPN, Ciudad de México, 07360, Mexico
| | - Andrea Brancaccio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR), Largo F. Vito, 00168, Roma, Italy; School of Biochemistry, University of Bristol, BS8 1TD, UK.
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4
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Pham TL, Thomas F. Design of Functional Globular β-Sheet Miniproteins. Chembiochem 2024; 25:e202300745. [PMID: 38275210 DOI: 10.1002/cbic.202300745] [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: 10/31/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/27/2024]
Abstract
The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.
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Affiliation(s)
- Truc Lam Pham
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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5
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Lu J, Rahman MI, Kazan IC, Halloran NR, Bobkov AA, Ozkan SB, Ghirlanda G. Engineering gain-of-function mutants of a WW domain by dynamics and structural analysis. Protein Sci 2023; 32:e4759. [PMID: 37574787 PMCID: PMC10464296 DOI: 10.1002/pro.4759] [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: 03/22/2023] [Revised: 07/17/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Proteins gain optimal fitness such as foldability and function through evolutionary selection. However, classical studies have found that evolutionarily designed protein sequences alone cannot guarantee foldability, or at least not without considering local contacts associated with the initial folding steps. We previously showed that foldability and function can be restored by removing frustration in the folding energy landscape of a model WW domain protein, CC16, which was designed based on Statistical Coupling Analysis (SCA). Substitutions ensuring the formation of five local contacts identified as "on-path" were selected using the closest homolog native folded sequence, N21. Surprisingly, the resulting sequence, CC16-N21, bound to Group I peptides, while N21 did not. Here, we identified single-point mutations that enable N21 to bind a Group I peptide ligand through structure and dynamic-based computational design. Comparison of the docked position of the CC16-N21/ligand complex with the N21 structure showed that residues at positions 9 and 19 are important for peptide binding, whereas the dynamic profiles identified position 10 as allosterically coupled to the binding site and exhibiting different dynamics between N21 and CC16-N21. We found that swapping these positions in N21 with matched residues from CC16-N21 recovers nature-like binding affinity to N21. This study validates the use of dynamic profiles as guiding principles for affecting the binding affinity of small proteins.
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Affiliation(s)
- Jin Lu
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | | | - I. Can Kazan
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | | | - Andrey A. Bobkov
- Conrad Prebys Center for Chemical GenomicsSanford Burnham Prebys Medical Discovery InstituteCaliforniaUSA
| | - S. Banu Ozkan
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
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6
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Wenz MT, Bertazzon M, Sticht J, Aleksić S, Gjorgjevikj D, Freund C, Keller BG. Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW. J Chem Inf Model 2022; 62:6586-6601. [PMID: 35347992 DOI: 10.1021/acs.jcim.1c01426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein-protein interactions often rely on specialized recognition domains, such as WW domains, which bind to specific proline-rich sequences. The specificity of these protein-protein interactions can be increased by tandem repeats, i.e., two WW domains connected by a linker. With a flexible linker, the WW domains can move freely with respect to each other. Additionally, the tandem WW domains can bind in two different orientations to their target sequences. This makes the elucidation of complex structures of tandem WW domains extremely challenging. Here, we identify and characterize two complex structures of the tandem WW domain of human formin-binding protein 21 and a peptide sequence from its natural binding partner, the core-splicing protein SmB/B'. The two structures differ in the ligand orientation and, consequently, also in the relative orientation of the two WW domains. We analyze and probe the interactions in the complexes by molecular simulations and NMR experiments. The workflow to identify the complex structures uses molecular simulations, density-based clustering, and peptide docking. It is designed to systematically generate possible complex structures for repeats of recognition domains. These structures will help us to understand the synergistic and multivalency effects that generate the astonishing versatility and specificity of protein-protein interactions.
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Affiliation(s)
- Marius T Wenz
- Institute for Chemistry and Biochemistry, Molecular Dynamics Group, Freie Universität Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Miriam Bertazzon
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Jana Sticht
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany.,Core Facility BioSupraMol, Freie Universität Berlin, Takustrasse 3, Berlin 14195, Germany
| | - Stevan Aleksić
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach, Germany
| | - Daniela Gjorgjevikj
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Christian Freund
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Bettina G Keller
- Institute for Chemistry and Biochemistry, Molecular Dynamics Group, Freie Universität Berlin, Arnimallee 22, Berlin 14195, Germany
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7
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Neitz H, Paul NB, Häge FR, Lindner C, Graebner R, Kovermann M, Thomas F. Identification of novel functional mini-receptors by combinatorial screening of split-WW domains. Chem Sci 2022; 13:9079-9090. [PMID: 36091217 PMCID: PMC9365081 DOI: 10.1039/d2sc01078j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
β-Sheet motifs such as the WW domain are increasingly being explored as building blocks for synthetic biological applications. Since the sequence-structure relationships of β-sheet motifs are generally complex compared to the well-studied α-helical coiled coil (CC), other approaches such as combinatorial screening should be included to vary the function of the peptide. In this study, we present a combinatorial approach to identify novel functional mini-proteins based on the WW-domain scaffold, which takes advantage of the successful reconstitution of the fragmented WW domain of hPin1 (hPin1WW) by CC association. Fragmentation of hPin1WW was performed in both loop 1 (CC-hPin1WW-L1) and loop 2 (CC-hPin1WW-L2), and the respective fragments were linked to the strands of an antiparallel heterodimeric CC. Structural analysis by CD and NMR spectroscopy revealed structural reconstitution of the WW-domain scaffold only in CC-hPin1WW-L1, but not in CC-hPin1WW-L2. Furthermore, by using 1H-15N HSQC NMR, fluorescence and CD spectroscopy, we demonstrated that binding properties of fragmented hPin1WW in CC-hPin1WW-L1 were fully restored by CC association. To demonstrate the power of this approach as a combinatorial screening platform, we synthesized a four-by-six library of N- and C-terminal hPin1WW-CC peptide fragments that was screened for a WW domain that preferentially binds to ATP over cAMP, phophocholine, or IP6. Using this screening platform, we identified one WW domain, which specifically binds ATP, and a phosphorylcholine-specific WW-based mini-receptor, both having binding dissociation constants in the lower micromolar range.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg Am Hubland Würzburg 97074 Germany
| | - Niels Benjamin Paul
- Institute of Organic and Biomolecular Chemistry, University of Göttingen Tammannstr. 2 Göttingen 37077 Germany
| | - Florian R Häge
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
| | - Christina Lindner
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
| | - Roman Graebner
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz Universitätsstraße 10 Konstanz 78457 Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
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8
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Musiała A, Donizy P, Augustyniak-Bartosik H, Jakuszko K, Banasik M, Kościelska-Kasprzak K, Krajewska M, Kamińska D. Biomarkers in Primary Focal Segmental Glomerulosclerosis in Optimal Diagnostic-Therapeutic Strategy. J Clin Med 2022; 11:jcm11123292. [PMID: 35743361 PMCID: PMC9225193 DOI: 10.3390/jcm11123292] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 02/01/2023] Open
Abstract
Focal segmental glomerulosclerosis (FSGS) involves podocyte injury. In patients with nephrotic syndrome, progression to end-stage renal disease often occurs over the course of 5 to 10 years. The diagnosis is based on a renal biopsy. It is presumed that primary FSGS is caused by an unknown plasma factor that might be responsible for the recurrence of FSGS after kidney transplantation. The nature of circulating permeability factors is not explained and particular biological molecules responsible for inducing FSGS are still unknown. Several substances have been proposed as potential circulating factors such as soluble urokinase-type plasminogen activator receptor (suPAR) and cardiolipin-like-cytokine 1 (CLC-1). Many studies have also attempted to establish which molecules are related to podocyte injury in the pathogenesis of FSGS such as plasminogen activator inhibitor type-1 (PAI-1), angiotensin II type 1 receptors (AT1R), dystroglycan(DG), microRNAs, metalloproteinases (MMPs), forkheadbox P3 (FOXP3), and poly-ADP-ribose polymerase-1 (PARP1). Some biomarkers have also been studied in the context of kidney tissue damage progression: transforming growth factor-beta (TGF-β), human neutrophil gelatinase-associated lipocalin (NGAL), malondialdehyde (MDA), and others. This paper describes molecules that could potentially be considered as circulating factors causing primary FSGS.
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Affiliation(s)
- Aleksandra Musiała
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, 50-556 Wroclaw, Poland; (H.A.-B.); (K.J.); (M.B.); (K.K.-K.); (M.K.); (D.K.)
- Correspondence: ; Tel.: +48-6-0172-8231
| | - Piotr Donizy
- Department of Clinical and Experimental Pathology, Division of Clinical Pathology, Wroclaw Medical University, 50-556 Wroclaw, Poland;
| | - Hanna Augustyniak-Bartosik
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, 50-556 Wroclaw, Poland; (H.A.-B.); (K.J.); (M.B.); (K.K.-K.); (M.K.); (D.K.)
| | - Katarzyna Jakuszko
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, 50-556 Wroclaw, Poland; (H.A.-B.); (K.J.); (M.B.); (K.K.-K.); (M.K.); (D.K.)
| | - Mirosław Banasik
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, 50-556 Wroclaw, Poland; (H.A.-B.); (K.J.); (M.B.); (K.K.-K.); (M.K.); (D.K.)
| | - Katarzyna Kościelska-Kasprzak
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, 50-556 Wroclaw, Poland; (H.A.-B.); (K.J.); (M.B.); (K.K.-K.); (M.K.); (D.K.)
| | - Magdalena Krajewska
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, 50-556 Wroclaw, Poland; (H.A.-B.); (K.J.); (M.B.); (K.K.-K.); (M.K.); (D.K.)
| | - Dorota Kamińska
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, 50-556 Wroclaw, Poland; (H.A.-B.); (K.J.); (M.B.); (K.K.-K.); (M.K.); (D.K.)
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9
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Viral Proteins with PxxP and PY Motifs May Play a Role in Multiple Sclerosis. Viruses 2022; 14:v14020281. [PMID: 35215874 PMCID: PMC8879583 DOI: 10.3390/v14020281] [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: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Multiple sclerosis (MS) is a debilitating disease that arises from immune system attacks to the protective myelin sheath that covers nerve fibers and ensures optimal communication between brain and body. Although the cause of MS is unknown, a number of factors, which include viruses, have been identified as increasing the risk of displaying MS symptoms. Specifically, the ubiquitous and highly prevalent Epstein–Barr virus, human herpesvirus 6, cytomegalovirus, varicella–zoster virus, and other viruses have been identified as potential triggering agents. In this review, we examine the specific role of proline-rich proteins encoded by these viruses and their potential role in MS at a molecular level.
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10
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Fujimoto T, Yaoi T, Tanaka H, Itoh K. Dystroglycan regulates proper expression, submembranous localization and subsequent phosphorylation of Dp71 through physical interaction. Hum Mol Genet 2021; 29:3312-3326. [PMID: 32996569 DOI: 10.1093/hmg/ddaa217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/28/2020] [Accepted: 09/25/2020] [Indexed: 11/12/2022] Open
Abstract
Dystrophin-dystroglycan complex (DGC) plays important roles for structural integrity and cell signaling, and its defects cause progressive muscular degeneration and intellectual disability. Dystrophin short product, Dp71, is abundantly expressed in multiple tissues other than muscle and is suspected of contributing to cognitive functions; however, its molecular characteristics and relation to dystroglycan (DG) remain unknown. Here, we report that DG physically interacts with Dp71 in cultured cells. Intriguingly, DG expression positively and DG knockdown negatively affected the steady-state expression, submembranous localization and subsequent phosphorylation of Dp71. Mechanistically, two EF-hand regions along with a ZZ motif of Dp71 mediate its association with the transmembrane proximal region, amino acid residues 788-806, of DG cytoplasmic domain. Most importantly, the pathogenic point mutations of Dp71, C272Y in the ZZ motif or L170del in the second EF-hand region, impaired its binding to DG, submembranous localization and phosphorylation of Dp71, indicating the relevance of DG-dependent Dp71 regulatory mechanism to pathophysiological conditions. Since Dp140, another dystrophin product, was also regulated by DG in the same manner as Dp71, our results uncovered a tight molecular relation between DG and dystrophin, which has broad implications for understanding the DGC-related cellular physiology and pathophysiology.
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Affiliation(s)
- Takahiro Fujimoto
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Takeshi Yaoi
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hidekazu Tanaka
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Kyoko Itoh
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
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11
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Rheinemann L, Thompson T, Mercenne G, Paine EL, Peterson FC, Volkman BF, Alam SL, Alian A, Sundquist WI. Interactions between AMOT PPxY motifs and NEDD4L WW domains function in HIV-1 release. J Biol Chem 2021; 297:100975. [PMID: 34284061 PMCID: PMC8368996 DOI: 10.1016/j.jbc.2021.100975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/23/2021] [Accepted: 07/15/2021] [Indexed: 12/03/2022] Open
Abstract
Like most enveloped viruses, HIV must acquire a lipid membrane as it assembles and buds through the plasma membrane of infected cells to spread infection. Several sets of host cell machinery facilitate this process, including proteins of the endosomal sorting complexes required for transport pathway, which mediates the membrane fission reaction required to complete viral budding, as well as angiomotin (AMOT) and NEDD4L, which bind one another and promote virion membrane envelopment. AMOT and NEDD4L interact through the four NEDD4L WW domains and three different AMOT Pro-Pro-x (any amino acid)-Tyr (PPxY) motifs, but these interactions are not yet well defined. Here, we report that individual AMOT PPxY and NEDD4L WW domains interact with the following general affinity hierarchies: AMOT PPxY1>PPxY2>PPxY3 and NEDD4L WW3>WW2>WW1∼WW4. The unusually high-affinity of the AMOT PPxY1–NEDD4L WW3 interaction accounts for most of the AMOT–NEDD4L binding and is critical for stimulating HIV-1 release. Comparative structural, binding, and virological analyses reveal that complementary ionic and hydrophobic contacts on both sides of the WW–PPxY core interaction account for the unusually high affinity of the AMOT PPxY1–NEDD4L WW3 interaction. Taken together, our studies reveal how the first AMOT PPxY1 motif binds the third NEDD4L WW domain to stimulate HIV-1 viral envelopment and promote infectivity.
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Affiliation(s)
- Lara Rheinemann
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Tuscan Thompson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Gaelle Mercenne
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Elliott L Paine
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Steven L Alam
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Akram Alian
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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12
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Kałuzińska Ż, Kołat D, Bednarek AK, Płuciennik E. PLEK2, RRM2, GCSH: A Novel WWOX-Dependent Biomarker Triad of Glioblastoma at the Crossroads of Cytoskeleton Reorganization and Metabolism Alterations. Cancers (Basel) 2021; 13:cancers13122955. [PMID: 34204789 PMCID: PMC8231639 DOI: 10.3390/cancers13122955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/30/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Glioblastoma is one of the deadliest human cancers. Its malignancy depends on cytoskeleton reorganization, which is related to, e.g., epithelial-to-mesenchymal transition and metastasis. The malignant phenotype of glioblastoma is also affected by the WWOX gene, which is lost in nearly a quarter of gliomas. Although the role of WWOX in the cytoskeleton rearrangement has been found in neural progenitor cells, its function as a modulator of cytoskeleton in gliomas was not investigated. Therefore, this study aimed to investigate the role of WWOX and its collaborators in cytoskeleton dynamics of glioblastoma. Methodology on RNA-seq data integrated the use of databases, bioinformatics tools, web-based platforms, and machine learning algorithm, and the obtained results were validated through microarray data. PLEK2, RRM2, and GCSH were the most relevant WWOX-dependent genes that could serve as novel biomarkers. Other genes important in the context of cytoskeleton (BMP4, CCL11, CUX2, DUSP7, FAM92B, GRIN2B, HOXA1, HOXA10, KIF20A, NF2, SPOCK1, TTR, UHRF1, and WT1), metabolism (MTHFD2), or correlation with WWOX (COL3A1, KIF20A, RNF141, and RXRG) were also discovered. For the first time, we propose that changes in WWOX expression dictate a myriad of alterations that affect both glioblastoma cytoskeleton and metabolism, rendering new therapeutic possibilities.
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13
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Zhang P, He W, Huang Y, Xiao K, Tang Y, Huang L, Huang X, Zhang J, Yang W, Liu R, Fu Q, Lu Y, Zhang M. Proteomic and phosphoproteomic profiles of Sertoli cells in buffalo. Theriogenology 2021; 170:1-14. [PMID: 33945957 DOI: 10.1016/j.theriogenology.2021.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/27/2021] [Accepted: 04/21/2021] [Indexed: 01/12/2023]
Abstract
Sertoli cells provide nutrients and support for germ cell differentiation and maintain a stable microenvironment for spermatogenesis. Comprehensive identification of Sertoli cellular proteins is important in understanding spermatogenesis. In this study, we performed an integrative analysis of the proteome and phosphoproteome to explore the role of Sertoli cells in spermatogenesis. A total of 2912 and 753 proteins were identified from the proteome and phosphoproteome in Sertoli cells, respectively; 438 proteins were common to the proteome and phosphoproteome. Data are available via ProteomeXchange with identifier PXD024984. In the proteome, ACTG1, ACTB, ACTA2, MYH9 were the most abundant proteins. Gene Ontology (GO) analysis indicated that most of the proteins were involved in the processes of localization, biosynthesis, gene expression, and transport. In addition, some of the proteins related to Sertoli cell functions were also enriched. In the phosphoproteome, most of the proteins were involved in gene expression and the RNA metabolic process; the pathways mainly involved the spliceosome, mitogen-activated protein kinase signaling pathway, focal adhesion, and tight junctions. The pleckstrin homology-like domain is the most highly enriched protein domain in phosphoproteins. Cyclin-dependent kinases and protein kinases C were found to be highly active kinases in the kinase-substrate network analysis. Ten proteins most closely related to network stability were found in the analysis of the network interactions of proteins identified jointly in the phosphoproteome and proteome. Through immunohistochemistry and immunofluorescence verification of vimentin, it was found that there were localization differences between phosphorylated and non-phosphorylated vimentin in testicular tissue. This study is the first in-depth proteomic and phosphoproteomic analysis of buffalo testicular Sertoli cells. The results provide insight into the role of Sertoli cells in spermatogenesis and provide clues for further study of male reproduction.
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Affiliation(s)
- Pengfei Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Wengtan He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Yulin Huang
- Department of Cell and Genetics, College of Basic Medicine, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Kai Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Yuyan Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Liangfeng Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Xingchen Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Junjun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Weihan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Runfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China
| | - Qiang Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China.
| | - Yangqing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China.
| | - Ming Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi, China.
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14
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The tumor suppressor role of salvador family WW domain-containing protein 1 (SAV1): one of the key pieces of the tumor puzzle. J Cancer Res Clin Oncol 2021; 147:1287-1297. [PMID: 33580421 DOI: 10.1007/s00432-021-03552-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/04/2021] [Indexed: 10/22/2022]
Abstract
PURPOSE In the complex tumor scenario, understanding the function of proteins with protumor or antitumor roles is essential to support advances in the cancer clinical area. Among them, the salvador family WW domain-containing protein 1 (SAV1) is highlighted. This protein plays a fundamental role in the tumor suppressor face of the Hippo pathway, which are responsible for controlling cell proliferation, organ size, development and tissue homeostasis. However, the functional dysregulation of this pathway may contribute to tumorigenesis and tumor progression. As SAV1 is a tumor suppressor scaffold protein, we explored the functions performed by SAV1 with its partners, the regulation of its expression, and its antitumor role in various types of cancer. METHODS We selected and analyzed 80 original articles and reviews from Pubmed that focuses on the study of SAV1 in cancer. RESULTS SAV1 interacts with several proteins, has different functions and acts as tumor suppressor by other mechanisms besides Hippo pathway. SAV1 expression regulation seems to occur by microRNAs and rarely by mutation or promoter methylation. It is downregulated in different types of cancer, which leads to cancer promotion and progression and is associated with poor prognosis. In vivo models have shown that the loss of SAV1 contributes to tumorigenesis. CONCLUSION SAV1 plays a relevant role as tumor suppressor in several types of cancer, highlighting SAV1 and the Hippo pathway's importance to cancer. Thus, encouraging further studies to include the SAV1 as a molecular key piece in cancer biology and in clinical approaches to cancer.
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15
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Massoud TF, Paulmurugan R. Molecular Imaging of Protein–Protein Interactions and Protein Folding. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00071-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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Zhang J, Liu S, Li H, Tian X, Li X. Tryptophan-Based Self-Assembling Peptides with Bacterial Flocculation and Antimicrobial Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11316-11323. [PMID: 32907333 DOI: 10.1021/acs.langmuir.0c01957] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tryptophan as an aromatic amino acid with a hydrophobic indole group plays important roles in stabilizing protein structures and enhancing molecular bindings in nature, but was rarely used in the molecular design of self-assembling peptides or gelators. Therefore, we prepared a series of short peptides from Trp amino acids and examined the potential roles of Trp residues for regulating peptide self-assembly and gelation. The introduced Trp amino acids not only diversify the molecular structures of peptide gelators, but also promote aromatic and hydrogen-bonding interactions for supramolecular self-assembling and gelation, which generates self-assembled nanostructures with twisted helical morphologies and supramolecular hydrogels with low minimal gelation concentrations. More importantly, the self-assembling peptides with Trp residues displayed strong preference for interacting with the lipidic membranes of bacteria, which resulted in bacterial flocculation and the death of E. coli and S. aureus.
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Affiliation(s)
- Jikun Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Shengnan Liu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Hang Li
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xin Tian
- School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Xinming Li
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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17
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Abstract
The WW domain is a modular protein structure that recognizes the proline-rich Pro-Pro-x-Tyr (PPxY) motif contained in specific target proteins. The compact modular nature of the WW domain makes it ideal for mediating interactions between proteins in complex networks and signaling pathways of the cell (e.g. the Hippo pathway). As a result, WW domains play key roles in a plethora of both normal and disease processes. Intriguingly, RNA and DNA viruses have evolved strategies to hijack cellular WW domain-containing proteins and thereby exploit the modular functions of these host proteins for various steps of the virus life cycle, including entry, replication, and egress. In this review, we summarize key findings in this rapidly expanding field, in which new virus-host interactions continue to be identified. Further unraveling of the molecular aspects of these crucial virus-host interactions will continue to enhance our fundamental understanding of the biology and pathogenesis of these viruses. We anticipate that additional insights into these interactions will help support strategies to develop a new class of small-molecule inhibitors of viral PPxY-host WW-domain interactions that could be used as antiviral therapeutics.
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Affiliation(s)
- Ariel Shepley-McTaggart
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Hao Fan
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore 138671.,Department of Biological Sciences (DBS), National University of Singapore, Singapore 119077.,Center for Computational Biology, DUKE-NUS Medical School, Singapore 169857
| | - Marius Sudol
- Department of Physiology, National University of Singapore, Singapore 119077.,Laboratory of Cancer Signaling and Domainopathies, Yong Loo Li School of Medicine, Block MD9, 2 Medical Drive #04-01, Singapore 117597.,Mechanobiology Institute, T-Lab, 5A Engineering Drive 1, Singapore 117411.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Ronald N Harty
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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18
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Gao XM, Zhang DD, Hou CC, Du C, Luo SY, Zhu JQ. Developmental and mRNA transcript relative abundance pattern of vitellogenin receptors, LR8-/Lrp13, during ovarian development in the large yellow croaker (Larimichthys crocea). Anim Reprod Sci 2020; 213:106271. [DOI: 10.1016/j.anireprosci.2019.106271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 12/06/2019] [Accepted: 12/27/2019] [Indexed: 12/13/2022]
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19
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Beltrán D, Anderson ME, Bharathy N, Settelmeyer TP, Svalina MN, Bajwa Z, Shern JF, Gultekin SH, Cuellar MA, Yonekawa T, Keller C, Campbell KP. Exogenous expression of the glycosyltransferase LARGE1 restores α-dystroglycan matriglycan and laminin binding in rhabdomyosarcoma. Skelet Muscle 2019; 9:11. [PMID: 31054580 PMCID: PMC6500046 DOI: 10.1186/s13395-019-0195-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 04/09/2019] [Indexed: 11/19/2022] Open
Abstract
Background α-Dystroglycan is the highly glycosylated component of the dystrophin-glycoprotein complex (DGC) that binds with high-affinity to extracellular matrix (ECM) proteins containing laminin-G-like (LG) domains via a unique heteropolysaccharide [-GlcA-beta1,3-Xyl-alpha1,3-]n called matriglycan. Changes in expression of components of the DGC or in the O-glycosylation of α-dystroglycan result in muscular dystrophy but are also observed in certain cancers. In mice, the loss of either of two DGC proteins, dystrophin or α-sarcoglycan, is associated with a high incidence of rhabdomyosarcoma (RMS). In addition, glycosylation of α-dystroglycan is aberrant in a small cohort of human patients with RMS. Since both the glycosylation of α-dystroglycan and its function as an ECM receptor require over 18 post-translational processing enzymes, we hypothesized that understanding its role in the pathogenesis of RMS requires a complete analysis of the expression of dystroglycan-modifying enzymes and the characterization of α-dystroglycan glycosylation in the context of RMS. Methods A series of cell lines and biopsy samples from human and mouse RMS were analyzed for the glycosylation status of α-dystroglycan and for expression of the genes encoding the responsible enzymes, in particular those required for the addition of matriglycan. Furthermore, the glycosyltransferase LARGE1 was ectopically expressed in RMS cells to determine its effects on matriglycan modifications and the ability of α-dystroglycan to function as a laminin receptor. Results Immunohistochemistry and immunoblotting of a collection of primary RMS tumors show that although α-dystroglycan is consistently expressed and glycosylated in these tumors, α-dystroglycan lacks matriglycan and the ability to bind laminin. Similarly, in a series of cell lines derived from human and mouse RMS, α-dystroglycan lacks matriglycan modification and the ability to bind laminin. RNAseq data from RMS cell lines was analyzed for expression of the genes known to be involved in α-dystroglycan glycosylation, which revealed that, for most cell lines, the lack of matriglycan can be attributed to the downregulation of the dystroglycan-modifying enzyme LARGE1. Ectopic expression of LARGE1 in these cell cultures restored matriglycan to levels comparable to those in muscle and restored high-affinity laminin binding to α-dystroglycan. Conclusions Collectively, our findings demonstrate that a lack of matriglycan on α-dystroglycan is a common feature in RMS due to the downregulation of LARGE1, and that ectopic expression of LARGE1 can restore matriglycan modifications and the ability of α-dystroglycan to function as an ECM receptor.
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Affiliation(s)
- Daniel Beltrán
- Department of Molecular Physiology and Biophysics, Department of Neurology, Howard Hughes Medical Institute, University of Iowa Roy J. and Lucille A. Carver College of Medicine, 4283 Carver Biomedical Research Building, 285 Newton Road, Iowa City, IA, 52242-1101, USA
| | - Mary E Anderson
- Department of Molecular Physiology and Biophysics, Department of Neurology, Howard Hughes Medical Institute, University of Iowa Roy J. and Lucille A. Carver College of Medicine, 4283 Carver Biomedical Research Building, 285 Newton Road, Iowa City, IA, 52242-1101, USA
| | - Narendra Bharathy
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road W, Beaverton, OR, 97005, USA
| | - Teagan P Settelmeyer
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road W, Beaverton, OR, 97005, USA
| | - Matthew N Svalina
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road W, Beaverton, OR, 97005, USA
| | - Zia Bajwa
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road W, Beaverton, OR, 97005, USA
| | - John F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sakir H Gultekin
- Department of Pathology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Marco A Cuellar
- Department of Molecular Physiology and Biophysics, Department of Neurology, Howard Hughes Medical Institute, University of Iowa Roy J. and Lucille A. Carver College of Medicine, 4283 Carver Biomedical Research Building, 285 Newton Road, Iowa City, IA, 52242-1101, USA
| | - Takahiro Yonekawa
- Department of Molecular Physiology and Biophysics, Department of Neurology, Howard Hughes Medical Institute, University of Iowa Roy J. and Lucille A. Carver College of Medicine, 4283 Carver Biomedical Research Building, 285 Newton Road, Iowa City, IA, 52242-1101, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road W, Beaverton, OR, 97005, USA.
| | - Kevin P Campbell
- Department of Molecular Physiology and Biophysics, Department of Neurology, Howard Hughes Medical Institute, University of Iowa Roy J. and Lucille A. Carver College of Medicine, 4283 Carver Biomedical Research Building, 285 Newton Road, Iowa City, IA, 52242-1101, USA.
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20
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Ehaideb SN, Al-Bu Ali MJ, Al-Obaid JJ, Aljassim KM, Alfadhel M. Novel Homozygous Mutation in the WWOX Gene Causes Seizures and Global Developmental Delay: Report and Review. Transl Neurosci 2018; 9:203-208. [PMID: 30746283 PMCID: PMC6368664 DOI: 10.1515/tnsci-2018-0029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/09/2018] [Indexed: 11/30/2022] Open
Abstract
The WWOX gene has a WW domain containing oxidoreductase, which is located at the common fragile site FRA16D at chromosome 16q23. WWOX is a tumor suppressor gene that has been associated with several types of cancer such as hepatic, breast, lung, prostate, gastric, and ovarian. Recently WWOX has been implicated in epilepsy, where studies show homozygous loss-of-function mutation lead to early-infantile epileptic encephalopathy, spinocerebellar ataxia, intractable seizures and developmental delay, and early lethal microcephaly syndrome with epilepsy. Here we investigate two consanguineous Saudi families and we identified three probands with epileptic encephalopathy. Whole exome sequencing revealed a novel homozygous mutation in the WWOX gene in one proband. In addition, we identified a previously reported WWOX mutation in two probands. Later on these findings were confirmed with Sanger sequencing. The underlying mechanism on how WWOX mutations lead to seizure remains elusive. To date very few WWOX mutations have been associated with neurological disorder and our newly identified mutations support the notion that WWOX play an important role in neurons and will aid in better diagnosis and genetic counseling.
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Affiliation(s)
- Salleh N Ehaideb
- King Abdullah International Medical Research Centre (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Majed J Al-Bu Ali
- Medical Genetic Unit, Pediatrics department, Maternity Children Hospital, Al-hassa Hofuf, Saudi Arabia
| | | | - Kareemah M Aljassim
- Medical Genetic Unit, Pediatrics department, Maternity Children Hospital, Al-hassa Hofuf, Saudi Arabia
| | - Majid Alfadhel
- King Abdullah International Medical Research Centre (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
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21
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BmYki is transcribed into four functional splicing isoforms in the silk glands of the silkworm Bombyx mori. Gene 2018; 646:39-46. [DOI: 10.1016/j.gene.2017.12.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/19/2017] [Accepted: 12/22/2017] [Indexed: 02/06/2023]
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22
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Vélez-Aguilera G, de Dios Gómez-López J, Jiménez-Gutiérrez GE, Vásquez-Limeta A, Laredo-Cisneros MS, Gómez P, Winder SJ, Cisneros B. Control of nuclear β-dystroglycan content is crucial for the maintenance of nuclear envelope integrity and function. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2018; 1865:406-420. [PMID: 29175376 DOI: 10.1016/j.bbamcr.2017.11.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/07/2017] [Accepted: 11/20/2017] [Indexed: 01/28/2023]
Abstract
β-Dystroglycan (β-DG) is a plasma membrane protein that has ability to target to the nuclear envelope (NE) to maintain nuclear architecture. Nevertheless, mechanisms controlling β-DG nuclear localization and the physiological consequences of a failure of trafficking are largely unknown. We show that β-DG has a nuclear export pathway in myoblasts that depends on the recognition of a nuclear export signal located in its transmembrane domain, by CRM1. Remarkably, NES mutations forced β-DG nuclear accumulation resulting in mislocalization and decreased levels of emerin and lamin B1 and disruption of various nuclear processes in which emerin (centrosome-nucleus linkage and β-catenin transcriptional activity) and lamin B1 (cell cycle progression and nucleoli structure) are critically involved. In addition to nuclear export, the lifespan of nuclear β-DG is restricted by its nuclear proteasomal degradation. Collectively our data show that control of nuclear β-DG content by the combination of CRM1 nuclear export and nuclear proteasome pathways is physiologically relevant to preserve proper NE structure and activity.
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Affiliation(s)
- Griselda Vélez-Aguilera
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Juan de Dios Gómez-López
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Guadalupe E Jiménez-Gutiérrez
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Alejandra Vásquez-Limeta
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico; Laboratory of Protein Dynamics and Signaling, Center for Cancer Research-Frederick, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Marco S Laredo-Cisneros
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Pablo Gómez
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Steve J Winder
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Bulmaro Cisneros
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico.
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Ubiquitin Ligase WWP1 Interacts with Ebola Virus VP40 To Regulate Egress. J Virol 2017; 91:JVI.00812-17. [PMID: 28768865 DOI: 10.1128/jvi.00812-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/24/2017] [Indexed: 01/05/2023] Open
Abstract
Ebola virus (EBOV) is a member of the Filoviridae family and the cause of hemorrhagic fever outbreaks. The EBOV VP40 (eVP40) matrix protein is the main driving force for virion assembly and budding. Indeed, expression of eVP40 alone in mammalian cells results in the formation and budding of virus-like particles (VLPs) which mimic the budding process and morphology of authentic, infectious EBOV. To complete the budding process, eVP40 utilizes its PPXY L-domain motif to recruit a specific subset of host proteins containing one or more modular WW domains that then function to facilitate efficient production and release of eVP40 VLPs. In this report, we identified additional host WW-domain interactors by screening for potential interactions between mammalian proteins possessing one or more WW domains and WT or PPXY mutant peptides of eVP40. We identified the HECT family E3 ubiquitin ligase WWP1 and all four of its WW domains as strong interactors with the PPXY motif of eVP40. The eVP40-WWP1 interaction was confirmed by both peptide pulldown and coimmunoprecipitation assays, which also demonstrated that modular WW domain 1 of WWP1 was most critical for binding to eVP40. Importantly, the eVP40-WWP1 interaction was found to be biologically relevant for VLP budding since (i) small interfering RNA (siRNA) knockdown of endogenous WWP1 resulted in inhibition of eVP40 VLP egress, (ii) coexpression of WWP1 and eVP40 resulted in ubiquitination of eVP40 and a subsequent increase in eVP40 VLP egress, and (iii) an enzymatically inactive mutant of WWP1 (C890A) did not ubiquitinate eVP40 or enhance eVP40 VLP egress. Last, our data show that ubiquitination of eVP40 by WWP1 enhances egress of VLPs and concomitantly decreases cellular levels of higher-molecular-weight oligomers of eVP40. In sum, these findings contribute to our fundamental understanding of the functional interplay between host E3 ligases, ubiquitination, and regulation of EBOV VP40-mediated egress.IMPORTANCE Ebola virus (EBOV) is a high-priority, emerging human pathogen that can cause severe outbreaks of hemorrhagic fever with high mortality rates. As there are currently no approved vaccines or treatments for EBOV, a better understanding of the biology and functions of EBOV-host interactions that promote or inhibit viral budding is warranted. Here, we describe a physical and functional interaction between EBOV VP40 (eVP40) and WWP1, a host E3 ubiquitin ligase that ubiquitinates VP40 and regulates VLP egress. This viral PPXY-host WW domain-mediated interaction represents a potential new target for host-oriented inhibitors of EBOV egress.
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Molecular mechanisms underlying the evolution of the slp76 signalosome. Sci Rep 2017; 7:1509. [PMID: 28473706 PMCID: PMC5431462 DOI: 10.1038/s41598-017-01660-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/29/2017] [Indexed: 02/07/2023] Open
Abstract
The well-defined mammalian slp76-signalosome is crucial for T-cell immune response, yet whether slp76-signalosome exists in invertebrates and how it evolved remain unknown. Here we investigated slp76-signalosome from an evolutionary perspective in amphioxus Branchiostoma belcheri (bb). We proved slp76-signalosome components bbslp76, bbGADS and bbItk are present in amphioxus and bbslp76 interacts with bbGADS and bbItk, but differences exist between the interaction manners within slp76-signalosome components of amphioxus and human (h). Specifically, bbslp76 has a unique WW-domain that blocked its association with hItk and decreased TCR-induced tyrosine-phosphorylation and NFAT-activation. Deletion of WW-domain shifted the constitutive association between bbslp76 and hPLCγ1 to a TCR-enhanced association. Among slp76-signalosome, the interaction between slp76 and PLCγ1 is the most conserved and the binding between Itk and slp76 evolved from constitutive to stimulation-regulated. Sequence alignment and 3D structural analysis of slp76-signalosome molecules from keystone species indicated slp76 evolved into a more unfolded and flexible adaptor due to lack of WW-domain and several low-complexity-regions (LCRs) while GADS turned into a larger protein by a LCR gain, thus preparing more space for nucleating the coevolving slp76-signalosome. Altogether, through deletion of WW-domain and manipulation of LCRs, slp76-signalosome evolves from a rigid and stimulation-insensitive to a more flexible and stimulation-responding complex.
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Liang J, Sagum CA, Bedford MT, Sidhu SS, Sudol M, Han Z, Harty RN. Chaperone-Mediated Autophagy Protein BAG3 Negatively Regulates Ebola and Marburg VP40-Mediated Egress. PLoS Pathog 2017; 13:e1006132. [PMID: 28076420 PMCID: PMC5226679 DOI: 10.1371/journal.ppat.1006132] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/15/2016] [Indexed: 12/18/2022] Open
Abstract
Ebola (EBOV) and Marburg (MARV) viruses are members of the Filoviridae family which cause outbreaks of hemorrhagic fever. The filovirus VP40 matrix protein is essential for virus assembly and budding, and its PPxY L-domain motif interacts with WW-domains of specific host proteins, such as Nedd4 and ITCH, to facilitate the late stage of virus-cell separation. To identify additional WW-domain-bearing host proteins that interact with VP40, we used an EBOV PPxY-containing peptide to screen an array of 115 mammalian WW-domain-bearing proteins. Using this unbiased approach, we identified BCL2 Associated Athanogene 3 (BAG3), a member of the BAG family of molecular chaperone proteins, as a specific VP40 PPxY interactor. Here, we demonstrate that the WW-domain of BAG3 interacts with the PPxY motif of both EBOV and MARV VP40 and, unexpectedly, inhibits budding of both eVP40 and mVP40 virus-like particles (VLPs), as well as infectious VSV-EBOV recombinants. BAG3 is a stress induced protein that regulates cellular protein homeostasis and cell survival through chaperone-mediated autophagy (CMA). Interestingly, our results show that BAG3 alters the intracellular localization of VP40 by sequestering VP40 away from the plasma membrane. As BAG3 is the first WW-domain interactor identified that negatively regulates budding of VP40 VLPs and infectious virus, we propose that the chaperone-mediated autophagy function of BAG3 represents a specific host defense strategy to counteract the function of VP40 in promoting efficient egress and spread of virus particles.
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Affiliation(s)
- Jingjing Liang
- Department of Pathobiology, School Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, China
| | - Cari A. Sagum
- Department of Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, University of Texas Smithville, Smithville, TX, United States of America
| | - Mark T. Bedford
- Department of Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, University of Texas Smithville, Smithville, TX, United States of America
| | - Sachdev S. Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marius Sudol
- Department of Physiology, National University of Singapore, Mechanobiology Institute and Institute for Molecular and Cell Biology (IMCB, A*STAR), Republic of Singapore
| | - Ziying Han
- Department of Pathobiology, School Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Ronald N. Harty
- Department of Pathobiology, School Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- * E-mail:
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ITCH E3 Ubiquitin Ligase Interacts with Ebola Virus VP40 To Regulate Budding. J Virol 2016; 90:9163-71. [PMID: 27489272 DOI: 10.1128/jvi.01078-16] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/25/2016] [Indexed: 01/27/2023] Open
Abstract
UNLABELLED Ebola virus (EBOV) and Marburg virus (MARV) belong to the Filoviridae family and can cause outbreaks of severe hemorrhagic fever, with high mortality rates in humans. The EBOV VP40 (eVP40) and MARV VP40 (mVP40) matrix proteins play a central role in virion assembly and egress, such that independent expression of VP40 leads to the production and egress of virus-like particles (VLPs) that accurately mimic the budding of infectious virus. Late (L) budding domains of eVP40 recruit host proteins (e.g., Tsg101, Nedd4, and Alix) that are important for efficient virus egress and spread. For example, the PPxY-type L domain of eVP40 and mVP40 recruits the host Nedd4 E3 ubiquitin ligase via its WW domains to facilitate budding. Here we sought to identify additional WW domain host interactors and demonstrate that the PPxY L domain motif of eVP40 interacts specifically with the WW domain of the host E3 ubiquitin ligase ITCH. ITCH, like Nedd4, is a member of the HECT class of E3 ubiquitin ligases, and the resultant physical and functional interaction with eVP40 facilitates VLP and virus budding. Identification of this novel eVP40 interactor highlights the functional interplay between cellular E3 ligases, ubiquitination, and regulation of VP40-mediated egress. IMPORTANCE The unprecedented magnitude and scope of the recent 2014-2015 EBOV outbreak in West Africa and its emergence here in the United States and other countries underscore the critical need for a better understanding of the biology and pathogenesis of this emerging pathogen. We have identified a novel and functional EBOV VP40 interactor, ITCH, that regulates VP40-mediated egress. This virus-host interaction may represent a new target for our previously identified small-molecule inhibitors of virus egress.
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Tsukasaki W, Saeki K, Katayama T, Maruyama JI, Kitamoto K. Molecular dissection of SO (SOFT) protein in stress-induced aggregation and cell-to-cell interactive functions in filamentous fungal multicellularity. Fungal Biol 2016; 120:775-82. [DOI: 10.1016/j.funbio.2016.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/25/2016] [Accepted: 02/02/2016] [Indexed: 11/26/2022]
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Abstract
The dystrophin complex stabilizes the plasma membrane of striated muscle cells. Loss of function mutations in the genes encoding dystrophin, or the associated proteins, trigger instability of the plasma membrane, and myofiber loss. Mutations in dystrophin have been extensively cataloged, providing remarkable structure-function correlation between predicted protein structure and clinical outcomes. These data have highlighted dystrophin regions necessary for in vivo function and fueled the design of viral vectors and now, exon skipping approaches for use in dystrophin restoration therapies. However, dystrophin restoration is likely more complex, owing to the role of the dystrophin complex as a broad cytoskeletal integrator. This review will focus on dystrophin restoration, with emphasis on the regions of dystrophin essential for interacting with its associated proteins and discuss the structural implications of these approaches.
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Affiliation(s)
- Quan Q Gao
- Committee on Development, Regeneration and Stem Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University, Chicago, Chicago, Illinois, USA
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Allen DG, Whitehead NP, Froehner SC. Absence of Dystrophin Disrupts Skeletal Muscle Signaling: Roles of Ca2+, Reactive Oxygen Species, and Nitric Oxide in the Development of Muscular Dystrophy. Physiol Rev 2016; 96:253-305. [PMID: 26676145 DOI: 10.1152/physrev.00007.2015] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Dystrophin is a long rod-shaped protein that connects the subsarcolemmal cytoskeleton to a complex of proteins in the surface membrane (dystrophin protein complex, DPC), with further connections via laminin to other extracellular matrix proteins. Initially considered a structural complex that protected the sarcolemma from mechanical damage, the DPC is now known to serve as a scaffold for numerous signaling proteins. Absence or reduced expression of dystrophin or many of the DPC components cause the muscular dystrophies, a group of inherited diseases in which repeated bouts of muscle damage lead to atrophy and fibrosis, and eventually muscle degeneration. The normal function of dystrophin is poorly defined. In its absence a complex series of changes occur with multiple muscle proteins showing reduced or increased expression or being modified in various ways. In this review, we will consider the various proteins whose expression and function is changed in muscular dystrophies, focusing on Ca(2+)-permeable channels, nitric oxide synthase, NADPH oxidase, and caveolins. Excessive Ca(2+) entry, increased membrane permeability, disordered caveolar function, and increased levels of reactive oxygen species are early changes in the disease, and the hypotheses for these phenomena will be critically considered. The aim of the review is to define the early damage pathways in muscular dystrophy which might be appropriate targets for therapy designed to minimize the muscle degeneration and slow the progression of the disease.
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Affiliation(s)
- David G Allen
- Sydney Medical School & Bosch Institute, University of Sydney, New South Wales, Australia; and Department of Physiology & Biophysics, University of Washington, Seattle, Washington
| | - Nicholas P Whitehead
- Sydney Medical School & Bosch Institute, University of Sydney, New South Wales, Australia; and Department of Physiology & Biophysics, University of Washington, Seattle, Washington
| | - Stanley C Froehner
- Sydney Medical School & Bosch Institute, University of Sydney, New South Wales, Australia; and Department of Physiology & Biophysics, University of Washington, Seattle, Washington
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30
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Melino S, Bellomaria A, Nepravishta R, Paci M, Melino G. p63 threonine phosphorylation signals the interaction with the WW domain of the E3 ligase Itch. Cell Cycle 2015; 13:3207-17. [PMID: 25485500 DOI: 10.4161/15384101.2014.951285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Both in epithelial development as well as in epithelial cancers, the p53 family member p63 plays a crucial role acting as a master transcriptional regulator. P63 steady state protein levels are regulated by the E3 ubiquitin ligase Itch, via a physical interaction between the PPxY consensus sequence (PY motif) of p63 and one of the 4 WW domains of Itch; this substrate recognition process leads to protein-ubiquitylation and p63 proteasomal degradation. The interaction of the WW domains, a highly compact protein-protein binding module, with the short proline-rich sequences is therefore a crucial regulatory event that may offer innovative potential therapeutic opportunity. Previous molecular studies on the Itch-p63 recognition have been performed in vitro using the Itch-WW2 domain and the peptide interacting fragment of p63 (pep63), which includes the PY motif. Itch-WW2-pep63 interaction is also stabilized in vitro by the conformational constriction of the S-S cyclization in the p63 peptide. The PY motif of p63, as also for other proteins, is characterized by the nearby presence of a (T/S)P motif, which is a potential recognition site of the WW domain of the IV group present in the prolyl-isomerase Pin1. In this study, we demonstrate, by in silico and spectroscopical studies using both the linear pep63 and its cyclic form, that the threonine phosphorylation of the (T/S)PPPxY motif may represent a crucial regulatory event of the Itch-mediated p63 ubiquitylation, increasing the Itch-WW domains-p63 recognition event and stabilizing in vivo the Itch-WW-p63 complex. Moreover, our studies confirm that the subsequently trans/cis proline isomerization of (T/S)P motif by the Pin1 prolyl-isomerase, could modulate the E3-ligase interaction, and that the (T/S)pPtransPPxY motif represent the best conformer for the ItchWW-(T/S)PPPxY motif recognition.
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Key Words
- CXCR4, chemokine receptor
- E3 ubiquitin ligases
- HECT, Homologous E6-AP Carboxyl Terminus
- IPTG, isopropyl-β-D-thiogalactoside
- Itch
- Pin1
- Ppep63, phosphorylated pep63
- RHS, Rapp-Hodgkin syndrome
- RP-HPLC, reverse phase high performance chromatography
- TFE, 2, 2, 2-trifluoroethanol
- TNF, tumor necrosis factor
- TRAF6, TNF receptor-associated factor 6
- cPpep63, cyclic phosphorylated pep63
- p53 family
- p63
- pep63, p63(534–551) peptide
- proline isomerization
- ubiquitynation
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Affiliation(s)
- Sonia Melino
- a Dipartimento di Scienze e Tecnologie Chimiche ; University of Rome "Tor Vergata" ; Rome , Italy
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Cerecedo D, Martínez‐Vieyra I, Maldonado‐García D, Hernández‐González E, Winder SJ. Association of Membrane/Lipid Rafts With the Platelet Cytoskeleton and the Caveolin PY14: Participation in the Adhesion Process. J Cell Biochem 2015; 116:2528-40. [DOI: 10.1002/jcb.25197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/14/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Doris Cerecedo
- Laboratorio de HematobiologíaEscuela Nacional de Medicina y Homeopatía (ENMH)Instituto Politécnico Nacional (IPN)Mexico CityMexico
| | - Ivette Martínez‐Vieyra
- Laboratorio de HematobiologíaEscuela Nacional de Medicina y Homeopatía (ENMH)Instituto Politécnico Nacional (IPN)Mexico CityMexico
| | - Deneb Maldonado‐García
- Departamento de Biología CelularCentro de Investigación y de Estudios Avanzados del IPN (Cinvestav‐IPN)Mexico CityMexico
| | - Enrique Hernández‐González
- Departamento de Biología CelularCentro de Investigación y de Estudios Avanzados del IPN (Cinvestav‐IPN)Mexico CityMexico
| | - Steve J. Winder
- Department of Biomedical ScienceUniversity of SheffieldSheffieldUK
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Holland A, Murphy S, Dowling P, Ohlendieck K. Pathoproteomic profiling of the skeletal muscle matrisome in dystrophinopathy associated myofibrosis. Proteomics 2015; 16:345-66. [PMID: 26256116 DOI: 10.1002/pmic.201500158] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/12/2015] [Accepted: 07/24/2015] [Indexed: 12/14/2022]
Abstract
The gradual accumulation of collagen and associated proteins of the extracellular matrix is a crucial myopathological parameter of many neuromuscular disorders. Progressive tissue damage and fibrosis play a key pathobiochemical role in the dysregulation of contractile functions and often correlates with poor motor outcome in muscular dystrophies. Following a brief introduction into the role of the extracellular matrix in skeletal muscles, we review here the proteomic profiling of myofibrosis and its intrinsic role in X-linked muscular dystrophy. Although Duchenne muscular dystrophy is primarily a disease of the membrane cytoskeleton, one of its most striking histopathological features is a hyperactive connective tissue and tissue scarring. We outline the identification of novel factors involved in the modulation of the extracellular matrix in muscular dystrophy, such as matricellular proteins. The establishment of novel proteomic markers will be helpful in improving the diagnosis, prognosis, and therapy monitoring in relation to fibrotic substitution of contractile tissue. In the future, the prevention of fibrosis will be crucial for providing optimum conditions to apply novel pharmacological treatments, as well as establish cell-based approaches or gene therapeutic interventions. The elimination of secondary abnormalities in the matrisome promises to reduce tissue scarring and the loss of skeletal muscle elasticity.
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Affiliation(s)
- Ashling Holland
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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Lo JY, Chou YT, Lai FJ, Hsu LJ. Regulation of cell signaling and apoptosis by tumor suppressor WWOX. Exp Biol Med (Maywood) 2015; 240:383-91. [PMID: 25595191 DOI: 10.1177/1535370214566747] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Human fragile WWOX gene encodes a tumor suppressor WW domain-containing oxidoreductase (named WWOX, FOR, or WOX1). Functional suppression of WWOX prevents apoptotic cell death induced by a variety of stress stimuli, such as tumor necrosis factor, UV radiation, and chemotherapeutic drug treatment. Loss of WWOX gene expression due to gene deletions, loss of heterozygosity, chromosomal translocations, or epigenetic silencing is frequently observed in human malignant cancer cells. Acquisition of chemoresistance in squamous cell carcinoma, osteosarcoma, and breast cancer cells is associated with WWOX deficiency. WWOX protein physically interacts with many signaling molecules and exerts its regulatory effects on gene transcription and protein stability and subcellular localization to control cell survival, proliferation, differentiation, autophagy, and metabolism. In this review, we provide an overview of the recent advances in understanding the molecular mechanisms by which WWOX regulates cellular functions and stress responses. A potential scenario is that activation of WWOX by anticancer drugs is needed to overcome chemoresistance and trigger cancer cell death, suggesting that WWOX can be regarded as a prognostic marker and a candidate molecule for targeted cancer therapies.
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Affiliation(s)
- Jui-Yen Lo
- Institute of Basic Medical Sciences, National Cheng Kung University Medical College, Tainan 70101, Taiwan
| | - Ying-Tsen Chou
- Institute of Basic Medical Sciences, National Cheng Kung University Medical College, Tainan 70101, Taiwan
| | - Feng-Jie Lai
- Department of Dermatology, Chimei Medical Center, Tainan 71004, Taiwan
| | - Li-Jin Hsu
- Department of Medical Laboratory Science and Biotechnology Center of Infectious Disease and Signaling Research and Research Center for Medical Laboratory Biotechnology, National Cheng Kung University Medical College, Tainan 70101, Taiwan
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Guilbert SM, Varlet AA, Fuchs M, Lambert H, Landry J, Lavoie JN. Regulation of Actin-Based Structure Dynamics by HspB Proteins and Partners. HEAT SHOCK PROTEINS 2015. [DOI: 10.1007/978-3-319-16077-1_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Oda T, Chiba S, Nagai T, Mizuno K. Binding to Cep164, but not EB1, is essential for centriolar localization of TTBK2 and its function in ciliogenesis. Genes Cells 2014; 19:927-40. [PMID: 25297623 DOI: 10.1111/gtc.12191] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 09/14/2014] [Indexed: 11/28/2022]
Abstract
Primary cilia are formed by extending the microtubule-based axoneme from the mother centriole-derived basal body. Recruitment of Tau tubulin kinase-2 (TTBK2) to the mother centriole and subsequent removal of CP110 and its interactor Cep97 are crucial for the initiation of ciliogenesis. We analyzed the roles of two TTBK2-binding proteins, EB1 and Cep164, in centriolar localization of TTBK2. TTBK2 bound EB1 and Cep164 through its SxIP motifs and a proline-rich motif, respectively. Using TTBK2 variants that contained mutations in the SxIP or proline-rich motifs, we obtained evidence that Cep164, but not EB1, is essential for centriolar localization of TTBK2. Depletion of TTBK2 inhibited CP110 removal and ciliogenesis, whereas expression of wild-type TTBK2, but not non-Cep164-binding mutants, rescued CP110 removal and ciliogenesis in TTBK2-depleted cells. Therefore, Cep164 binding is essential for the function of TTBK2 in promoting CP110 removal and ciliogenesis. We also provide evidence that TTBK2 has the potential to effectively phosphorylate Cep164 and Cep97 and inhibits the interaction between Cep164 and its binding partner Dishevelled-3 (an important regulator of ciliogenesis) in a kinase activity-dependent manner.
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Affiliation(s)
- Toshiaki Oda
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
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Reading BJ, Hiramatsu N, Schilling J, Molloy KT, Glassbrook N, Mizuta H, Luo W, Baltzegar DA, Williams VN, Todo T, Hara A, Sullivan CV. Lrp13 is a novel vertebrate lipoprotein receptor that binds vitellogenins in teleost fishes. J Lipid Res 2014; 55:2287-95. [PMID: 25217480 DOI: 10.1194/jlr.m050286] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcripts encoding a novel member of the lipoprotein receptor superfamily, termed LDL receptor-related protein (Lrp)13, were sequenced from striped bass (Morone saxatilis) and white perch (Morone americana) ovaries. Receptor proteins were purified from perch ovary membranes by protein-affinity chromatography employing an immobilized mixture of vitellogenins Aa and Ab. RT-PCR revealed lrp13 to be predominantly expressed in striped bass ovary, and in situ hybridization detected lrp13 transcripts in the ooplasm of early secondary growth oocytes. Quantitative RT-PCR confirmed peak lrp13 expression in the ovary during early secondary growth. Quantitative mass spectrometry revealed peak Lrp13 protein levels in striped bass ovary during late-vitellogenesis, and immunohistochemistry localized Lrp13 to the oolemma and zona radiata of vitellogenic oocytes. Previously unreported orthologs of lrp13 were identified in genome sequences of fishes, chicken (Gallus gallus), mouse (Mus musculus), and dog (Canis lupus familiaris). Zebrafish (Danio rerio) and Nile tilapia (Oreochromis niloticus) lrp13 loci are discrete and share genomic synteny. The Lrp13 appears to function as a vitellogenin receptor and may be an important mediator of yolk formation in fishes and other oviparous vertebrates. The presence of lrp13 orthologs in mammals suggests that this lipoprotein receptor is widely distributed among vertebrates, where it may generally play a role in lipoprotein metabolism.
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Affiliation(s)
- Benjamin J Reading
- Departments of Applied Ecology North Carolina State University, Raleigh, NC
| | - Naoshi Hiramatsu
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Justin Schilling
- Departments of Applied Ecology North Carolina State University, Raleigh, NC
| | - Katelyn T Molloy
- Departments of Applied Ecology North Carolina State University, Raleigh, NC
| | - Norm Glassbrook
- Genomic Sciences Laboratory, North Carolina State University, Raleigh, NC
| | - Hiroko Mizuta
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Wenshu Luo
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | | | - Valerie N Williams
- Departments of Applied Ecology North Carolina State University, Raleigh, NC
| | - Takashi Todo
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Akihiko Hara
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Craig V Sullivan
- Biological Sciences, North Carolina State University, Raleigh, NC Carolina AquaGyn, Raleigh, NC
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MLL partner genes in secondary acute lymphoblastic leukemia: report of a new partner PRRC1 and review of the literature. Leuk Res 2014; 38:1316-9. [PMID: 25205603 DOI: 10.1016/j.leukres.2014.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/17/2014] [Accepted: 08/18/2014] [Indexed: 11/23/2022]
Abstract
Secondary acute lymphoblastic leukemia (sALL) following chemotherapy and/or radiotherapy of previous malignancies represents 2-10% of all cases of ALL. A 72-year-old female patient was diagnosed with acute lymphoblastic leukemia following chemotherapy for a diffuse large B cell lymphoma. Banding cytogenetics showed a t(t(5;11)(q23-31;q23) in 20 of the 21 metaphases examined and fluorescent in situ hybridization confirmed rearrangement of MLL. Long distance inverse-polymerase chain reaction revealed an in-frame fusion between 5'MLL and 3'PRRC1. Sixty-five cases of sALL associated with 11q23/MLL rearrangement, including 47 with a t(4;11)(q21;q23), were retrieved from the literature. Drug regimen used to treat the primary neoplasm was available for 54 patients; 52 had received a topoisomerase II inhibitor, known to induce MLL rearrangement.
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39
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Characterization of human gene locus CYYR1: a complex multi-transcript system. Mol Biol Rep 2014; 41:6025-38. [PMID: 24981926 DOI: 10.1007/s11033-014-3480-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/17/2014] [Indexed: 01/19/2023]
Abstract
Cysteine/tyrosine-rich 1 (CYYR1) is a gene we previously identified on human chromosome 21 starting from an in-depth bioinformatics analysis of chromosome 21 segment 40/105 (21q21.3), where no coding region had previously been predicted. CYYR1 was initially characterized as a four-exon gene, whose brain-derived cDNA sequencing predicts a 154-amino acid product. In this study we provide, with in silico and in vitro analyses, the first detailed description of the human CYYR1 locus. The analysis of this locus revealed that it is composed of a multi-transcript system, which includes at least seven CYYR1 alternative spliced isoforms and a new CYYR1 antisense gene (named CYYR1-AS1). In particular, we cloned, for the first time, the following isoforms: CYYR1-1,2,3,4b and CYYR1-1,2,3b, which present a different 3' transcribed region, with a consequent different carboxy-terminus of the predicted proteins; CYYR1-1,2,4 lacks exon 3; CYYR1-1,2,2bis,3,4 presents an additional exon between exon 2 and exon 3; CYYR1-1b,2,3,4 presents a different 5' untranslated region when compared to CYYR1. The complexity of the locus is enriched by the presence of an antisense transcript. We have cloned a long transcript overlapping with CYYR1 as an antisense RNA, probably a non-coding RNA. Expression analysis performed in different normal tissues, tumour cell lines as well as in trisomy 21 and euploid fibroblasts has confirmed a quantitative and qualitative variability in the expression pattern of the multi-transcript locus, suggesting a possible role in complex diseases that should be further investigated.
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40
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Chen J, Zhang Y, Liu J, Xia M, Wang W, Shen F. Genome-wide analysis of the RNA helicase gene family in Gossypium raimondii. Int J Mol Sci 2014; 15:4635-56. [PMID: 24642883 PMCID: PMC3975418 DOI: 10.3390/ijms15034635] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 02/25/2014] [Accepted: 02/27/2014] [Indexed: 12/15/2022] Open
Abstract
The RNA helicases, which help to unwind stable RNA duplexes, and have important roles in RNA metabolism, belong to a class of motor proteins that play important roles in plant development and responses to stress. Although this family of genes has been the subject of systematic investigation in Arabidopsis, rice, and tomato, it has not yet been characterized in cotton. In this study, we identified 161 putative RNA helicase genes in the genome of the diploid cotton species Gossypium raimondii. We classified these genes into three subfamilies, based on the presence of either a DEAD-box (51 genes), DEAH-box (52 genes), or DExD/H-box (58 genes) in their coding regions. Chromosome location analysis showed that the genes that encode RNA helicases are distributed across all 13 chromosomes of G. raimondii. Syntenic analysis revealed that 62 of the 161 G. raimondii helicase genes (38.5%) are within the identified syntenic blocks. Sixty-six (40.99%) helicase genes from G. raimondii have one or several putative orthologs in tomato. Additionally, GrDEADs have more conserved gene structures and more simple domains than GrDEAHs and GrDExD/Hs. Transcriptome sequencing data demonstrated that many of these helicases, especially GrDEADs, are highly expressed at the fiber initiation stage and in mature leaves. To our knowledge, this is the first report of a genome-wide analysis of the RNA helicase gene family in cotton.
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Affiliation(s)
- Jie Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Yujuan Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Jubo Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Minxuan Xia
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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41
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Renal biopsy: use of biomarkers as a tool for the diagnosis of focal segmental glomerulosclerosis. DISEASE MARKERS 2014; 2014:192836. [PMID: 24719498 PMCID: PMC3955602 DOI: 10.1155/2014/192836] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/15/2014] [Accepted: 01/15/2014] [Indexed: 12/12/2022]
Abstract
Focal segmental glomerulosclerosis (FSGS) is a glomerulopathy associated with nephrotic syndrome and podocyte injury. FSGS occurs both in children and adults and it is considered the main idiopathic nephrotic syndrome nowadays. It is extremely difficult to establish a morphological diagnosis, since some biopsies lack a considerable quantifiable number of sclerotic glomeruli, given their focal aspect and the fact that FSGS occurs in less than half of the glomeruli. Therefore, many biological molecules have been evaluated as potential markers that would enhance the diagnosis of FSGS. Some of these molecules and receptors are associated with the pathogenesis of FSGS and have potential use in diagnosis.
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42
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Kanai Y, Wang D, Hirokawa N. KIF13B enhances the endocytosis of LRP1 by recruiting LRP1 to caveolae. ACTA ACUST UNITED AC 2014; 204:395-408. [PMID: 24469637 PMCID: PMC3912526 DOI: 10.1083/jcb.201309066] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The motor protein KIF13B has an unconventional role as a scaffold that recruits lipoprotein receptor–related protein 1 to caveolae, thereby enhancing its endocytosis. Multifunctional low-density lipoprotein (LDL) receptor-related protein 1 (LRP1) recognizes and internalizes a large number of diverse ligands, including LDL and factor VIII. However, little is known about the regulation of LRP1 endocytosis. Here, we show that a microtubule-based motor protein, KIF13B, in an unexpected and unconventional function, enhances caveolin-dependent endocytosis of LRP1. KIF13B was highly expressed in the liver and was localized on the sinusoidal plasma membrane of hepatocytes. KIF13B knockout (KO) mice showed elevated levels of serum cholesterol and factor VIII, and KO MEFs showed decreased uptake of LDL. Exogenous KIF13B, initially localized on the plasma membrane with caveolae, was translocated to the vesicles in the cytoplasm with LRP1 and caveolin-1. KIF13B bound to hDLG1 and utrophin, which, in turn, bound to LRP1 and caveolae, respectively. These linkages were required for the KIF13B-enhanced endocytosis of LRP1. Thus, we propose that KIF13B, working as a scaffold, recruits LRP1 to caveolae via LRP1–hDLG1–KIF13B–utrophin–caveolae linkage and enhances the endocytosis of LRP1.
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Affiliation(s)
- Yoshimitsu Kanai
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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43
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44
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Hu JP, He HQ, Jiao X, Chang S. Understanding the folding and stability of a designed WW domain protein with replica exchange molecular dynamics simulations. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.773431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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45
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Huang H, Bae C, Sachs F, Suchyna TM. Caveolae regulation of mechanosensitive channel function in myotubes. PLoS One 2013; 8:e72894. [PMID: 24023653 PMCID: PMC3758351 DOI: 10.1371/journal.pone.0072894] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/15/2013] [Indexed: 01/07/2023] Open
Abstract
Mutations that lead to muscular dystrophy often create deficiencies in cytoskeletal support of the muscle sarcolemma causing hyperactive mechanosensitive cation channel (MSC) activity and elevated intracellular Ca(2+). Caveolae are cholesterol-rich microdomains that form mechanically deformable invaginations of the sarcolemma. Mutations to caveolin-3, the main scaffolding protein of caveolae in muscle, cause Limbe-Girdle muscular dystrophy. Using genetic and acute chemical perturbations of developing myotubes we investigated whether caveolae are functionally linked to MSCs. MSC sensitivity was assayed using suction application to patches and probe-induced indentation during whole-cell recordings. Membrane mechanical stress in patches was monitored using patch capacitance/impedance. Cholesterol depletion disrupted caveolae and caused a large increase in MSC current. It also decreased the membrane mechanical relaxation time, likely reflecting cytoskeleton dissociation from the bilayer. Reduction of Cav3 expression with miRNA also increased MSC current and decreased patch relaxation time. In contrast Cav3 overexpression produced a small decrease in MSC currents. To acutely and specifically inhibit Cav3 interactions, we made a chimeric peptide containing the antennapedia membrane translocation domain and the Cav3 scaffolding domain (A-CSD3). A-CSD3 action was time dependent initially producing a mild Ca(2+) leak and increased MSC current, while longer exposures decreased MSC currents coinciding with increased patch stiffening. Images of GFP labeled Cav3 in patches showed that Cav3 doesn't enter the pipette, showing patch composition differed from the cell surface. However, disruption via cholesterol depletion caused Cav3 to become uniformly distributed over the sarcolemma and Cav3 appearance in the patch dome. The whole-cell indentation currents elicited under the different caveolae modifying conditions mirror the patch response supporting the role of caveolae in MSC function. These studies show that normal expression levels of Cav3 are mechanoprotective to the sarcolemma through multiple mechanisms, and Cav3 upregulation observed in some dystrophies may compensate for other mechanical deficiencies.
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Affiliation(s)
- Haixia Huang
- Capital Medical University, Department of Physiology, Beijing, China
| | - Chilman Bae
- SUNY at Buffalo, Department of Physiology and Biophysics, Buffalo, New York, United States of America
| | - Frederick Sachs
- SUNY at Buffalo, Department of Physiology and Biophysics, Buffalo, New York, United States of America
| | - Thomas M. Suchyna
- SUNY at Buffalo, Department of Physiology and Biophysics, Buffalo, New York, United States of America
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46
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Gene expression of WWOX, FHIT and p73 in acute lymphoblastic leukemia. Oncol Lett 2013; 6:963-969. [PMID: 24137446 PMCID: PMC3796419 DOI: 10.3892/ol.2013.1514] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 07/08/2013] [Indexed: 12/22/2022] Open
Abstract
The aim of the present study was to analyze the expression of WW-domain oxidoreductase (WWOX), fragile histidine triad (FHIT) and p73 in acute lymphoblastic leukemia (ALL). Samples from 122 ALL patients and 35 non-ALL control patients were collected in this study. RT-PCR was performed to detect the mRNA expression of WWOX, FHIT and p73. The methylation status of the WWOX promoter region, FHIT promoter region and the first exon region of p73 were also analyzed using the methylation-specific PCR method. The mRNA expression of WWOX, FHIT and p73 was significantly lower in the ALL samples compared with the controls (48.2, 42.9 and 55.4%, respectively). By contrast, the methylation frequency of WWOX, FHIT and p73 was significantly higher in the ALL samples compared with the controls (44.6, 46.4 and 37.5%, respectively). The mRNA expression of these three genes was inversely correlated with the methylation frequency in the ALL samples (correlation coefficients, −0.661, −0.685 and −0.536 for WWOX, FHIT and p73, respectively). Moreover, the mRNA expression of WWOX was positively correlated with that of FHIT and p73 (correlation coefficients, 0.569 and 0.556, respectively). However, the methylation status of WWOX had no correlation with that of FHIT or p73. It was concluded that the high methylation status of WWOX, FHIT and p73 may lead to the inactivation of expression and the silencing of these genes, promoting the occurrence and development of ALL. The determination of the mRNA expression and methylation status of WWOX, FHIT and p73 may aid in the development of treatment approaches for ALL.
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The E3 ubiquitin ligase Itch regulates tumor suppressor protein RASSF5/NORE1 stability in an acetylation-dependent manner. Cell Death Dis 2013; 4:e565. [PMID: 23538446 PMCID: PMC3615736 DOI: 10.1038/cddis.2013.91] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ras association (RalGDS/AF-6) domain family member RASSF5 is a non-enzymatic RAS effector super family protein, known to be involved in cell growth regulation. Expression of RASSF5 is found to be extinguished by promoter hypermethylation in different human cancers, and its ectopic expression suppresses cell proliferation and tumorigenicity. Interestingly, this role in tumorigenesis has been confounded by the fact that regulation at molecular level remains unclear and many transformed cells actually display elevated RASSF5 expression. Here, we demonstrate that E3 ubiquitin ligase Itch is a unique binding partner of RASSF5. Itch can interact with PPxY motif in RASSF5 both in vivo and in vitro through its WW domains. Importantly, the overexpression of Itch induces RASSF5 degradation by poly-ubiquitination via 26S proteasome pathway. In addition, our results indicate that the elevated levels of RASSF5 found in tumor cells due to acetylation, which restricts its binding to Itch and results in a more stable inert protein. Inhibition of RASSF5 acetylation permits its interaction with Itch and provokes proteasomal degradation. These data suggest that apart from promoter methylation, hyperacetylation could also be downregulating RASSF5 function in different human cancer. Finally, results from functional assays suggest that the overexpression of wild type, not the ligase activity defective Itch negatively regulate RASSF5-mediated G1 phase transition of cell cycle as well as apoptosis, suggesting that Itch alone is sufficient to alter RASSF5 function. Collectively, the present investigation identifies a HECT class E3 ubiquitin ligase Itch as a unique negative regulator of RASSF5, and suggests the possibility that acetylation as a potential therapeutic target for human cancer.
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48
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Hung FC, Cheng YC, Sun NK, Chao CCK. Identification and functional characterization of zebrafish Gas7 gene in early development. J Neurosci Res 2012; 91:51-61. [PMID: 23086717 DOI: 10.1002/jnr.23145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 08/07/2012] [Accepted: 08/22/2012] [Indexed: 12/17/2022]
Abstract
Growth arrest-specific 7 (Gas7) is preferentially expressed in the nervous system and plays an important role during neuritogenesis in mammals. However, the structure and function of Gas7 homologs have not been studied in nonmammalian vertebrates used as models. In this report, we identify a Gas7 gene in zebrafish that we termed zfGas7. The transcript of this gene was produced by canonical splicing, and its protein product contained a Fes/CIP4 homology and a coiled-coil domain. In early zebrafish embryos, RT-PCR analyses revealed that zfGas7 was initially expressed at 5.3 hr postfertilization (hpf), followed by an increase of expression at 10 hpf and further accumulation during somitogenesis at 48 hpf. Spatiotemporal analyses further showed that Gas7 mRNA was detected in the brain, somite, and posterior presomitic mesoderm regions during somitogenesis. At 36 hpf, zfGas7 mRNA was detected in the brain and somite but was later found only in neuronal clusters of the brain at 52 hpf. Gas7 knockdown with morpholino antisense oligonucleotides (Gas7MO) reduced the number of HuC-positive neurons in the trigeminal and statoacoustic ganglions and produced deformed phenotypes, such as flattening of the top of the head. Notably, the neuron reduction and deformed phenotypes observed in Gas7MO embryos were partially rescued by ectopic expression of Gas7. Because altered somitogenesis and pigmentation were also found in the morphants, the neuronal phenotypes observed likely are due to a general developmental delay of embryogenesis. These results indicate that Gas7 is expressed in neuronal cells but is not specifically required for neuronal development in vertebrates.
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Affiliation(s)
- Feng-Chun Hung
- Department of Biochemistry and Molecular Biology, Chang Gung University, Gueishan, Taiwan, Republic of China
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49
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Jasnovidova O, Stefl R. The CTD code of RNA polymerase II: a structural view. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:1-16. [DOI: 10.1002/wrna.1138] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Chithra C, Devaraj H. Purification and characterisation of a 48kDa protein involved in the molting cycle of Penaeus monodon. Food Chem 2012. [DOI: 10.1016/j.foodchem.2012.01.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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