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Wu LY, Song YJ, Zhang CL, Liu J. K V Channel-Interacting Proteins in the Neurological and Cardiovascular Systems: An Updated Review. Cells 2023; 12:1894. [PMID: 37508558 PMCID: PMC10377897 DOI: 10.3390/cells12141894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
KV channel-interacting proteins (KChIP1-4) belong to a family of Ca2+-binding EF-hand proteins that are able to bind to the N-terminus of the KV4 channel α-subunits. KChIPs are predominantly expressed in the brain and heart, where they contribute to the maintenance of the excitability of neurons and cardiomyocytes by modulating the fast inactivating-KV4 currents. As the auxiliary subunit, KChIPs are critically involved in regulating the surface protein expression and gating properties of KV4 channels. Mechanistically, KChIP1, KChIP2, and KChIP3 promote the translocation of KV4 channels to the cell membrane, accelerate voltage-dependent activation, and slow the recovery rate of inactivation, which increases KV4 currents. By contrast, KChIP4 suppresses KV4 trafficking and eliminates the fast inactivation of KV4 currents. In the heart, IKs, ICa,L, and INa can also be regulated by KChIPs. ICa,L and INa are positively regulated by KChIP2, whereas IKs is negatively regulated by KChIP2. Interestingly, KChIP3 is also known as downstream regulatory element antagonist modulator (DREAM) because it can bind directly to the downstream regulatory element (DRE) on the promoters of target genes that are implicated in the regulation of pain, memory, endocrine, immune, and inflammatory reactions. In addition, all the KChIPs can act as transcription factors to repress the expression of genes involved in circadian regulation. Altered expression of KChIPs has been implicated in the pathogenesis of several neurological and cardiovascular diseases. For example, KChIP2 is decreased in failing hearts, while loss of KChIP2 leads to increased susceptibility to arrhythmias. KChIP3 is increased in Alzheimer's disease and amyotrophic lateral sclerosis, but decreased in epilepsy and Huntington's disease. In the present review, we summarize the progress of recent studies regarding the structural properties, physiological functions, and pathological roles of KChIPs in both health and disease. We also summarize the small-molecule compounds that regulate the function of KChIPs. This review will provide an overview and update of the regulatory mechanism of the KChIP family and the progress of targeted drug research as a reference for researchers in related fields.
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Affiliation(s)
- Le-Yi Wu
- Department of Pathophysiology, Shenzhen University Medical School, Shenzhen 518060, China
| | - Yu-Juan Song
- Department of Pathophysiology, Shenzhen University Medical School, Shenzhen 518060, China
| | - Cheng-Lin Zhang
- Department of Pathophysiology, Shenzhen University Medical School, Shenzhen 518060, China
| | - Jie Liu
- Department of Pathophysiology, Shenzhen University Medical School, Shenzhen 518060, China
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2
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Molinaro P, Sanguigno L, Casamassa A, Valsecchi V, Sirabella R, Pignataro G, Annunziato L, Formisano L. Emerging Role of DREAM in Healthy Brain and Neurological Diseases. Int J Mol Sci 2023; 24:ijms24119177. [PMID: 37298129 DOI: 10.3390/ijms24119177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023] Open
Abstract
The downstream regulatory element antagonist modulator (DREAM) is a multifunctional Ca2+-sensitive protein exerting a dual mechanism of action to regulate several Ca2+-dependent processes. Upon sumoylation, DREAM enters in nucleus where it downregulates the expression of several genes provided with a consensus sequence named dream regulatory element (DRE). On the other hand, DREAM could also directly modulate the activity or the localization of several cytosolic and plasma membrane proteins. In this review, we summarize recent advances in the knowledge of DREAM dysregulation and DREAM-dependent epigenetic remodeling as a central mechanism in the progression of several diseases affecting central nervous system, including stroke, Alzheimer's and Huntington's diseases, amyotrophic lateral sclerosis, and neuropathic pain. Interestingly, DREAM seems to exert a common detrimental role in these diseases by inhibiting the transcription of several neuroprotective genes, including the sodium/calcium exchanger isoform 3 (NCX3), brain-derived neurotrophic factor (BDNF), pro-dynorphin, and c-fos. These findings lead to the concept that DREAM might represent a pharmacological target to ameliorate symptoms and reduce neurodegenerative processes in several pathological conditions affecting central nervous system.
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Affiliation(s)
- Pasquale Molinaro
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, Federico II University of Naples, Via Pansini, 5, 80131 Naples, Italy
| | - Luca Sanguigno
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, Federico II University of Naples, Via Pansini, 5, 80131 Naples, Italy
| | | | - Valeria Valsecchi
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, Federico II University of Naples, Via Pansini, 5, 80131 Naples, Italy
| | - Rossana Sirabella
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, Federico II University of Naples, Via Pansini, 5, 80131 Naples, Italy
| | - Giuseppe Pignataro
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, Federico II University of Naples, Via Pansini, 5, 80131 Naples, Italy
| | | | - Luigi Formisano
- Division of Pharmacology, Department of Neuroscience, Reproductive and Dentistry Sciences, School of Medicine, Federico II University of Naples, Via Pansini, 5, 80131 Naples, Italy
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3
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Abstract
Kv channel-interacting proteins (KChIPs) belong to the neuronal calcium sensor (NCS) family of Ca2+-binding EF-hand proteins. KChIPs constitute a group of specific auxiliary β-subunits for Kv4 channels, the molecular substrate of transient potassium currents in both neuronal and non-neuronal tissues. Moreover, KChIPs can interact with presenilins to control ER calcium signaling and apoptosis, and with DNA to control gene transcription. Ca2+ binding via their EF-hands, with the consequence of conformational changes, is well documented for KChIPs. Moreover, the Ca2+ dependence of the presenilin/KChIP complex may be related to Alzheimer’s disease and the Ca2+ dependence of the DNA/KChIP complex to pain sensing. However, only in few cases could the Ca2+ binding to KChIPs be directly linked to the control of excitability in nerve and muscle cells known to express Kv4/KChIP channel complexes. This review summarizes current knowledge about the Ca2+ binding properties of KChIPs and the Ca2+ dependencies of macromolecular complexes containing KChIPs, including those with presenilins, DNA and especially Kv4 channels. The respective physiological or pathophysiolgical roles of Ca2+ binding to KChIPs are discussed.
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Affiliation(s)
- Robert Bähring
- a Institut für Zelluläre und Integrative Physiologie, Zentrum für Experimentelle Medizin , Universitätsklinikum Hamburg-Eppendorf , Hamburg , Germany
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4
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The interaction between RE1-silencing transcription factor (REST) and heat shock protein 90 as new therapeutic target against Huntington's disease. PLoS One 2019; 14:e0220393. [PMID: 31361762 PMCID: PMC6667143 DOI: 10.1371/journal.pone.0220393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 07/14/2019] [Indexed: 12/18/2022] Open
Abstract
The wild type huntingtin protein (Htt), supports the production of brain-derived neurotrophic factor (BDNF), a survival factor for striatal neurons, through cytoplasmic sequestering of RE-1silencing transcription factor (REST). In Huntington´s Disease an inherited degenerative disease, caused by a CAG expansion in the 5´coding region of the gene, the mutant huntingtin protein (mHtt), causes that REST enters pathologically into the nucleus of cells, resulting in the repression of neuronal genes including BDNF, resulting in the progressive neuronal death. It has been reported that Htt associates with Hsp90 and this interaction is involved in regulation of huntingtin aggregation. Discovering mechanisms to reduce the cellular levels of mutant huntingtin and REST provide promising strategies for treating Huntington disease. Here, we use the yeast two-hybrid system to show that N-terminus or REST interacts with the heat shock protein 90 (Hsp90) and identifies REST as an Hsp90 Client Protein. To assess the effects of Hsp90 we used antisense oligonucleotide, and evaluated the levels mHtt and REST levels. Our results show that direct knockdown of endogenous Hsp90 significantly reduces the levels of REST and mutant Huntingtin, decreased the percentage of cells with mHtt in nucleus and rescued cells from mHtt-induced cellular cytotoxicity. Additionally Hsp90–specific inhibitors geldanamicyn and PUH71 dramatically reduced mHtt and REST levels, thereby providing neuroprotective activity. Our data show that Hsp90 is necessary to maintain the levels of REST and mHtt, which suggests that the interactions between Hsp90-REST and Hsp90-Huntingtin could be potential therapeutic targets in Huntington's disease.
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5
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Momtazi G, Lambrecht BN, Naranjo JR, Schock BC. Regulators of A20 (TNFAIP3): new drug-able targets in inflammation. Am J Physiol Lung Cell Mol Physiol 2018; 316:L456-L469. [PMID: 30543305 DOI: 10.1152/ajplung.00335.2018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Persistent activation of the transcription factor Nuclear factor-κB (NF-κB) is central to the pathogenesis of many inflammatory disorders, including those of the lung such as cystic fibrosis (CF), asthma, and chronic obstructive pulmonary disease (COPD). Despite recent advances in treatment, management of the inflammatory component of these diseases still remains suboptimal. A20 is an endogenous negative regulator of NF-κB signaling, which has been widely described in several autoimmune and inflammatory disorders and more recently in terms of chronic lung disorders. However, the underlying mechanism for the apparent lack of A20 in CF, COPD, and asthma has not been investigated. Transcriptional regulation of A20 is complex and requires coordination of different transcription factors. In this review we examine the existing body of research evidence on the regulation of A20, concentrating on pulmonary inflammation. Special focus is given to the repressor downstream regulatory element antagonist modulator (DREAM) and its nuclear and cytosolic action to regulate inflammation. We provide evidence that would suggest the A20-DREAM axis to be an important player in (airway) inflammatory responses and point to DREAM as a potential future therapeutic target for the modification of phenotypic changes in airway inflammatory disorders. A schematic summary describing the role of DREAM in inflammation with a focus on chronic lung diseases as well as the possible consequences of altered DREAM expression on immune responses is provided.
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Affiliation(s)
- G Momtazi
- Centre for Experimental Medicine, Queen's University of Belfast , Belfast , United Kingdom
| | - B N Lambrecht
- VIB Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - J R Naranjo
- Spanish Network for Biomedical Research in Neurodegenerative Diseases (Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas), Instituto de Salud Carlos III, Madrid, Spain.,National Biotechnology Center, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
| | - B C Schock
- Centre for Experimental Medicine, Queen's University of Belfast , Belfast , United Kingdom
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6
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Naranjo R, González P, Lopez-Hurtado A, Dopazo XM, Mellström B, Naranjo JR. Inhibition of the Neuronal Calcium Sensor DREAM Modulates Presenilin-2 Endoproteolysis. Front Mol Neurosci 2018; 11:449. [PMID: 30559648 PMCID: PMC6287014 DOI: 10.3389/fnmol.2018.00449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/21/2018] [Indexed: 11/14/2022] Open
Abstract
Deregulated intracellular Ca2+ and protein homeostasis underlie synaptic dysfunction and are common features in neurodegenerative diseases. DREAM, also known as calsenilin or KChIP-3, is a multifunctional Ca2+ binding protein of the neuronal calcium sensor superfamily with specific functions through protein-DNA and protein-protein interactions. Small-molecules able to bind DREAM, like the anti-diabetic drug repaglinide, disrupt some of the interactions with other proteins and modulate DREAM activity on Kv4 channels or on the processing of activating transcription factor 6 (ATF6). Here, we show the interaction of endogenous DREAM and presenilin-2 (PS2) in mouse brain and, using DREAM deficient mice or transgenic mice overexpressing a dominant active DREAM (daDREAM) mutant in the brain, we provide genetic evidence of the role of DREAM in the endoproteolysis of endogenous PS2. We show that repaglinide disrupts the interaction between DREAM and the C-terminal PS2 fragment (Ct-PS2) by coimmunoprecipitation assays. Exposure to sub-micromolar concentrations of repaglinide reduces the levels of Ct-PS2 fragment in N2a neuroblastoma cells. These results suggest that the interaction between DREAM and PS2 may represent a new target for modulation of PS2 processing, which could have therapeutic potential in Alzheimer’s disease (AD) treatment.
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Affiliation(s)
- Rocío Naranjo
- Spanish Network for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain.,National Biotechnology Center (CNB), CSIC, Madrid, Spain
| | - Paz González
- Spanish Network for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain.,National Biotechnology Center (CNB), CSIC, Madrid, Spain
| | - Alejandro Lopez-Hurtado
- Spanish Network for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain.,National Biotechnology Center (CNB), CSIC, Madrid, Spain
| | - Xosé M Dopazo
- Spanish Network for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain.,National Biotechnology Center (CNB), CSIC, Madrid, Spain
| | - Britt Mellström
- Spanish Network for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain.,National Biotechnology Center (CNB), CSIC, Madrid, Spain
| | - José R Naranjo
- Spanish Network for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain.,National Biotechnology Center (CNB), CSIC, Madrid, Spain
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7
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Kim HJ, Lee WH, Kim MJ, Shin S, Jang B, Park JB, Wasco W, Buxbaum JD, Kim YS, Choi EK. Calsenilin, a Presenilin Interactor, Regulates RhoA Signaling and Neurite Outgrowth. Int J Mol Sci 2018; 19:ijms19041196. [PMID: 29652865 PMCID: PMC5979497 DOI: 10.3390/ijms19041196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 11/24/2022] Open
Abstract
Calsenilin modulates A-type potassium channels, regulates presenilin-mediated γ-secretase activity, and represses prodynorphin and c-fos genes expression. RhoA is involved in various cellular functions including proliferation, differentiation, migration, transcription, and regulation of the actin cytoskeleton. Although recent studies demonstrate that calsenilin can directly interact with RhoA and that RhoA inactivation is essential for neuritogenesis, it is uncertain whether there is a link between calsenilin and RhoA-regulated neuritogenesis. Here, we investigated the role of calsenilin in RhoA-regulated neuritogenesis using in vitro and in vivo systems. We found that calsenilin induced RhoA inactivation, which accompanied RhoA phosphorylation and the reduced phosphorylation levels of LIM kinase (LIMK) and cofilin. Interestingly, PC12 cells overexpressing either full-length (FL) or the caspase 3-derived C-terminal fragment (CTF) of calsenilin significantly inactivated RhoA through its interaction with RhoA and p190 Rho GTPase-activating protein (p190RhoGAP). In addition, cells expressing FL and the CTF of calsenilin had increased neurite outgrowth compared to cells expressing the N-terminal fragment (NTF) of calsenilin or vector alone. Moreover, Tat-C3 and Y27632 treatment significantly increased the percentage of neurite-bearing cells, neurite length, and the number of neurites in cells. Finally, calsenilin deficiency in the brains of calsenilin-knockout mice significantly interfered with RhoA inactivation. These findings suggest that calsenilin contributes to neuritogenesis through RhoA inactivation.
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Affiliation(s)
- Hee-Jun Kim
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do 14066, Korea.
| | - Won-Haeng Lee
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do 14066, Korea.
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Gangwon-do 24252, Korea.
| | - Mo-Jong Kim
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do 14066, Korea.
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Gangwon-do 24252, Korea.
| | - Sunmee Shin
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do 14066, Korea.
| | - Byungki Jang
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do 14066, Korea.
| | - Jae-Bong Park
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Gangwon-do 24252, Korea.
| | - Wilma Wasco
- Genetics and Aging Research Unit, Mass General Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Yong-Sun Kim
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do 14066, Korea.
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Gangwon-do 24252, Korea.
| | - Eun-Kyoung Choi
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do 14066, Korea.
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Gangwon-do 24252, Korea.
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8
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Stankiewicz TR, Schroeder EK, Kelsey NA, Bouchard RJ, Linseman DA. C-terminal binding proteins are essential pro-survival factors that undergo caspase-dependent downregulation during neuronal apoptosis. Mol Cell Neurosci 2013; 56:322-332. [PMID: 23859824 DOI: 10.1016/j.mcn.2013.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 06/25/2013] [Accepted: 07/08/2013] [Indexed: 12/20/2022] Open
Abstract
C-terminal binding proteins (CtBPs) are transcriptional co-repressors that are subject to proteasome-dependent downregulation during apoptosis. Alternative mechanisms that regulate CtBP expression are currently under investigation and the role of CtBPs in neuronal survival is largely unexplored. Here, we show that CtBPs are downregulated in cerebellar granule neurons (CGNs) induced to undergo apoptosis by a variety of stressors. Moreover, antisense-mediated downregulation of CtBP1 is sufficient to cause CGN apoptosis. Similarly, the CtBP inhibitor, 4-methylthio-2-oxobutyric acid, induces expression of the CtBP target Noxa and causes actinomycin-sensitive CGN apoptosis. Unexpectedly, we found that the mechanism of CtBP downregulation in CGNs undergoing apoptosis varies in a stimulus-specific manner involving either the proteasome or caspases. In the case of CGNs deprived of depolarizing potassium (5K apoptotic condition), caspases appear to play a dominant role in CtBP downregulation. However, incubation in 5K does not enhance the kinetics of CtBP1 degradation and recombinant CtBP1 is not cleaved in vitro by caspase-3. In addition, 5K has no significant effect on CtBP transcript expression. Finally, mouse embryonic stem cells display caspase-dependent downregulation of CtBP1 following exposure to staurosporine, an effect that is not observed in DGCR8 knockout cells which are deficient in miRNA processing. These data identify caspase-dependent downregulation of CtBPs as an alternative mechanism to the proteasome for regulation of these transcriptional co-repressors in neurons undergoing apoptosis. Moreover, caspases appear to regulate CtBP expression indirectly, at a post-transcriptional level, and via a mechanism that is dependent upon miRNA processing. We conclude that CtBPs are essential pro-survival proteins in neurons and their downregulation contributes significantly to neuronal apoptosis via the de-repression of pro-apoptotic genes.
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Affiliation(s)
- Trisha R Stankiewicz
- Research Service, Veterans Affairs Medical Center, Denver, Colorado, 80220, USA.,Department of Biological Sciences and Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, 80208, USA
| | - Emily K Schroeder
- Research Service, Veterans Affairs Medical Center, Denver, Colorado, 80220, USA
| | - Natalie A Kelsey
- Department of Biological Sciences and Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, 80208, USA
| | - Ron J Bouchard
- Research Service, Veterans Affairs Medical Center, Denver, Colorado, 80220, USA
| | - Daniel A Linseman
- Research Service, Veterans Affairs Medical Center, Denver, Colorado, 80220, USA.,Department of Biological Sciences and Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, 80208, USA.,Division of Clinical Pharmacology and Toxicology, Department of Medicine and Neuroscience Program, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
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9
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Protein-Protein Interactions: Gene Acronym Redundancies and Current Limitations Precluding Automated Data Integration. Proteomes 2013; 1:3-24. [PMID: 28250396 PMCID: PMC5314489 DOI: 10.3390/proteomes1010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 05/16/2013] [Accepted: 05/21/2013] [Indexed: 12/31/2022] Open
Abstract
Understanding protein interaction networks and their dynamic changes is a major challenge in modern biology. Currently, several experimental and in silico approaches allow the screening of protein interactors in a large-scale manner. Therefore, the bulk of information on protein interactions deposited in databases and peer-reviewed published literature is constantly growing. Multiple databases interfaced from user-friendly web tools recently emerged to facilitate the task of protein interaction data retrieval and data integration. Nevertheless, as we evidence in this report, despite the current efforts towards data integration, the quality of the information on protein interactions retrieved by in silico approaches is frequently incomplete and may even list false interactions. Here we point to some obstacles precluding confident data integration, with special emphasis on protein interactions, which include gene acronym redundancies and protein synonyms. Three human proteins (choline kinase, PPIase and uromodulin) and three different web-based data search engines focused on protein interaction data retrieval (PSICQUIC, DASMI and BIPS) were used to explain the potential occurrence of undesired errors that should be considered by researchers in the field. We demonstrate that, despite the recent initiatives towards data standardization, manual curation of protein interaction networks based on literature searches are still required to remove potential false positives. A three-step workflow consisting of: (i) data retrieval from multiple databases, (ii) peer-reviewed literature searches, and (iii) data curation and integration, is proposed as the best strategy to gather updated information on protein interactions. Finally, this strategy was applied to compile bona fide information on human DREAM protein interactome, which constitutes liable training datasets that can be used to improve computational predictions.
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10
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C-Terminal Binding Protein: A Molecular Link between Metabolic Imbalance and Epigenetic Regulation in Breast Cancer. Int J Cell Biol 2013; 2013:647975. [PMID: 23762064 PMCID: PMC3671672 DOI: 10.1155/2013/647975] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 04/14/2013] [Accepted: 04/15/2013] [Indexed: 12/21/2022] Open
Abstract
The prevalence of obesity has given rise to significant global concerns as numerous population-based studies demonstrate an incontrovertible association between obesity and breast cancer. Mechanisms proposed to account for this linkage include exaggerated levels of carbohydrate substrates, elevated levels of circulating mitogenic hormones, and inflammatory cytokines that impinge on epithelial programming in many tissues. Moreover, recently many scientists have rediscovered the observation, first described by Otto Warburg nearly a century ago, that most cancer cells undergo a dramatic metabolic shift in energy utilization and expenditure that fuels and supports the cellular expansion associated with malignant proliferation. This shift in substrate oxidation comes at the cost of sharp changes in the levels of the high energy intermediate, nicotinamide adenine dinucleotide (NADH). In this review, we discuss a novel example of how shifts in the concentration and flux of substrates metabolized and generated during carbohydrate metabolism represent components of a signaling network that can influence epigenetic regulatory events in the nucleus. We refer to this regulatory process as "metabolic transduction" and describe how the C-terminal binding protein (CtBP) family of NADH-dependent nuclear regulators represents a primary example of how cellular metabolic status can influence epigenetic control of cellular function and fate.
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11
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Pruunsild P, Timmusk T. Subcellular localization and transcription regulatory potency of KCNIP/Calsenilin/DREAM/KChIP proteins in cultured primary cortical neurons do not provide support for their role in CRE-dependent gene expression. J Neurochem 2012; 123:29-43. [PMID: 22612322 DOI: 10.1111/j.1471-4159.2012.07796.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
KCNIP3/KChIP3 (voltage-dependent K+ channel interacting protein 3), alias Calsenilin and downstream regulatory element antagonist modulator (DREAM), is a multifunctional protein that modulates A-type potassium channels, affects processing of amyloid precursor protein and regulates transcription. KCNIP3 has been described to negatively influence the activity of CREB (cAMP/Ca(2+)-response element binding protein), an essential factor in neuronal activity-dependent gene expression regulation. However, reports on intracellular localization of KCNIP3 in neurons are diverse and necessitate additional analyses of distribution of KCNIPs in cells to clarify the potential of KCNIP3 to fulfill its functions in different cell compartments. Here, we examined localization of the entire family of highly similar KCNIP proteins in neuronal cells and show that over-expressed isoforms of KCNIP1/KChIP1, KCNIP2/KChIP2, KCNIP3/KChIP3, and KCNIP4/KChIP4 had varied, yet partially overlapping subcellular localization. In addition, although some of the over-expressed KCNIP isoforms localized to the nucleus, endogenous KCNIPs were not detected in nuclei of rat primary cortical neurons. Moreover, we analyzed the role of KCNIP proteins in cAMP/Ca(2+)-response element (CRE)-dependent transcription by luciferase reporter assay and electrophoretic mobility shift assay and report that our results do not support the role for KCNIPs, including DREAM/Calsenilin/KChIP3, in modulation of CREB-mediated transcription in neurons.
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Affiliation(s)
- Priit Pruunsild
- Department of Gene Technology, Tallinn University of Technology, Estonia.
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12
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Dierssen M, Fedrizzi L, Gomez-Villafuertes R, de Lagran MM, Gutierrez-Adan A, Sahún I, Pintado B, Oliveros JC, Dopazo XM, Gonzalez P, Brini M, Mellström B, Carafoli E, Naranjo JR. Reduced Mid1 Expression and Delayed Neuromotor Development in daDREAM Transgenic Mice. Front Mol Neurosci 2012; 5:58. [PMID: 22563308 PMCID: PMC3342529 DOI: 10.3389/fnmol.2012.00058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 04/11/2012] [Indexed: 11/21/2022] Open
Abstract
Downstream regulatory element antagonist modulator (DREAM) is a Ca2+-binding protein that binds DNA and represses transcription in a Ca2+-dependent manner. Previous work has shown a role for DREAM in cerebellar function regulating the expression of the sodium/calcium exchanger 3 (NCX3) in cerebellar granular neurons to control Ca2+ homeostasis and survival of these neurons. To achieve a global view of the genes regulated by DREAM in the cerebellum, we performed a genome-wide analysis in transgenic cerebellum expressing a Ca2+-insensitive/CREB-independent dominant active mutant DREAM (daDREAM). Here we show that DREAM regulates the expression of the midline 1 (Mid1) gene early after birth. As a consequence, daDREAM mice exhibit a significant shortening of the rostro-caudal axis of the cerebellum and a delay in neuromotor development early after birth. Our results indicate a role for DREAM in cerebellar function.
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Affiliation(s)
- Mara Dierssen
- Genomic Regulation Center, Parc de Recerca Biomèdica de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras Barcelona, Spain
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13
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Burgoyne RD, Haynes LP. Understanding the physiological roles of the neuronal calcium sensor proteins. Mol Brain 2012; 5:2. [PMID: 22269068 PMCID: PMC3271974 DOI: 10.1186/1756-6606-5-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 01/23/2012] [Indexed: 01/22/2023] Open
Abstract
Calcium signalling plays a crucial role in the control of neuronal function and plasticity. Changes in neuronal Ca2+ concentration are detected by Ca2+-binding proteins that can interact with and regulate target proteins to modify their function. Members of the neuronal calcium sensor (NCS) protein family have multiple non-redundant roles in the nervous system. Here we review recent advances in the understanding of the physiological roles of the NCS proteins and the molecular basis for their specificity.
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Affiliation(s)
- Robert D Burgoyne
- Department of Cellular and Molecular Physiology, The Physiological Laboratory, Institute of Translational Medicine, University of Liverpool, Liverpool, UK.
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Rivas M, Villar D, González P, Dopazo XM, Mellstrom B, Naranjo JR. Building the DREAM interactome. SCIENCE CHINA-LIFE SCIENCES 2011; 54:786-92. [DOI: 10.1007/s11427-011-4196-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 06/07/2011] [Indexed: 12/28/2022]
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Visinin-like proteins (VSNLs): interaction partners and emerging functions in signal transduction of a subfamily of neuronal Ca2+ -sensor proteins. Cell Tissue Res 2008; 335:301-16. [PMID: 18989702 DOI: 10.1007/s00441-008-0716-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 09/29/2008] [Indexed: 10/21/2022]
Abstract
The visinin-like protein (VSNL) subfamily, including VILIP-1 (the founder protein), VILIP-2, VILIP-3, hippocalcin, and neurocalcin delta, constitute a highly homologous subfamily of neuronal calcium sensor (NCS) proteins. Comparative studies have shown that VSNLs are expressed predominantly in the brain with restricted expression patterns in various subsets of neurons but are also found in peripheral organs. In addition, the proteins display differences in their calcium affinities, in their membrane-binding kinetics, and in the intracellular targets to which they associate after calcium binding. Even though the proteins use a similar calcium-myristoyl switch mechanism to translocate to cellular membranes, they show calcium-dependent localization to various subcellular compartments when expressed in the same neuron. These distinct calcium-myristoyl switch properties might be explained by specificity for defined phospholipids and membrane-bound targets; this enables VSNLs to modulate various cellular signal transduction pathways, including cyclic nucleotide and MAPK signaling. An emerging theme is the direct or indirect effect of VSNLs on gene expression and their interaction with components of membrane trafficking complexes, with a possible role in membrane trafficking of different receptors and ion channels, such as glutamate receptors of the kainate and AMPA subtype, nicotinic acetylcholine receptors, and Ca(2+)-channels. One hypothesis is that the highly homologous VSNLs have evolved to fulfil specialized functions in membrane trafficking and thereby affect neuronal signaling and differentiation in defined subsets of neurons. VSNLs are involved in differentiation processes showing a tumor-invasion-suppressor function in peripheral organs. Finally, VSNLs play neuroprotective and neurotoxic roles and have been implicated in neurodegenerative diseases.
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Haverkamp S, Specht D, Majumdar S, Zaidi NF, Brandstätter JH, Wasco W, Wässle H, Tom Dieck S. Type 4 OFF cone bipolar cells of the mouse retina express calsenilin and contact cones as well as rods. J Comp Neurol 2008; 507:1087-101. [PMID: 18095322 DOI: 10.1002/cne.21612] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Immunocytochemical discrimination of distinct bipolar cell types in the mouse retina is a prerequisite for analyzing retinal circuitry in wild-type and transgenic mice. Here we demonstrate that among the more than 10 anatomically defined mouse bipolar cell types, type 4 bipolar cells are specifically recognized by anti-calsenilin antibodies. Axon terminals in the inner plexiform layer are not readily identifiable because calsenilin is also expressed in a subset of amacrine and ganglion cells. In contrast, in the outer plexiform layer calsenilin immunoreactivity allows the analysis of photoreceptor to type 4 bipolar cell contacts. A dense plexus of calsenilin-positive dendrites makes several basal contacts at cone pedicles. An individual calsenilin-positive bipolar cell contacts five to seven cones. In addition, some calsenilin-positive dendrites contact rod photoreceptors. On average we counted 10 rod spherule contacts per type 4 bipolar cell, and approximately 10% of rods contacted type 4 bipolar cells. We suggest that type 4 bipolar cells, together with the recently described type 3a and b cells, provide an alternative and direct route from rods to OFF cone bipolar cells. In the Bassoon DeltaEx4/5 mouse, a mouse mutant that shows extensive remodeling of the rod system including sprouting of horizontal and rod bipolar cells into the outer nuclear layer due to impaired synaptic transmission, we found that in addition mixed-input (type 3 and 4) OFF bipolar cells sprout to ectopic sites. In contrast, true cone-selective type 1 and 2 OFF cone bipolar cells did not show sprouting in the Bassoon mouse mutant.
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Affiliation(s)
- Silke Haverkamp
- Department of Neuroanatomy, Max Planck Institute for Brain Research, 60528 Frankfurt/Main, Germany
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Lusin JD, Vanarotti M, Li C, Valiveti A, Ames JB. NMR structure of DREAM: Implications for Ca(2+)-dependent DNA binding and protein dimerization. Biochemistry 2008; 47:2252-64. [PMID: 18201103 DOI: 10.1021/bi7017267] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DREAM (calsenilin/KChIP3) is an EF-hand calcium-binding protein that binds to specific DNA sequences and regulates Ca2+-induced transcription of prodynorphin and c-fos genes. Here, we present the atomic-resolution structure of Ca2+-bound DREAM in solution determined by nuclear magnetic resonance (NMR) spectroscopy. Pulsed-field gradient NMR diffusion experiments and 15N NMR relaxation analysis indicate that Ca2+-bound DREAM forms a stable dimer in solution. The structure of the first 77 residues from the N-terminus could not be determined by our NMR analysis. The C-terminal DREAM structure (residues 78-256) contains four EF-hand motifs arranged in a tandem linear array, similar to that seen in KChIP1, recoverin, and other structures of the neuronal calcium sensor (NCS) branch of the calmodulin superfamily. Mg2+ is bound at the second EF-hand, whereas Ca2+ is bound functionally at the third and fourth sites. The first and second EF-hands form an exposed hydrophobic groove on the protein surface lined by side-chain atoms of L96, F100, F114, I117, Y118, F121, F122, Y151, L155, L158, and L159 that are highly conserved in all NCS proteins. An exposed leucine near the C-terminus (L251) is suggested to form intermolecular contacts with leucine residues in the hydrophobic groove (L155, L158, and L159). Positively charged side chains of Arg and Lys (Lys87, Lys90, Lys91, Arg98, Lys101, Arg160, and Lys166) are clustered on one side of the protein surface and may mediate electrostatic contacts with DNA targets. We propose that Ca2+-induced dimerization of DREAM may partially block the putative DNA-binding site, which may suggest as to how Ca2+ abolishes DREAM binding to DNA to activate the transcription of prodynorphin and other downstream genes in pain control.
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Affiliation(s)
- Jacqueline D Lusin
- Department of Chemistry, University of California, Davis, California 95616, USA
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Leclerc GM, Boockfor FR. Calcium influx and DREAM protein are required for GnRH gene expression pulse activity. Mol Cell Endocrinol 2007; 267:70-9. [PMID: 17241740 PMCID: PMC1852481 DOI: 10.1016/j.mce.2006.12.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 10/28/2006] [Accepted: 12/19/2006] [Indexed: 12/19/2022]
Abstract
Recent evidence using GT1-7 cells indicates that GnRH pulsatility depends on exocytotic-release and gene transcription events. To determine whether calcium or DREAM may play a role in linking these processes, we used an L-type Ca(2+)-blocker (nimodipine) and found that not only GnRH gene expression (GnRH-GE) pulse activity was abolished but also that binding of proteins to OCT1BS-a (essential site for GnRH-GE pulses) was reduced. We further found that only EF-hand forms of DREAM were expressed in GT1-7 and that DREAM was part of the complex binding to OCT1BS-a. Finally, microinjection of DREAM antibody into cells abolished GnRH-GE pulses demonstrating its importance in pulsatility. These results reveal that calcium and DREAM may bridge cytoplasmic and nuclear events enabling temporal coordination of intermittent activity. Expression of DREAM in various cell types coupled with the universal role of calcium raise the possibility that these factors may play similar role in other secretory cells.
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Affiliation(s)
- Gilles M Leclerc
- Laboratory of Molecular Dynamics, Department of Cell Biology and Anatomy Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA
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Burgoyne RD. Neuronal calcium sensor proteins: generating diversity in neuronal Ca2+ signalling. Nat Rev Neurosci 2007; 8:182-93. [PMID: 17311005 PMCID: PMC1887812 DOI: 10.1038/nrn2093] [Citation(s) in RCA: 426] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In neurons, intracellular calcium signals have crucial roles in activating neurotransmitter release and in triggering alterations in neuronal function. Calmodulin has been widely studied as a Ca(2+) sensor that has several defined roles in neuronal Ca(2+) signalling, but members of the neuronal calcium sensor protein family have also begun to emerge as key components in a number of regulatory pathways and have increased the diversity of neuronal Ca(2+) signalling pathways. The differing properties of these proteins allow them to have discrete, non-redundant functions.
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Affiliation(s)
- Robert D Burgoyne
- The Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, UK.
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