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Fuentes Y, Olguín V, López-Ulloa B, Mendonça D, Ramos H, Abdalla A, Guajardo-Contreras G, Niu M, Rojas-Araya B, Mouland A, López-Lastra M. Heterogeneous nuclear ribonucleoprotein K promotes cap-independent translation initiation of retroviral mRNAs. Nucleic Acids Res 2024; 52:2625-2647. [PMID: 38165048 PMCID: PMC10954487 DOI: 10.1093/nar/gkad1221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 12/07/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024] Open
Abstract
Translation initiation of the human immunodeficiency virus-type 1 (HIV-1) genomic mRNA (vRNA) is cap-dependent or mediated by an internal ribosome entry site (IRES). The HIV-1 IRES requires IRES-transacting factors (ITAFs) for function. In this study, we evaluated the role of the heterogeneous nuclear ribonucleoprotein K (hnRNPK) as a potential ITAF for the HIV-1 IRES. In HIV-1-expressing cells, the depletion of hnRNPK reduced HIV-1 vRNA translation. Furthermore, both the depletion and overexpression of hnRNPK modulated HIV-1 IRES activity. Phosphorylations and protein arginine methyltransferase 1 (PRMT1)-induced asymmetrical dimethylation (aDMA) of hnRNPK strongly impacted the protein's ability to promote the activity of the HIV-1 IRES. We also show that hnRNPK acts as an ITAF for the human T cell lymphotropic virus-type 1 (HTLV-1) IRES, present in the 5'UTR of the viral sense mRNA, but not for the IRES present in the antisense spliced transcript encoding the HTLV-1 basic leucine zipper protein (sHBZ). This study provides evidence for a novel role of the host hnRNPK as an ITAF that stimulates IRES-mediated translation initiation for the retroviruses HIV-1 and HTLV-1.
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Affiliation(s)
- Yazmín Fuentes
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Valeria Olguín
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Brenda López-Ulloa
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Dafne Mendonça
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Hade Ramos
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Ana Luiza Abdalla
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Gabriel Guajardo-Contreras
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Meijuan Niu
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
| | - Barbara Rojas-Araya
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H4A 3J1, Canada
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
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2
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Benoit B, Baillet A, Poüs C. Cytoskeleton and Associated Proteins: Pleiotropic JNK Substrates and Regulators. Int J Mol Sci 2021; 22:8375. [PMID: 34445080 PMCID: PMC8395060 DOI: 10.3390/ijms22168375] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022] Open
Abstract
This review extensively reports data from the literature concerning the complex relationships between the stress-induced c-Jun N-terminal kinases (JNKs) and the four main cytoskeleton elements, which are actin filaments, microtubules, intermediate filaments, and septins. To a lesser extent, we also focused on the two membrane-associated cytoskeletons spectrin and ESCRT-III. We gather the mechanisms controlling cytoskeleton-associated JNK activation and the known cytoskeleton-related substrates directly phosphorylated by JNK. We also point out specific locations of the JNK upstream regulators at cytoskeletal components. We finally compile available techniques and tools that could allow a better characterization of the interplay between the different types of cytoskeleton filaments upon JNK-mediated stress and during development. This overview may bring new important information for applied medical research.
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Affiliation(s)
- Béatrice Benoit
- Université Paris-Saclay, INSERM UMR-S-1193, 5 Rue Jean-Baptiste Clément, 92296 Châtenay-Malabry, France; (A.B.); (C.P.)
| | - Anita Baillet
- Université Paris-Saclay, INSERM UMR-S-1193, 5 Rue Jean-Baptiste Clément, 92296 Châtenay-Malabry, France; (A.B.); (C.P.)
| | - Christian Poüs
- Université Paris-Saclay, INSERM UMR-S-1193, 5 Rue Jean-Baptiste Clément, 92296 Châtenay-Malabry, France; (A.B.); (C.P.)
- Biochimie-Hormonologie, AP-HP Université Paris-Saclay, Site Antoine Béclère, 157 Rue de la Porte de Trivaux, 92141 Clamart, France
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3
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Velázquez-Cruz A, Baños-Jaime B, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Post-translational Control of RNA-Binding Proteins and Disease-Related Dysregulation. Front Mol Biosci 2021; 8:658852. [PMID: 33987205 PMCID: PMC8111222 DOI: 10.3389/fmolb.2021.658852] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Cell signaling mechanisms modulate gene expression in response to internal and external stimuli. Cellular adaptation requires a precise and coordinated regulation of the transcription and translation processes. The post-transcriptional control of mRNA metabolism is mediated by the so-called RNA-binding proteins (RBPs), which assemble with specific transcripts forming messenger ribonucleoprotein particles of highly dynamic composition. RBPs constitute a class of trans-acting regulatory proteins with affinity for certain consensus elements present in mRNA molecules. However, these regulators are subjected to post-translational modifications (PTMs) that constantly adjust their activity to maintain cell homeostasis. PTMs can dramatically change the subcellular localization, the binding affinity for RNA and protein partners, and the turnover rate of RBPs. Moreover, the ability of many RBPs to undergo phase transition and/or their recruitment to previously formed membrane-less organelles, such as stress granules, is also regulated by specific PTMs. Interestingly, the dysregulation of PTMs in RBPs has been associated with the pathophysiology of many different diseases. Abnormal PTM patterns can lead to the distortion of the physiological role of RBPs due to mislocalization, loss or gain of function, and/or accelerated or disrupted degradation. This Mini Review offers a broad overview of the post-translational regulation of selected RBPs and the involvement of their dysregulation in neurodegenerative disorders, cancer and other pathologies.
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Affiliation(s)
- Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Blanca Baños-Jaime
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
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Du JX, Zhu GQ, Cai JL, Wang B, Luo YH, Chen C, Cai CZ, Zhang SJ, Zhou J, Fan J, Zhu W, Dai Z. Splicing factors: Insights into their regulatory network in alternative splicing in cancer. Cancer Lett 2020; 501:83-104. [PMID: 33309781 DOI: 10.1016/j.canlet.2020.11.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022]
Abstract
More than 95% of all human genes are alternatively spliced after transcription, which enriches the diversity of proteins and regulates transcript and/or protein levels. The splicing isoforms produced from the same gene can manifest distinctly, even exerting opposite effects. Mounting evidence indicates that the alternative splicing (AS) mechanism is ubiquitous in various cancers and drives the generation and maintenance of various hallmarks of cancer, such as enhanced proliferation, inhibited apoptosis, invasion and metastasis, and angiogenesis. Splicing factors (SFs) play pivotal roles in the recognition of splice sites and the assembly of spliceosomes during AS. In this review, we mainly discuss the similarities and differences of SF domains, the details of SF function in AS, the effect of SF-driven pathological AS on different hallmarks of cancer, and the main drivers of SF expression level and subcellular localization. In addition, we briefly introduce the application prospects of targeted therapeutic strategies, including small-molecule inhibitors, siRNAs and splice-switching oligonucleotides (SSOs), from three perspectives (drivers, SFs and pathological AS). Finally, we share our insights into the potential direction of research on SF-centric AS-related regulatory networks.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
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5
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Xu Y, Wu W, Han Q, Wang Y, Li C, Zhang P, Xu H. Post-translational modification control of RNA-binding protein hnRNPK function. Open Biol 2020; 9:180239. [PMID: 30836866 PMCID: PMC6451366 DOI: 10.1098/rsob.180239] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNPK), a ubiquitously occurring RNA-binding protein (RBP), can interact with numerous nucleic acids and various proteins and is involved in a number of cellular functions including transcription, translation, splicing, chromatin remodelling, etc. Through its abundant biological functions, hnRNPK has been implicated in cellular events including proliferation, differentiation, apoptosis, DNA damage repair and the stress and immune responses. Thus, it is critical to understand the mechanism of hnRNPK regulation and its downstream effects on cancer and other diseases. A number of recent studies have highlighted that several post-translational modifications (PTMs) possibly play an important role in modulating hnRNPK function. Phosphorylation is the most widely occurring PTM in hnRNPK. For example, in vivo analyses of sites such as S116 and S284 illustrate the purpose of PTM of hnRNPK in altering its subcellular localization and its ability to bind target nucleic acids or proteins. Other PTMs such as methylation, ubiquitination, sumoylation, glycosylation and proteolytic cleavage are increasingly implicated in the regulation of DNA repair, cellular stresses and tumour growth. In this review, we describe the PTMs that impact upon hnRNPK function on gene expression programmes and different disease states. This knowledge is key in allowing us to better understand the mechanism of hnRNPK regulation.
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Affiliation(s)
- Yongjie Xu
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Wei Wu
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Qiu Han
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Yaling Wang
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Cencen Li
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Pengpeng Zhang
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Haixia Xu
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
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6
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Wang Z, Qiu H, He J, Liu L, Xue W, Fox A, Tickner J, Xu J. The emerging roles of hnRNPK. J Cell Physiol 2019; 235:1995-2008. [PMID: 31538344 DOI: 10.1002/jcp.29186] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an DNA/RNA-binding protein and regulates a wide range of biological processes and disease pathogenesis. It contains 3 K-homologous (KH) domains, which are conserved in other RNA-binding proteins, mediate nucleic acid binding activity, and function as an enhancer or repressor of gene transcription. Phosphorylation of the protein alters its regulatory function, which also enables the protein to serve as a docking platform for the signal transduction proteins. In terms of the function of hnRNPK, it is central to many cellular events, including long noncoding RNA (lncRNA) regulation, cancer development and bone homoeostasis. Many studies have identified hnRNPK as an oncogene, where it is overexpressed in cancer tissues compared with the nonneoplastic tissues and its expression level is related to the prognosis of different types of host malignancies. However, hnRNPK has also been identified as a tumour suppressor, as it is important for the activation of the p53/p21 pathway. Recently, the protein is also found to be exclusively related to the regulation of paraspeckles and lncRNAs such as Neat1, Lncenc1 and Xist. Interestingly, hnRNPK has been found to associate with the Kabuki-like syndrome and Au-Kline syndrome with prominent skeletal abnormalities. In vitro study revealed that the hnRNPK protein is essential for the formation of osteoclast, in line with its importance in the skeletal system.
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Affiliation(s)
- Ziyi Wang
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Heng Qiu
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jianbo He
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Langxia Liu
- Key laboratory of functional protein research of Guangdong higher education institutes, Institute of life and health engineering, Jinan University, Guangzhou, China
| | - Wei Xue
- Department of Biomedical Engineering, Jinan University, Guangzhou, China
| | - Archa Fox
- School of Human Sciences and Molecular Sciences, The University of Western Australia and Harry Perkins Institute of Medical Research, Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Jennifer Tickner
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jiake Xu
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
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7
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Shah K, Kim H. The significant others: Global search for direct kinase substrates using chemical approaches. IUBMB Life 2019; 71:721-737. [PMID: 30801966 DOI: 10.1002/iub.2023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/27/2019] [Indexed: 12/16/2022]
Abstract
Protein kinases function as key signaling hubs in the intricate network of biochemical signaling processes in the living cell. More than two-thirds of the human proteome is estimated to be phosphorylated at ~960,000 phosphosites, which makes it challenging to identify the direct contribution of any desired kinase in generating this phosphoproteome. In this review, we discuss some of the methods that have been developed over the years for global identification of kinase substrates. The methods are essentially categorized into two classes, namely, (i) direct tagging of kinase substrates and (ii) indirect phosphoproteomics-based approaches. We discuss the advantages and limitations entailed to each of the method introduced, with a special emphasis on the analog-sensitive (as) kinase approach method. © 2019 IUBMB Life, 71(6):721-737, 2019.
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Affiliation(s)
- Kavita Shah
- Department of Chemistry and Purdue University Center for Cancer Research, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Hyunjin Kim
- Department of Chemistry and Purdue University Center for Cancer Research, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
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8
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Capaia M, Granata I, Guarracino M, Petretto A, Inglese E, Cattrini C, Ferrari N, Boccardo F, Barboro P. A hnRNP K⁻AR-Related Signature Reflects Progression toward Castration-Resistant Prostate Cancer. Int J Mol Sci 2018; 19:ijms19071920. [PMID: 29966326 PMCID: PMC6073607 DOI: 10.3390/ijms19071920] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 06/27/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022] Open
Abstract
The major challenge in castration-resistant prostate cancer (CRPC) remains the ability to predict the clinical responses to improve patient selection for appropriate treatments. The finding that androgen deprivation therapy (ADT) induces alterations in the androgen receptor (AR) transcriptional program by AR coregulators activity in a context-dependent manner, offers the opportunity for identifying signatures discriminating different clinical states of prostate cancer (PCa) progression. Gel electrophoretic analyses combined with western blot showed that, in androgen-dependent PCa and CRPC in vitro models, the subcellular distribution of spliced and serine-phosphorylated heterogeneous nuclear ribonucleoprotein K (hnRNP K) isoforms can be associated with different AR activities. Using mass spectrometry and bioinformatic analyses, we showed that the protein sets of androgen-dependent (LNCaP) and ADT-resistant cell lines (PDB and MDB) co-immunoprecipitated with hnRNP K varied depending on the cell type, unravelling a dynamic relationship between hnRNP K and AR during PCa progression to CRPC. By comparing the interactome of LNCaP, PDB, and MDB cell lines, we identified 51 proteins differentially interacting with hnRNP K, among which KLK3, SORD, SPON2, IMPDH2, ACTN4, ATP1B1, HSPB1, and KHDRBS1 were associated with AR and differentially expressed in normal and tumor human prostate tissues. This hnRNP K–AR-related signature, associated with androgen sensitivity and PCa progression, may help clinicians to better manage patients with CRPC.
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Affiliation(s)
- Matteo Capaia
- Academic Unit of Medical Oncology, Ospedale Policlinico San Martino-IRCCS, L.go R. Benzi 10, 16132 Genova, Italy.
| | - Ilaria Granata
- Institute for High Performance Computing and Networking (ICAR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy.
| | - Mario Guarracino
- Institute for High Performance Computing and Networking (ICAR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy.
| | - Andrea Petretto
- Core Facilities-Proteomics Laboratory, Giannina Gaslini Institute, L.go G. Gaslini 5, 16147 Genova, Italy.
| | - Elvira Inglese
- Core Facilities-Proteomics Laboratory, Giannina Gaslini Institute, L.go G. Gaslini 5, 16147 Genova, Italy.
| | - Carlo Cattrini
- Academic Unit of Medical Oncology, Ospedale Policlinico San Martino-IRCCS, L.go R. Benzi 10, 16132 Genova, Italy.
- Department of Internal Medicine and Medical Specialties, School of Medicine, University of Genova, L.go R. Benzi 10, 16132 Genova, Italy.
| | - Nicoletta Ferrari
- Molecular Oncology and Angiogenesis, Ospedale Policlinico San Martino-IRCCS, L.go R. Benzi 10, 16132 Genova, Italy.
| | - Francesco Boccardo
- Academic Unit of Medical Oncology, Ospedale Policlinico San Martino-IRCCS, L.go R. Benzi 10, 16132 Genova, Italy.
- Department of Internal Medicine and Medical Specialties, School of Medicine, University of Genova, L.go R. Benzi 10, 16132 Genova, Italy.
| | - Paola Barboro
- Academic Unit of Medical Oncology, Ospedale Policlinico San Martino-IRCCS, L.go R. Benzi 10, 16132 Genova, Italy.
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9
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Enari M, Matsushima-Hibiya Y, Miyazaki M, Otomo R. Studies of ATM Kinase Activity Using Engineered ATM Sensitive to ATP Analogues (ATM-AS). Methods Mol Biol 2018; 1599:145-156. [PMID: 28477117 DOI: 10.1007/978-1-4939-6955-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ataxia-telangiectasia mutated (ATM) protein is a member of the phosphatidylinositol 3-phosphate kinase (PI3-K)-related protein kinase (PIKK) family and is implicated in the initiation of signaling pathways following DNA double strand breaks (DSBs) elicited by exposure to ionizing irradiation (IR) or radiomimetic compounds. Loss of function of the ATM gene product results in the human genetic disorder ataxia-telangiectasia (A-T) characterized by neurodegeneration, immunodeficiency, genomic instability, and cancer predisposition. In response to DSBs, ATM is activated and phosphorylates Ser/Thr-Gln (S/T-Q) sequences on numerous proteins participating in DNA-damage responses. Among these proteins, phosphorylation of the tumor suppressor p53 at Ser15 is known as a target for ATM, which leads to the dissociation of MDM2, an E3 ubiquitin ligase, from p53 to prevent MDM2-dependent p53 degradation. Ser46 on p53 is phosphorylated in response to DSBs and contributes to the preferential transactivation of pro-apoptotic genes, such as p53AIP1, Noxa, and PUMA, to prevent tumor formation. Our group have shown that not only ATM preferentially phosphorylates S/T-Q sequences, but also Ser46, which is a noncanonical site with an S-P sequence for ATM. Ser46 on p53 is directly phosphorylated by ATM in a p53 conformation-dependent manner using the ATP analogue-accepting ATM mutant (ATM-AS) system. This protocol summarizes an approach to identify direct numerous targets for ATM kinase and is used to elucidate ATM signaling pathways in the DNA damage responses.
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Affiliation(s)
- Masato Enari
- Division of Refractory and Advanced Cancer, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Yuko Matsushima-Hibiya
- Division of Refractory and Advanced Cancer, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Makoto Miyazaki
- Division of Refractory and Advanced Cancer, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Medical Genome Sciences, Laboratory of Tumor Cell Biology, Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Ryo Otomo
- Division of Refractory and Advanced Cancer, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
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Kim HJ, Lee JJ, Cho JH, Jeong J, Park AY, Kang W, Lee KJ. Heterogeneous nuclear ribonucleoprotein K inhibits heat shock-induced transcriptional activity of heat shock factor 1. J Biol Chem 2017; 292:12801-12812. [PMID: 28592492 DOI: 10.1074/jbc.m117.774992] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 06/06/2017] [Indexed: 12/22/2022] Open
Abstract
When cells are exposed to heat shock and various other stresses, heat shock factor 1 (HSF1) is activated, and the heat shock response (HSR) is elicited. To better understand the molecular regulation of the HSR, we used 2D-PAGE-based proteome analysis to screen for heat shock-induced post-translationally modified cellular proteins. Our analysis revealed that two protein spots typically present on 2D-PAGE gels and containing heterogeneous nuclear ribonucleoprotein K (hnRNP K) with trioxidized Cys132 disappeared after the heat shock treatment and reappeared during recovery, but the total amount of hnRNP K protein remained unchanged. We next tested whether hnRNP K plays a role in HSR by regulating HSF1 and found that hnRNP K inhibits HSF1 activity, resulting in reduced expression of hsp70 and hsp27 mRNAs. hnRNP K also reduced binding affinity of HSF1 to the heat shock element by directly interacting with HSF1 but did not affect HSF1 phosphorylation-dependent activation or nuclear localization. hnRNP K lost its ability to induce these effects when its Cys132 was substituted with Ser, Asp, or Glu. These findings suggest that hnRNP K inhibits transcriptional activity of HSF1 by inhibiting its binding to heat shock element and that the oxidation status of Cys132 in hnRNP K is critical for this inhibition.
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Affiliation(s)
- Hee-Jung Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea
| | - Jae-Jin Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea
| | - Jin-Hwan Cho
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea
| | - Jaeho Jeong
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea
| | - A Young Park
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea
| | - Wonmo Kang
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea.
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11
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Cooke M, Magimaidas A, Casado-Medrano V, Kazanietz MG. Protein kinase C in cancer: The top five unanswered questions. Mol Carcinog 2017; 56:1531-1542. [PMID: 28112438 DOI: 10.1002/mc.22617] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/04/2017] [Accepted: 01/20/2017] [Indexed: 12/29/2022]
Abstract
Few kinases have been studied as extensively as protein kinase C (PKC), particularly in the context of cancer. As major cellular targets for the phorbol ester tumor promoters and diacylglycerol (DAG), a second messenger generated by stimulation of membrane receptors, PKC isozymes play major roles in the control of signaling pathways associated with proliferation, migration, invasion, tumorigenesis, and metastasis. However, despite decades of research, fundamental questions remain to be answered or are the subject of intense controversy. Primary among these unresolved issues are the role of PKC isozymes as either tumor promoter or tumor suppressor kinases and the incomplete understanding on isozyme-specific substrates and effectors. The involvement of PKC isozymes in cancer progression needs to be reassessed in the context of specific oncogenic and tumor suppressing alterations. In addition, there are still major hurdles in addressing isozyme-specific function due to the limited specificity of most pharmacological PKC modulators and the lack of validated predictive biomarkers for response, which impacts the translation of these agents to the clinic. In this review we focus on key controversial issues and upcoming challenges, with the expectation that understanding the intricacies of PKC function will help fulfill the yet unsuccessful promise of targeting PKCs for cancer therapeutics.
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Affiliation(s)
- Mariana Cooke
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew Magimaidas
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Victoria Casado-Medrano
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Marcelo G Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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12
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Romano V, de Beer TAP, Schwede T. A computational protocol to evaluate the effects of protein mutants in the kinase gatekeeper position on the binding of ATP substrate analogues. BMC Res Notes 2017; 10:104. [PMID: 28219448 PMCID: PMC5319021 DOI: 10.1186/s13104-017-2428-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/15/2017] [Indexed: 11/11/2022] Open
Abstract
Background The determination of specific kinase substrates in vivo is challenging due to the large number of protein kinases in cells, their substrate specificity overlap, and the lack of highly specific inhibitors. In the late 90s, Shokat and coworkers developed a protein engineering-based method addressing the question of identification of substrates of protein kinases. The approach was based on the mutagenesis of the gatekeeper residue within the binding site of a protein kinase to change the co-substrate specificity from ATP to ATP analogues. One of the challenges in applying this method to other kinase systems is to identify the optimal combination of mutation in the enzyme and chemical derivative such that the ATP analogue acts as substrate for the engineered, but not the native kinase enzyme. In this study, we developed a computational protocol for estimating the effect of mutations at the gatekeeper position on the accessibility of ATP analogues within the binding site of engineered kinases. Results We tested the protocol on a dataset of tyrosine and serine/threonine protein kinases from the scientific literature where Shokat’s method was applied and experimental data were available. Our protocol correctly identified gatekeeper residues as the positions to mutate within the binding site of the studied kinase enzymes. Furthermore, the approach well reproduced the experimental data available in literature. Conclusions We have presented a computational protocol that scores how different mutations at the gatekeeper position influence the accommodation of various ATP analogues within the binding site of protein kinases. We have assessed our approach on protein kinases from the scientific literature and have verified the ability of the approach to well reproduce the available experimental data and identify suitable combinations of engineered kinases and ATP analogues.
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Affiliation(s)
- Valentina Romano
- Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Tjaart A P de Beer
- Biozentrum, University of Basel, Basel, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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13
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Spangler SM, Bruchas MR. Optogenetic approaches for dissecting neuromodulation and GPCR signaling in neural circuits. Curr Opin Pharmacol 2017; 32:56-70. [PMID: 27875804 PMCID: PMC5395328 DOI: 10.1016/j.coph.2016.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/29/2016] [Accepted: 11/02/2016] [Indexed: 12/19/2022]
Abstract
Optogenetics has revolutionized neuroscience by providing means to control cell signaling with spatiotemporal control in discrete cell types. In this review, we summarize four major classes of optical tools to manipulate neuromodulatory GPCR signaling: opsins (including engineered chimeric receptors); photoactivatable proteins; photopharmacology through caging-photoswitchable molecules; fluorescent protein based reporters and biosensors. Additionally, we highlight technologies to utilize these tools in vitro and in vivo, including Cre dependent viral vector expression and two-photon microscopy. These emerging techniques targeting specific members of the GPCR signaling pathway offer an expansive base for investigating GPCR signaling in behavior and disease states, in addition to paving a path to potential therapeutic developments.
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Affiliation(s)
- Skylar M Spangler
- Department of Anesthesiology, Basic Research Division, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael R Bruchas
- Department of Anesthesiology, Basic Research Division, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA.
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14
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Reduced Activity of Mutant Calcium-Dependent Protein Kinase 1 Is Compensated in Plasmodium falciparum through the Action of Protein Kinase G. mBio 2016; 7:mBio.02011-16. [PMID: 27923926 PMCID: PMC5142624 DOI: 10.1128/mbio.02011-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We used a sensitization approach that involves replacement of the gatekeeper residue in a protein kinase with one with a different side chain. The activity of the enzyme with a bulky gatekeeper residue, such as methionine, cannot be inhibited using bumped kinase inhibitors (BKIs). Here, we have used this approach to study Plasmodium falciparum calcium-dependent protein kinase 1 (PfCDPK1). The methionine gatekeeper substitution, T145M, although it led to a 47% reduction in transphosphorylation, was successfully introduced into the CDPK1 locus using clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9. As methionine is a bulky residue, BKI 1294 had a 10-fold-greater effect in vitro on the wild-type enzyme than on the methionine mutant. However, in contrast to in vitro data with recombinant enzymes, BKI 1294 had a slightly greater inhibition of the growth of CDPK1 T145M parasites than the wild type. Moreover, the CDPK1 T145M parasites were more sensitive to the action of compound 2 (C2), a specific inhibitor of protein kinase G (PKG). These results suggest that a reduction in the activity of CDPK1 due to methionine substitution at the gatekeeper position is compensated through the direct action of PKG or of another kinase under the regulation of PKG. The transcript levels of CDPK5 and CDPK6 were significantly upregulated in the CDPK1 T145M parasites. The increase in CDPK6 or some other kinase may compensate for decrease in CDPK1 activity during invasion. This study suggests that targeting two kinases may be more effective in chemotherapy to treat malaria so as not to select for mutations in one of the enzymes. Protein kinases of Plasmodium falciparum are being actively pursued as drug targets to treat malaria. However, compensatory mechanisms may reverse the drug activity against a kinase. In this study, we show that replacement of the wild-type threonine gatekeeper residue with methionine reduces the transphosphorylation activity of CDPK1. Mutant parasites with methionine gatekeeper residue compensate the reduced activity of CDPK1 through the action of PKG possibly by upregulation of CDPK6 or some other kinase. This study highlights that targeting one enzyme may lead to changes in transcript expression of other kinases that compensate for its function and may select for mutants that are less dependent on the target enzyme activity. Thus, inhibiting two kinases is a better strategy to protect the antimalarial activity of each, similar to artemisinin combination therapy or malarone (atovaquone and proguanil).
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15
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JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships. Microbiol Mol Biol Rev 2016; 80:793-835. [PMID: 27466283 DOI: 10.1128/mmbr.00043-14] [Citation(s) in RCA: 321] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The c-Jun N-terminal kinases (JNKs), as members of the mitogen-activated protein kinase (MAPK) family, mediate eukaryotic cell responses to a wide range of abiotic and biotic stress insults. JNKs also regulate important physiological processes, including neuronal functions, immunological actions, and embryonic development, via their impact on gene expression, cytoskeletal protein dynamics, and cell death/survival pathways. Although the JNK pathway has been under study for >20 years, its complexity is still perplexing, with multiple protein partners of JNKs underlying the diversity of actions. Here we review the current knowledge of JNK structure and isoforms as well as the partnerships of JNKs with a range of intracellular proteins. Many of these proteins are direct substrates of the JNKs. We analyzed almost 100 of these target proteins in detail within a framework of their classification based on their regulation by JNKs. Examples of these JNK substrates include a diverse assortment of nuclear transcription factors (Jun, ATF2, Myc, Elk1), cytoplasmic proteins involved in cytoskeleton regulation (DCX, Tau, WDR62) or vesicular transport (JIP1, JIP3), cell membrane receptors (BMPR2), and mitochondrial proteins (Mcl1, Bim). In addition, because upstream signaling components impact JNK activity, we critically assessed the involvement of signaling scaffolds and the roles of feedback mechanisms in the JNK pathway. Despite a clarification of many regulatory events in JNK-dependent signaling during the past decade, many other structural and mechanistic insights are just beginning to be revealed. These advances open new opportunities to understand the role of JNK signaling in diverse physiological and pathophysiological states.
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16
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Hardie DG, Schaffer BE, Brunet A. AMPK: An Energy-Sensing Pathway with Multiple Inputs and Outputs. Trends Cell Biol 2016; 26:190-201. [PMID: 26616193 PMCID: PMC5881568 DOI: 10.1016/j.tcb.2015.10.013] [Citation(s) in RCA: 634] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/15/2015] [Accepted: 10/22/2015] [Indexed: 12/20/2022]
Abstract
AMP-activated protein kinase (AMPK) is a key regulator of energy balance expressed ubiquitously in eukaryotic cells. Here we review the canonical adenine nucleotide-dependent mechanism that activates AMPK when cellular energy status is compromised, as well as other, noncanonical activation mechanisms. Once activated, AMPK acts to restore energy homeostasis by promoting catabolic pathways, resulting in ATP generation, and inhibiting anabolic pathways that consume ATP. We also review the various hypothesis-driven and unbiased approaches that have been used to identify AMPK substrates and have revealed substrates involved in both metabolic and non-metabolic processes. We particularly focus on methods for identifying the AMPK target recognition motif and how it can be used to predict new substrates.
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Affiliation(s)
- D Grahame Hardie
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - Bethany E Schaffer
- Department of Genetics and the Cancer Biology Program, Stanford University, 300 Pasteur Drive, Stanford, CA, USA
| | - Anne Brunet
- Department of Genetics and the Cancer Biology Program, Stanford University, 300 Pasteur Drive, Stanford, CA, USA
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Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation. Genes Dev 2016; 29:2054-66. [PMID: 26443849 PMCID: PMC4604346 DOI: 10.1101/gad.267245.115] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this study, Martinez et al. find a positive feedback loop in the JNK signaling pathway through the alternative splicing of MKK7, identify the RNA-binding protein CELF2 as a major regulator of MKK7 splicing, and show that ∼25% of T-cell receptor-mediated alternative splicing events are dependent on JNK signaling. This study provides insight into a novel paradigm for the reciprocal interplay of signaling and splicing. Alternative splicing is prevalent among genes encoding signaling molecules; however, the functional consequence of differential isoform expression remains largely unknown. Here we demonstrate that, in response to T-cell activation, the Jun kinase (JNK) kinase MAP kinase kinase 7 (MKK7) is alternatively spliced to favor an isoform that lacks exon 2. This isoform restores a JNK-docking site within MKK7 that is disrupted in the larger isoform. Consistently, we show that skipping of MKK7 exon 2 enhances JNK pathway activity, as indicated by c-Jun phosphorylation and up-regulation of TNF-α. Moreover, this splicing event is itself dependent on JNK signaling. Thus, MKK7 alternative splicing represents a positive feedback loop through which JNK promotes its own signaling. We further show that repression of MKK7 exon 2 is dependent on the presence of flanking sequences and the JNK-induced expression of the RNA-binding protein CELF2, which binds to these regulatory elements. Finally, we found that ∼25% of T-cell receptor-mediated alternative splicing events are dependent on JNK signaling. Strikingly, these JNK-dependent events are also significantly enriched for responsiveness to CELF2. Together, our data demonstrate a widespread role for the JNK–CELF2 axis in controlling splicing during T-cell activation, including a specific role in propagating JNK signaling.
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18
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Hutchins EJ, Belrose JL, Szaro BG. Phosphorylation of heterogeneous nuclear ribonucleoprotein K at an extracellular signal-regulated kinase phosphorylation site promotes neurofilament-medium protein expression and axon outgrowth in Xenopus. Neurosci Lett 2015; 607:59-65. [DOI: 10.1016/j.neulet.2015.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/27/2015] [Accepted: 09/22/2015] [Indexed: 12/18/2022]
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19
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Tiedje C, Holtmann H, Gaestel M. The role of mammalian MAPK signaling in regulation of cytokine mRNA stability and translation. J Interferon Cytokine Res 2015; 34:220-32. [PMID: 24697200 DOI: 10.1089/jir.2013.0146] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Extracellular-regulated kinases and p38 mitogen-activated protein kinases are activated in innate (and adaptive) immunity and signal via different routes to alter the stability and translation of various cytokine mRNAs, enabling immune cells to respond promptly. This regulation involves mRNA elements, such as AU-rich motifs, and mRNA-binding proteins, such as tristetraprolin (TTP), HuR, and hnRNPK-homology (KH) type splicing regulatory protein (KSRP). Signal-dependent phosphorylation of mRNA-binding proteins often alters their subcellular localization or RNA-binding affinity. Furthermore, it could lead to an altered interaction with other mRNA-binding proteins and altered scaffolding properties for mRNA-modifying enzymes, such as deadenylases, polyadenylases, decapping enzymes, poly(A) binding proteins, exo- or endonucleases, and proteins of the exosome machinery. In many cases, this results in unstable mRNAs being stabilized, with their translational arrest being released and cytokine production being stimulated. Hence, components of these mechanisms are potential targets for the modulation of the inflammatory response.
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Affiliation(s)
- Christopher Tiedje
- Institute of Physiological Chemistry, Hannover Medical School , Hannover, Germany
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20
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Weng YC, Wang G, Messing RO, Chou WH. Identification of lipocalin-2 as a PKCδ phosphorylation substrate in neutrophils. J Biomed Sci 2015; 22:21. [PMID: 25890235 PMCID: PMC4396066 DOI: 10.1186/s12929-015-0129-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/13/2015] [Indexed: 01/05/2023] Open
Abstract
Background PKCδ expressed in neutrophils is implicated in promoting reperfusion injury after ischemic stroke. To understand the molecular and cellular actions of PKCδ, we employed a chemical-genetics approach to identify PKCδ substrates in neutrophils. Results We recently generated knock-in mice endogenously expressing analog-specific PKCδ (AS-PKCδ) that can utilize ATP analogs as phosphate donors. Using neutrophils isolated from the knock-in mice, we identified several PKCδ substrates, one of which was lipocalin-2 (LCN2), which is an iron-binding protein that can trigger apoptosis by reducing intracellular iron concentrations. We found that PKCδ phosphorylated LCN2 at T115 and this phosphorylation was reduced in Prkcd−/− mice. PKCδ colocalized with LCN2 in resting and stimulated neutrophils. LCN2 release from neutrophils after cerebral ischemia was reduced in PKCδ null mice. Conclusions These findings suggest that PKCδ phosphorylates LCN2 and mediates its release from neutrophils during ischemia-reperfusion injury.
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Affiliation(s)
- Yi-Chinn Weng
- Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, OH, 44224, USA.
| | - Guona Wang
- Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, OH, 44224, USA.
| | - Robert O Messing
- Department of Neurology, University of California, San Francisco, CA, 94608, USA. .,Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Wen-Hai Chou
- Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, OH, 44224, USA. .,Department of Neurology, University of California, San Francisco, CA, 94608, USA.
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Kumar V, Weng YC, Geldenhuys WJ, Wang D, Han X, Messing RO, Chou WH. Generation and characterization of ATP analog-specific protein kinase Cδ. J Biol Chem 2014; 290:1936-51. [PMID: 25505183 DOI: 10.1074/jbc.m114.598698] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To better study the role of PKCδ in normal function and disease, we developed an ATP analog-specific (AS) PKCδ that is sensitive to specific kinase inhibitors and can be used to identify PKCδ substrates. AS PKCδ showed nearly 200 times higher affinity (Km) and 150 times higher efficiency (kcat/Km) than wild type (WT) PKCδ toward N(6)-(benzyl)-ATP. AS PKCδ was uniquely inhibited by 1-(tert-butyl)-3-(1-naphthyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine (1NA-PP1) and 1-(tert-butyl)-3-(2-methylbenzyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine (2MB-PP1) but not by other 4-amino-5-(4-methylphenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP1) analogs tested, whereas WT PKCδ was insensitive to all PP1 analogs. To understand the mechanisms for specificity and affinity of these analogs, we created in silico WT and AS PKCδ homology models based on the crystal structure of PKCι. N(6)-(Benzyl)-ATP and ATP showed similar positioning within the purine binding pocket of AS PKCδ, whereas N(6)-(benzyl)-ATP was displaced from the pocket of WT PKCδ and was unable to interact with the glycine-rich loop that is required for phosphoryl transfer. The adenine rings of 1NA-PP1 and 2MB-PP1 matched the adenine ring of ATP when docked in AS PKCδ, and this interaction prevented the potential interaction of ATP with Lys-378, Glu-428, Leu-430, and Phe-633 residues. 1NA-PP1 failed to effectively dock within WT PKCδ. Other PP1 analogs failed to interact with either AS PKCδ or WT PKCδ. These results provide a structural basis for the ability of AS PKCδ to efficiently and specifically utilize N(6)-(benzyl)-ATP as a phosphate donor and for its selective inhibition by 1NA-PP1 and 2MB-PP1. Such homology modeling could prove useful in designing molecules to target PKCδ and other kinases to understand their function in cell signaling and to identify unique substrates.
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Affiliation(s)
- Varun Kumar
- From the Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, Ohio 44242
| | - Yi-Chinn Weng
- From the Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, Ohio 44242
| | - Werner J Geldenhuys
- the Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Dan Wang
- the Ernest Gallo Clinic and Research Center, Department of Neurology, University of California, San Francisco, Emeryville, California 94608, and
| | - Xiqian Han
- From the Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, Ohio 44242
| | - Robert O Messing
- the Ernest Gallo Clinic and Research Center, Department of Neurology, University of California, San Francisco, Emeryville, California 94608, and the Division of Pharmacology and Toxicology, College of Pharmacy, University of Texas, Austin, Texas 78712
| | - Wen-Hai Chou
- From the Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, the Ernest Gallo Clinic and Research Center, Department of Neurology, University of California, San Francisco, Emeryville, California 94608, and
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Moujalled D, James JL, Yang S, Zhang K, Duncan C, Moujalled DM, Parker SJ, Caragounis A, Lidgerwood G, Turner BJ, Atkin JD, Grubman A, Liddell JR, Proepper C, Boeckers TM, Kanninen KM, Blair I, Crouch PJ, White AR. Phosphorylation of hnRNP K by cyclin-dependent kinase 2 controls cytosolic accumulation of TDP-43. Hum Mol Genet 2014; 24:1655-69. [PMID: 25410660 DOI: 10.1093/hmg/ddu578] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cytosolic accumulation of TAR DNA binding protein 43 (TDP-43) is a major neuropathological feature of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). However, the mechanisms involved in TDP-43 accumulation remain largely unknown. Previously, we reported that inhibitors of cyclin-dependent kinases (CDKs) prevented cytosolic stress granule accumulation of TDP-43, correlating with depletion of heterogeneous ribonucleoprotein (hnRNP) K from stress granules. In the present study, we further investigated the relationship between TDP-43 and hnRNP K and their control by CDKs. Inhibition of CDK2 abrogated the accumulation of TDP-43 into stress granules. Phosphorylated CDK2 co-localized with accumulated TDP-43 and phosphorylated hnRNP K in stress granules. Inhibition of CDK2 phosphorylation blocked phosphorylation of hnRNP K, preventing its incorporation into stress granules. Due to interaction between hnRNP K with TDP-43, the loss of hnRNP K from stress granules prevented accumulation of TDP-43. Mutation of Ser216 and Ser284 phosphorylation sites on hnRNP K inhibited hnRNP K- and TDP-43-positive stress granule formation in transfected cells. The interaction between hnRNP K and TDP-43 was further confirmed by the loss of TDP-43 accumulation following siRNA-mediated inhibition of hnRNP K expression. A substantial decrease of CDK2 and hnRNP K expression in spinal cord motor neurons in ALS patients demonstrates a potential key role for these proteins in ALS and TDP-43 accumulation, indicating that further investigation of the association between hnRNP K and TDP-43 is warranted. Understanding how kinase activity modulates TDP-43 accumulation may provide new pharmacological targets for disease intervention.
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Affiliation(s)
| | | | - Shu Yang
- The Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Katharine Zhang
- The Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | | | - Donia M Moujalled
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Melbourne, VIC 3052, Australia
| | | | | | | | - Bradley J Turner
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC 3010, Australia
| | - Julie D Atkin
- The Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | | | | | - Christian Proepper
- Anatomy and Cell Biology, University of Ulm, Albert-Einstein Allee 11, 89081 Ulm, Germany
| | - Tobias M Boeckers
- Anatomy and Cell Biology, University of Ulm, Albert-Einstein Allee 11, 89081 Ulm, Germany
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, Laboratory of Molecular Brain Research, University of Eastern Finland, Kuopio, Finland
| | - Ian Blair
- The Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
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Barboro P, Ferrari N, Balbi C. Emerging roles of heterogeneous nuclear ribonucleoprotein K (hnRNP K) in cancer progression. Cancer Lett 2014; 352:152-9. [DOI: 10.1016/j.canlet.2014.06.019] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/26/2014] [Accepted: 06/29/2014] [Indexed: 12/18/2022]
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Moujalled D, White AR. Heterogeneous nuclear ribonucleoproteins in amyotrophic
lateral sclerosis: what do we know? FUTURE NEUROLOGY 2014. [DOI: 10.2217/fnl.14.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ABSTRACT: Amyotrophic lateral sclerosis (ALS) is a fatal adult-onset motor neuron disease that results from the progressive loss of motor neurons in the brainstem and spinal cord, and of upper motor neurons in the motor cortex. TDP-43 was the first protein identified in ALS. It is present in cytoplasmic inclusions in motor neurons of affected patient brains and spinal cords, a hallmark feature of this disease. Successive studies have identified missense mutations in TARDBP, and, to date, more than 40 mutations have been identified. Recent studies have indicated that altered RNA metabolism is a key feature of ALS. This article reviews an emerging role of heterogeneous nuclear ribonucleoproteins driving disease pathogenesis that include TDP-43, FUS, hnRNPA1, hnRNPA2/B1 and hnRNPA3. Determining the molecular pathways involved may provide a promising prospect for heterogeneous nuclear ribonucleoproteins being potential biomarkers in ALS in order to develop therapeutic strategies for mitigating this disease, for which there is currently no cure.
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Affiliation(s)
- Diane Moujalled
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Anthony R White
- Department of Pathology, The University of Melbourne, Victoria, Australia
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Couzens AL, Gill RM, Scheid MP. Characterization of a modified ROCK2 protein that allows use of N6-ATP analogs for the identification of novel substrates. BMC Biotechnol 2014; 14:2. [PMID: 24405853 PMCID: PMC3913329 DOI: 10.1186/1472-6750-14-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 01/07/2014] [Indexed: 12/18/2022] Open
Abstract
Background The Rho-associated coiled-coil kinase-2 (ROCK2) is an important signaling transducer in the transmission of extracellular signals effecting organization of the actin cytoskeleton. ROCK2 has been implicated in numerous pathologies and the current focus is on understanding the molecular events that couple ROCK2 activity to biological function. To aid in the search for new ROCK2 substrates, we have developed an analog-sensitive (AS) ROCK2 protein that allows the use of selective ATP analogs that are not efficiently utilized by other protein kinases. Results The analog sensitive protein, M160A ROCK2, was highly active and could phosphorylate proteins from a cellular homogenate with γ32P-N6 (benzyl)ATP. We show the utility of this approach by identifying a putative ROCK2 substrate, elongation initiation factor-1-α1. We further show that the major site of ROCK2 phosphorylation of EIF1α1 is Thr432. Conclusions Our work demonstrates that AS-ROCK2 could be useful in a systematic proteomic approach for identifying novel ROCK2 substrates.
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Affiliation(s)
| | | | - Michael P Scheid
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J1P3, Canada.
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c-Jun N-terminal kinase phosphorylation of heterogeneous nuclear ribonucleoprotein K regulates vertebrate axon outgrowth via a posttranscriptional mechanism. J Neurosci 2013; 33:14666-80. [PMID: 24027268 DOI: 10.1523/jneurosci.4821-12.2013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
c-Jun N-terminal kinase (JNK) mediates cell signaling essential for axon outgrowth, but the associated substrates and underlying mechanisms are poorly understood. We identified in Xenopus laevis embryos a novel posttranscriptional mechanism whereby JNK regulates axonogenesis by phosphorylating a specific site on heterogeneous nuclear ribonucleoprotein K (hnRNP K). Both JNK inhibition and hnRNP K knockdown inhibited axon outgrowth and translation of hnRNP K-regulated cytoskeletal RNAs (tau and neurofilament medium), effects that were alleviated by expressing phosphomimetic, but not phosphodeficient, forms of hnRNP K. Immunohistochemical and biochemical analyses indicated that JNK phosphorylation of hnRNP K occurred within the cytoplasm and was necessary for the translational initiation of hnRNP K-targeted RNAs but not for hnRNP K intracellular localization or RNA binding. Thus, in addition to its known roles in transcription and cytoskeletal organization, JNK acts posttranscriptionally through hnRNP K to regulate translation of proteins crucial for axonogenesis.
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Barboro P, Borzì L, Repaci E, Ferrari N, Balbi C. Androgen receptor activity is affected by both nuclear matrix localization and the phosphorylation status of the heterogeneous nuclear ribonucleoprotein K in anti-androgen-treated LNCaP cells. PLoS One 2013; 8:e79212. [PMID: 24236111 PMCID: PMC3827347 DOI: 10.1371/journal.pone.0079212] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/20/2013] [Indexed: 11/19/2022] Open
Abstract
The androgen receptor (AR) plays a central role in the development and progression of prostate cancer (PCa) and anti-androgen therapy is a standard treatment. Unfortunately, after a few years, the majority of patients progress, developing androgen-independent PCa. AR-driven gene transcription recruits a large number of co-activator/co-repressor complexes; among these, the heterogeneous nuclear ribonucleoprotein K (hnRNP K) directly interacts with and regulates the AR translational apparatus. Here we examined AR and hnRNP K expression in response to the treatment of LNCaP cells with anti-androgen cyproterone acetate (CPA) or bicalutamide (BIC). AR and hnRNP K modulation and compartmentalization were studied by Western blot and confocal microscopy. Phosphate-affinity gel electrophoresis was employed to examine how anti-androgens modified hnRNP K phosphorylation. 10(-6) M CPA significantly stimulated LNCaP proliferation, whereas for 10(-4) M CPA or 10(-5) M BIC an antagonistic effect was observed. After anti-androgen treatment, AR expression was remarkably down-regulated within both the cytoplasm and the nucleus; however, when CPA had an agonist activity, the AR associated with the nuclear matrix (NM) increased approximately 2.5 times. This increase was synchronous with a higher PSA expression, indicating that the NM-associated AR represents the active complex. After BIC treatment, hnRNP K expression was significantly lower in the NM, the protein was hypophosphorylated and the co-localization of AR and hnRNP K decreased. In contrast, CPA as an agonist caused hnRNP K hyperphosphorylation and an increase in the co-localization of two proteins. These findings demonstrate that, in vitro, there is a strong relationship between NM-associated AR and both cell viability and PSA levels, indicating that AR transcriptional activity is critically dependent on its subnuclear localization. Moreover, the agonistic/antagonistic activity of anti-androgens is associated with modifications in hnRNP K phosphorylation, indicating an involvement of this protein in the AR transcriptional activity and likely in the onset of the androgen-independent phenotype.
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Affiliation(s)
- Paola Barboro
- Translational Urologic Research Unit, IRCCS Azienda Ospedaliera Universitaria San Martino IST-Instituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Luana Borzì
- Translational Urologic Research Unit, IRCCS Azienda Ospedaliera Universitaria San Martino IST-Instituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Erica Repaci
- Translational Urologic Research Unit, IRCCS Azienda Ospedaliera Universitaria San Martino IST-Instituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Nicoletta Ferrari
- Molecular Oncology and Angiogenesis Unit, IRCCS Azienda Ospedaliera Universitaria San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Cecilia Balbi
- Translational Urologic Research Unit, IRCCS Azienda Ospedaliera Universitaria San Martino IST-Instituto Nazionale per la Ricerca sul Cancro, Genova, Italy
- * E-mail:
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Moujalled D, James JL, Parker SJ, Lidgerwood GE, Duncan C, Meyerowitz J, Nonaka T, Hasegawa M, Kanninen KM, Grubman A, Liddell JR, Crouch PJ, White AR. Kinase Inhibitor Screening Identifies Cyclin-Dependent Kinases and Glycogen Synthase Kinase 3 as Potential Modulators of TDP-43 Cytosolic Accumulation during Cell Stress. PLoS One 2013; 8:e67433. [PMID: 23840699 PMCID: PMC3694067 DOI: 10.1371/journal.pone.0067433] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/21/2013] [Indexed: 12/13/2022] Open
Abstract
Abnormal processing of TAR DNA binding protein 43 (TDP-43) has been identified as a major factor in neuronal degeneration during amyotrophic lateral sclerosis (ALS) or frontotemporal lobar degeneration (FTLD). It is unclear how changes to TDP-43, including nuclear to cytosolic translocation and subsequent accumulation, are controlled in these diseases. TDP-43 is a member of the heterogeneous ribonucleoprotein (hnRNP) RNA binding protein family and is known to associate with cytosolic RNA stress granule proteins in ALS and FTLD. hnRNP trafficking and accumulation is controlled by the action of specific kinases including members of the mitogen-activated protein kinase (MAPK) pathway. However, little is known about how kinase pathways control TDP-43 movement and accumulation. In this study, we used an in vitro model of TDP-43-positve stress granule formation to screen for the effect of kinase inhibitors on TDP-43 accumulation. We found that while a number of kinase inhibitors, particularly of the MAPK pathways modulated both TDP-43 and the global stress granule marker, human antigen R (HuR), multiple inhibitors were more specific to TDP-43 accumulation, including inhibitors of cyclin-dependent kinases (CDKs) and glycogen synthase kinase 3 (GSK3). Close correlation was observed between effects of these inhibitors on TDP-43, hnRNP K and TIAR, but often with different effects on HuR accumulation. This may indicate a potential interaction between TDP-43, hnRNP K and TIAR. CDK inhibitors were also found to reverse pre-formed TDP-43-positive stress granules and both CDK and GSK3 inhibitors abrogated the accumulation of C-terminal TDP-43 (219–414) in transfected cells. Further studies are required to confirm the specific kinases involved and whether their action is through phosphorylation of the TDP-43 binding partner hnRNP K. This knowledge provides a valuable insight into the mechanisms controlling abnormal cytoplasmic TDP-43 accumulation and may herald new opportunities for kinase modulation-based therapeutic intervention in ALS and FTLD.
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Affiliation(s)
- Diane Moujalled
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Janine L. James
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Sarah J. Parker
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Grace E. Lidgerwood
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Clare Duncan
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Jodi Meyerowitz
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Takashi Nonaka
- Department of Neuropathology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Masato Hasegawa
- Department of Neuropathology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Katja M. Kanninen
- A.I. Virtanen Institute for Molecular Sciences, Laboratory of Molecular Brain Research, University of Eastern Finland, Kuopio, Finland
| | - Alexandra Grubman
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Jeffrey R. Liddell
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Peter J. Crouch
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Anthony R. White
- Department of Pathology, The University of Melbourne, Victoria, Australia and Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
- * E-mail:
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Anxiety-associated alternative polyadenylation of the serotonin transporter mRNA confers translational regulation by hnRNPK. Proc Natl Acad Sci U S A 2013; 110:11624-9. [PMID: 23798440 DOI: 10.1073/pnas.1301485110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The serotonin transporter (SERT) is a major regulator of serotonergic neurotransmission and anxiety-related behaviors. SERT is expressed in two alternative polyadenylation forms that differ by an evolutionarily conserved element in the 3' untranslated region of its mRNA. Expression of SERT mRNA containing the distal polyadenylation element is associated with decreased anxiety-related behaviors in mice and humans, suggesting that this element has behaviorally relevant modulatory effects on SERT expression. We have identified heterogeneous nuclear ribonucleoprotein K (hnRNPK), a protein known to integrate multiple signal transduction pathways with gene expression, as a SERT distal polyadenylation element binding protein. This interaction is functionally meaningful because genetic manipulation of hnRNPK alters expression of the SERT protein. Furthermore, the trophic factor S100β induces Src-family kinase-mediated tyrosine phosphorylation of hnRNPK and increased SERT expression. These results identify a previously unknown mechanism of regulated SERT expression and provide a putative mechanism by which the SERT distal polyadenylation element modulates anxiety-related behaviors.
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Xue L, Tao WA. Current technologies to identify protein kinase substrates in high throughput. ACTA ACUST UNITED AC 2013; 8:216-227. [PMID: 25110472 DOI: 10.1007/s11515-013-1257-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Since the discovery of protein phosphorylation as an important modulator of many cellular processes, the involvement of protein kinases in diseases, such as cancer, diabetes, cardiovascular diseases, and central nervous system pathologies, has been extensively documented. Our understanding of many disease pathologies at the molecular level, therefore, requires the comprehensive identification of substrates targeted by protein kinases. In this review, we focus on recent techniques for kinase substrate identification in high throughput, in particular on genetic and proteomic approaches. Each method with its inherent advantages and limitations is discussed.
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Affiliation(s)
- Liang Xue
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA ; Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA ; Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA ; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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31
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Martić S, Kraatz HB. Chemical biology toolkit for exploring protein kinase catalyzed phosphorylation reactions. Chem Sci 2013. [DOI: 10.1039/c2sc20846f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Abstract
The neurexin genes (NRXN1, NRXN2, and NRXN3) encode polymorphic presynaptic proteins that are implicated in synaptic plasticity and memory processing. In rat brain neurons grown in culture, depolarization induces reversible, calcium-dependent, repression of NRXN2α exon 11 (E11) splicing. Using Neuro2a cells as a model, we explored E11 cis elements and trans-acting factors involved in alternative splicing of NRXN2α E11 pre-mRNA under basal and depolarization conditions. E11 mutation studies revealed two motifs, CTGCCTG (enhancer) and GCACCCA (suppressor) regulating NRXN2α E11 alternative splicing. Subsequent E11 RNA affinity pull-down experiments demonstrated heterogeneous nuclear ribonucleoprotein (hnRNP) K and hnRNP L binding to this exon. Under depolarization, the amount of E11-bound hnRNP L (but not of hnRNP K) increased, in parallel to NRXN2α E11 splicing repression. Depletion of hnRNP K or hnRNP L in the Neuro2a cells by specific siRNAs enhanced NRXN2α E11 splicing and ablated the depolarization-induced repression of this exon. In addition, depolarization suppressed whereas hnRNP K depletion enhanced NRXN2α expression. These results indicate a role for hnRNP K in regulation of NRXN2α expression and of hnRNP L in the activity-dependent alternative splicing of neurexins which may potentially govern trans-synaptic signaling required for memory processing.
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Chen X, Zhao X, Abeyweera TP, Rotenberg SA. Analysis of substrates of protein kinase C isoforms in human breast cells by the traceable kinase method. Biochemistry 2012; 51:7087-97. [PMID: 22897107 DOI: 10.1021/bi300999c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A previous report [Abeyweera, T. P., and Rotenberg, S. A. (2007) Biochemistry 46, 2364-2370] described the application of the traceable kinase method in identifying substrates of protein kinase Cα (PKC-α) in nontransformed human breast MCF-10A cells. Here, a nonradioactive variation of this method compared the phosphoprotein profiles of three traceable PKC isoforms (α, δ, and ζ) for the purpose of identifying novel, isoform-selective substrates. Each FLAG-tagged traceable kinase was expressed and co-immunoprecipitated along with high-affinity substrates. The isolated kinase and its associated substrates were subjected to an in vitro phosphorylation reaction with traceable kinase-specific N(6)-phenyl-ATP, and the resulting phosphoproteins were analyzed by Western blotting with an antibody that recognizes the phosphorylated PKC consensus site. Phosphoprotein profiles generated by PKC-α and -δ were similar and differed markedly from that of PKC-ζ. Mass spectrometry of selected bands revealed known PKC substrates and several potential substrates that included the small GTPase-associated Cdc42 effector protein-4 (CEP4). Of those potential substrates tested, only CEP4 was phosphorylated by pure PKC-α, -δ, and -ζ isoforms in vitro, and by endogenous PKC isoforms in MCF-10A cells treated with DAG-lactone, a membrane permeable PKC activator. Under these conditions, the stoichiometry of CEP4 phosphorylation was 3.2 ± 0.5 (moles of phospho-CEP4 per mole of CEP4). Following knockdown with isoform-specific shRNA-encoding plasmids, the level of phosphorylation of CEP4 was substantially decreased in response to silencing of each of the three isoforms (PKC-α, -δ, and -ζ), whereas testing of kinase-dead mutants supported a role for only PKC-α and -δ in CEP4 phosphorylation. These findings identify CEP4 as a novel intracellular PKC substrate that is phosphorylated by multiple PKC isoforms.
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Affiliation(s)
- Xiangyu Chen
- Department of Chemistry and Biochemistry, Queens College, The City University of New York, 65-30 Kissena Boulevard, Flushing, NY 11367, USA
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Chiou YY, Fu SL, Lin WJ, Lin CH. Proteomics analysis of in vitro protein methylation during Src-induced transformation. Electrophoresis 2012; 33:451-61. [DOI: 10.1002/elps.201100280] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 09/14/2011] [Accepted: 10/07/2011] [Indexed: 11/11/2022]
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Dittrich ACN, Devarenne TP. An ATP analog-sensitive version of the tomato cell death suppressor protein kinase Adi3 for use in substrate identification. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:269-73. [PMID: 22027266 DOI: 10.1016/j.bbapap.2011.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 10/03/2011] [Accepted: 10/06/2011] [Indexed: 01/19/2023]
Abstract
Adi3 is a protein kinase from tomato that functions as a cell death suppressor and its substrates are not well defined. As a step toward identifying Adi3 substrates we developed an ATP analog-sensitive version of Adi3 in which the ATP-binding pocket is mutated to allow use of bulky ATP analogs. Met385 was identified as the "gatekeeper" residue and the M385G mutation allows for the use of two bulky ATP analogs. Adi3(M385G) can also specifically utilize N(6)-benzyl-ATP to phosphorylate a known substrate and provides a tool for identifying Adi3 substrates.
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Affiliation(s)
- Anna C Nelson Dittrich
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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Moffat LD, Brown SBA, Grassie ME, Ulke-Lemée A, Williamson LM, Walsh MP, MacDonald JA. Chemical genetics of zipper-interacting protein kinase reveal myosin light chain as a bona fide substrate in permeabilized arterial smooth muscle. J Biol Chem 2011; 286:36978-91. [PMID: 21880706 DOI: 10.1074/jbc.m111.257949] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Zipper-interacting protein kinase (ZIPK) has been implicated in Ca(2+)-independent smooth muscle contraction, although its specific role is unknown. The addition of ZIPK to demembranated rat caudal arterial strips induced an increase in force, which correlated with increases in LC(20) and MYPT1 phosphorylation. However, because of the number of kinases capable of phosphorylating LC(20) and MYPT1, it has proven difficult to identify the mechanism underlying ZIPK action. Therefore, we set out to identify bona fide ZIPK substrates using a chemical genetics method that takes advantage of ATP analogs with bulky substituents at the N(6) position and an engineered ZIPK capable of utilizing such substrates. (32)P-Labeled 6-phenyl-ATP and ZIPK-L93G mutant protein were added to permeabilized rat caudal arterial strips, and substrate proteins were detected by autoradiography following SDS-PAGE. Mass spectrometry identified LC(20) as a direct target of ZIPK in situ for the first time. Tissues were also exposed to 6-phenyl-ATP and ZIPK-L93G in the absence of endogenous ATP, and putative ZIPK substrates were identified by Western blotting. LC(20) was thereby confirmed as a direct target of ZIPK; however, no phosphorylation of MYPT1 was detected. We conclude that ZIPK is involved in the regulation of smooth muscle contraction through direct phosphorylation of LC(20).
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Affiliation(s)
- Lori D Moffat
- Smooth Muscle Research Group and the Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
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Meyerowitz J, Parker SJ, Vella LJ, Ng DC, Price KA, Liddell JR, Caragounis A, Li QX, Masters CL, Nonaka T, Hasegawa M, Bogoyevitch MA, Kanninen KM, Crouch PJ, White AR. C-Jun N-terminal kinase controls TDP-43 accumulation in stress granules induced by oxidative stress. Mol Neurodegener 2011; 6:57. [PMID: 21819629 PMCID: PMC3162576 DOI: 10.1186/1750-1326-6-57] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 08/08/2011] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND TDP-43 proteinopathies are characterized by loss of nuclear TDP-43 expression and formation of C-terminal TDP-43 fragmentation and accumulation in the cytoplasm. Recent studies have shown that TDP-43 can accumulate in RNA stress granules (SGs) in response to cell stresses and this could be associated with subsequent formation of TDP-43 ubiquinated protein aggregates. However, the initial mechanisms controlling endogenous TDP-43 accumulation in SGs during chronic disease are not understood. In this study we investigated the mechanism of TDP-43 processing and accumulation in SGs in SH-SY5Y neuronal-like cells exposed to chronic oxidative stress. Cell cultures were treated overnight with the mitochondrial inhibitor paraquat and examined for TDP-43 and SG processing. RESULTS We found that mild stress induced by paraquat led to formation of TDP-43 and HuR-positive SGs, a proportion of which were ubiquitinated. The co-localization of TDP-43 with SGs could be fully prevented by inhibition of c-Jun N-terminal kinase (JNK). JNK inhibition did not prevent formation of HuR-positive SGs and did not prevent diffuse TDP-43 accumulation in the cytosol. In contrast, ERK or p38 inhibition prevented formation of both TDP-43 and HuR-positive SGs. JNK inhibition also inhibited TDP-43 SG localization in cells acutely treated with sodium arsenite and reduced the number of aggregates per cell in cultures transfected with C-terminal TDP-43 162-414 and 219-414 constructs. CONCLUSIONS Our studies are the first to demonstrate a critical role for kinase control of TDP-43 accumulation in SGs and may have important implications for development of treatments for FTD and ALS, targeting cell signal pathway control of TDP-43 aggregation.
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Affiliation(s)
- Jodi Meyerowitz
- Department of Pathology, The University of Melbourne, Victoria, 3010, Australia.
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Fujimoto T, Hatano N, Nozaki N, Yurimoto S, Kobayashi R, Tokumitsu H. Identification of a novel CaMKK substrate. Biochem Biophys Res Commun 2011; 410:45-51. [PMID: 21640082 DOI: 10.1016/j.bbrc.2011.05.102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 05/16/2011] [Indexed: 11/27/2022]
Abstract
Ca(2+)/calmodulin-dependent protein kinase kinase (CaMKK) phosphorylates and activates specific downstream protein kinases including CaMKI, CaMKIV and 5'-AMP-activated protein kinase. In order to examine the variety of CaMKK-mediated signaling pathways, we searched for novel CaMKK substrate(s) using N(6)-(1-methylbutyl)-ATP and genetically engineered CaMKKα mutant, CaMKKα (Phe(230)Gly), that was capable of utilizing this ATP analogue as a phosphate donor. Incubation of rat brain extracts with recombinant CaMKKα (Phe(230)Gly), but not with wild-type kinase, in the presence of N(6)-(1-methylbutyl)-ATP and Ca(2+)/CaM, induced significant threonine phosphorylation of a 50kDa protein as well as CaMKI phosphorylation at Thr(177). The 50kDa CaMKK substrate was partially purified by using serial column chromatography, and was identified as Syndapin I by LC-MS/MS analysis. We confirmed that recombinant Syndapin I was phosphorylated by CaMKKα and β isoforms at Thr(355)in vitro. Phosphorylation of HA-Syndapin I at Thr(355) in transfected HeLa cells was significantly induced by co-expression of constitutively active mutants of CaMKK isoforms. This is the first report that CaMKK is capable of phosphorylating a non-kinase substrate suggesting the possibility of CaMKK-mediated novel Ca(2+)-signaling pathways that are independent of downstream protein kinases.
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Affiliation(s)
- Tomohito Fujimoto
- Department of Signal Transduction Sciences, Faculty of Medicine, Kagawa University, Kagawa 761-0793, Japan
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Kimura Y, Nagata K, Suzuki N, Yokoyama R, Yamanaka Y, Kitamura H, Hirano H, Ohara O. Characterization of multiple alternative forms of heterogeneous nuclear ribonucleoprotein K by phosphate-affinity electrophoresis. Proteomics 2011; 10:3884-95. [PMID: 20960454 DOI: 10.1002/pmic.201000349] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The phosphorylation of heterogeneous nuclear ribonucleoprotein K (hnRNP K) is thought to play an important role in cell regulation and signal transduction. However, the relationship between hnRNP K phosphorylation and cellular events has only been indirectly examined, and the phosphorylated forms of endogenous hnRNP K have not been biochemically characterized in detail. In this study, we extensively examined the phosphorylated forms of endogenous hnRNP K by direct protein-chemical characterization using phosphate-affinity electrophoresis followed by immunoblotting and MS. Phosphate-affinity electrophoresis enabled us to sensitively detect and separate the phosphorylated forms of hnRNP K. When we used 2-DE with phosphate-affinity SDS-PAGE in the second dimension, the nuclear fraction contained more than 20 spots of endogenous hnRNP K on the 2-D map. We determined that the multiple forms of hnRNP K were produced mainly by alternative splicing of the single hnRNP K gene and phosphorylation of Ser116 and/or Ser284. Furthermore, the subcellular localization of these proteins revealed by the 2-D gel correlated with their phosphorylation states and alternative splicing patterns. The results also indicated that the multiple forms of hnRNP K were differentially modulated in response to external stimulation with bacterial lipopolysaccharide or serum.
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Affiliation(s)
- Yayoi Kimura
- Laboratory for Immunogenomics, RIKEN Research Center for Allergy and Immunology, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
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Carlson SM, White FM. Using small molecules and chemical genetics to interrogate signaling networks. ACS Chem Biol 2011; 6:75-85. [PMID: 21077690 DOI: 10.1021/cb1002834] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The limited clinical success of therapeutics targeting cellular signaling processes is due to multiple factors, including off-target effects and complex feedback regulation encoded within the signaling network. To understand these effects, chemical proteomics and chemical genetics tools have been developed to map the direct targets of kinase inhibitors, determine the network-level response to inhibitor treatment, and to infer network topology. Here we provide an overview of chemical phosphoproteomic and chemical genetic methods, including specific examples where these methods have been applied to yield biological insight regarding network structure and the system-wide effects of targeted therapeutics. The challenges and caveats associated with each method are described, along with approaches being used to resolve some of these issues. With the broad array of available techniques the next decade should see a rapid improvement in our understanding of signaling networks regulation and response to targeted perturbations, leading to more efficacious therapeutic strategies.
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Affiliation(s)
- Scott M. Carlson
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Forest M. White
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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41
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Identification of the methylation preference region in heterogeneous nuclear ribonucleoprotein K by protein arginine methyltransferase 1 and its implication in regulating nuclear/cytoplasmic distribution. Biochem Biophys Res Commun 2011; 404:865-9. [DOI: 10.1016/j.bbrc.2010.12.076] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 12/15/2010] [Indexed: 11/20/2022]
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Zheng H, Al-Ayoubi A, Eblen ST. Identification of novel substrates of MAP Kinase cascades using bioengineered kinases that uniquely utilize analogs of ATP to phosphorylate substrates. Methods Mol Biol 2010; 661:167-83. [PMID: 20811983 DOI: 10.1007/978-1-60761-795-2_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The Mitogen-Activated Protein Kinase (MAPK) family of signaling molecules regulates a number of cellular processes through the direct phosphorylation and regulation of a plethora of cellular proteins. Identifying the direct substrates of the MAPK pathway proteins is important for determining how the effects of MAPK activation have such profound effects on cell biology. In this chapter, we describe one method for specific labeling and identification of direct MAPK substrates. A single or double point mutation is generated within the ATP binding domain at a particular residue(s) termed the "gatekeeper" that comes into close contact with the N6 position of ATP. Most kinases contain an amino acid larger than alanine at this position. Mutation of the residue(s) to glycine or alanine generates a "pocket" that allows the mutant kinase to bind and uniquely utilize an analog of ATP that contains a chemical substituent at the N6 position. When radiolabeled analog is added to the mutant kinase and a complex mixture of cellular proteins, the only proteins that become radiolabeled are direct substrates of the mutant kinase. To label biologically relevant substrates, we take advantage of the direct binding of MAPKs to their substrates. An epitope tagged mutant kinase is expressed in cells and immunoprecipitated with associated substrates, which are then radiolabeled in an in vitro kinase reaction using (gamma-(32)P) ATP analog. Larger, unlabeled kinase reactions are run in parallel and used to identify the substrates by mass spectrometry.
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Affiliation(s)
- Hui Zheng
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
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43
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Mechanisms of mRNA translation of interferon stimulated genes. Cytokine 2010; 52:123-7. [DOI: 10.1016/j.cyto.2010.03.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 03/30/2010] [Indexed: 01/06/2023]
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Computational prediction and experimental verification of new MAP kinase docking sites and substrates including Gli transcription factors. PLoS Comput Biol 2010; 6. [PMID: 20865152 PMCID: PMC2928751 DOI: 10.1371/journal.pcbi.1000908] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2010] [Accepted: 07/28/2010] [Indexed: 12/14/2022] Open
Abstract
In order to fully understand protein kinase networks, new methods are needed to identify regulators and substrates of kinases, especially for weakly expressed proteins. Here we have developed a hybrid computational search algorithm that combines machine learning and expert knowledge to identify kinase docking sites, and used this algorithm to search the human genome for novel MAP kinase substrates and regulators focused on the JNK family of MAP kinases. Predictions were tested by peptide array followed by rigorous biochemical verification with in vitro binding and kinase assays on wild-type and mutant proteins. Using this procedure, we found new ‘D-site’ class docking sites in previously known JNK substrates (hnRNP-K, PPM1J/PP2Czeta), as well as new JNK-interacting proteins (MLL4, NEIL1). Finally, we identified new D-site-dependent MAPK substrates, including the hedgehog-regulated transcription factors Gli1 and Gli3, suggesting that a direct connection between MAP kinase and hedgehog signaling may occur at the level of these key regulators. These results demonstrate that a genome-wide search for MAP kinase docking sites can be used to find new docking sites and substrates. Protein kinases are enzymes that regulate key cellular processes by covalently attaching a phosphate group to substrate proteins; they are crucial components of signaling pathways involved in cancer, diabetes, and many other diseases. Identifying the substrates of particular protein kinases is challenging, and many existing biochemical methods are biased against weakly expressed proteins like transcription factors. Here we exploited the observation that mitogen-activated protein kinases (MAPKs) briefly attach to many of their substrates before phosphorylating them, docking onto a sequence known as the ‘D-site’. We developed D-finder, a computational tool that uses a combination of expert knowledge and machine learning to search genome databases for D-sites. We then verified several of D-finder's predictions using rigorous and well-established biochemical assays. The most intriguing predicted and verified substrates were the Gli1 and Gli3 transcription factors of the ‘hedgehog’ signaling pathway. Gli transcription factors are involved in embryonic development and stem cell differentiation, and have also been found to be hyperactive in several types of cancer. There is emerging evidence that crosstalk with MAPK pathways is important in Gli-mediated regulation. Our study, however, is the first to show that MAPKs directly phosphorylate Gli transcription factors.
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45
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Control of cell cycle progression by phosphorylation of cyclin-dependent kinase (CDK) substrates. Biosci Rep 2010; 30:243-55. [DOI: 10.1042/bsr20090171] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The eukaryotic cell cycle is a fundamental evolutionarily conserved process that regulates cell division from simple unicellular organisms, such as yeast, through to higher multicellular organisms, such as humans. The cell cycle comprises several phases, including the S-phase (DNA synthesis phase) and M-phase (mitotic phase). During S-phase, the genetic material is replicated, and is then segregated into two identical daughter cells following mitotic M-phase and cytokinesis. The S- and M-phases are separated by two gap phases (G1 and G2) that govern the readiness of cells to enter S- or M-phase. Genetic and biochemical studies demonstrate that cell division in eukaryotes is mediated by CDKs (cyclin-dependent kinases). Active CDKs comprise a protein kinase subunit whose catalytic activity is dependent on association with a regulatory cyclin subunit. Cell-cycle-stage-dependent accumulation and proteolytic degradation of different cyclin subunits regulates their association with CDKs to control different stages of cell division. CDKs promote cell cycle progression by phosphorylating critical downstream substrates to alter their activity. Here, we will review some of the well-characterized CDK substrates to provide mechanistic insights into how these kinases control different stages of cell division.
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Requirement of ATM for rapid p53 phosphorylation at Ser46 without Ser/Thr-Gln sequences. Mol Cell Biol 2010; 30:1620-33. [PMID: 20123963 DOI: 10.1128/mcb.00810-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
p53 phosphorylation at Ser46 following DNA damage is important for preferential transactivation of proapoptotic genes. Here, we report that ataxia-telangiectasia mutated (ATM) kinase is responsible for Ser46 phosphorylation of p53 during early-phase response to DNA damage. To elucidate the direct phosphorylation of p53 at Ser46 by ATM, an ATM mutant (ATM-AS) sensitive to ATP analogues was engineered. In vitro kinase assays revealed that p53 was phosphorylated at Ser46 by ATM-AS, even when ATP analogues were used as phosphate donors, although this phosphorylation site is not in an SQ motif, a consensus ATM site. Furthermore, Ser46 phosphorylation by ATM was dependent on the N- and C-terminal domains of p53, unlike Ser15 phosphorylation. Immunofluorescence analyses showed that Ser46-phosphorylated p53 was observed as foci in response to DNA damage and colocalized with gamma-H2AX or Ser1981-phosphorylated ATM. These results suggest that ATM phosphorylates a noncanonical serine residue on p53 by mechanisms different from those for the phosphorylation of Ser15.
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Haan C, Behrmann I, Haan S. Perspectives for the use of structural information and chemical genetics to develop inhibitors of Janus kinases. J Cell Mol Med 2010; 14:504-27. [PMID: 20132407 PMCID: PMC3823453 DOI: 10.1111/j.1582-4934.2010.01018.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Gain-of-function mutations in the genes encoding Janus kinases have been discovered in various haematologic diseases. Jaks are composed of a FERM domain, an SH2 domain, a pseudokinase domain and a kinase domain, and a complex interplay of the Jak domains is involved in regulation of catalytic activity and association to cytokine receptors. Most activating mutations are found in the pseudokinase domain. Here we present recently discovered mutations in the context of our structural models of the respective domains. We describe two structural hotspots in the pseudokinase domain of Jak2 that seem to be associated either to myeloproliferation or to lymphoblastic leukaemia, pointing at the involvement of distinct signalling complexes in these disease settings. The different domains of Jaks are discussed as potential drug targets. We present currently available inhibitors targeting Jaks and indicate structural differences in the kinase domains of the different Jaks that may be exploited in the development of specific inhibitors. Moreover, we discuss recent chemical genetic approaches which can be applied to Jaks to better understand the role of these kinases in their biological settings and as drug targets.
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Affiliation(s)
- Claude Haan
- Life Sciences Research Unit, University of Luxembourg, 162A, av. de la Faïencerie, 1511 Luxembourg, Luxembourg.
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Koch A, Hauf S. Strategies for the identification of kinase substrates using analog-sensitive kinases. Eur J Cell Biol 2010; 89:184-93. [PMID: 20061049 DOI: 10.1016/j.ejcb.2009.11.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Phosphorylation of proteins is a prevalent post-translational modification, which affects intracellular signaling in many ways. About 2% of all eukaryotic genes code for protein kinases catalyzing phosphorylation events. Despite technological advances that have made it possible to identify thousands of phosphorylation sites simultaneously, identification of the substrates of a given kinase remains an exceptionally challenging task. Here, we summarize approaches for substrate identification that make use of genetically engineered 'analog-sensitive' kinases.
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Affiliation(s)
- André Koch
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
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Liu W, Wu S, Hou S, Zhao Z(K. Synthesis of phosphodiester-type nicotinamide adenine dinucleotide analogs. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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50
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Abeyweera TP, Chen X, Rotenberg SA. Phosphorylation of alpha6-tubulin by protein kinase Calpha activates motility of human breast cells. J Biol Chem 2009; 284:17648-56. [PMID: 19406749 PMCID: PMC2719404 DOI: 10.1074/jbc.m902005200] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Indexed: 11/06/2022] Open
Abstract
Engineered overexpression of protein kinase Calpha (PKCalpha) was previously shown to endow nonmotile MCF-10A human breast cells with aggressive motility. A traceable mutant of PKCalpha (Abeyweera, T. P., and Rotenberg, S. A. (2007) Biochemistry 46, 2364-2370) revealed that alpha6-tubulin is phosphorylated in cells expressing traceable PKCalpha and in vitro by wild type PKCalpha. Gain-of-function, single site mutations (Ser-->Asp) were constructed at each PKC consensus site in alpha6-tubulin (Ser158, Ser165, Ser241, and Thr337) to simulate phosphorylation. Following expression of each construct in MCF-10A cells, motility assays identified Ser165 as the only site in alpha6-tubulin whose pseudophosphorylation reproduced the motile behavior engendered by PKCalpha. Expression of a phosphorylation-resistant mutant (S165N-alpha6-tubulin) resulted in suppression of MCF-10A cell motility stimulated either by expression of PKCalpha or by treatment with PKCalpha-selective activator diacylglycerol-lactone. MCF-10A cells treated with diacylglycerol-lactone showed strong phosphorylation of endogenous alpha-tubulin that could be blocked when S165N-alpha6-tubulin was expressed. The S165N mutant also inhibited intrinsically motile human breast tumor cells that express high endogenous PKCalpha levels (MDA-MB-231 cells) or lack PKCalpha and other conventional isoforms (MDA-MB-468 cells). Comparison of Myc-tagged wild type alpha6-tubulin and S165N-alpha6-tubulin expressed in MDA-MB-468 cells demonstrated that Ser165 is also a major site of phosphorylation for endogenously active, nonconventional PKC isoforms. PKC-stimulated motility of MCF-10A cells was nocodazole-sensitive, thereby implicating microtubule elongation in the mechanism. These findings support a model in which PKC phosphorylates alpha-tubulin at Ser165, leading to microtubule elongation and motility.
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Affiliation(s)
- Thushara P. Abeyweera
- From the Department of Chemistry and Biochemistry of Queens College and
- the Graduate Center of the City University of New York, Flushing, New York 11367
| | - Xiangyu Chen
- From the Department of Chemistry and Biochemistry of Queens College and
- the Graduate Center of the City University of New York, Flushing, New York 11367
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