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Rochín-Hernández LJ, Jiménez-Acosta MA, Ramírez-Reyes L, Figueroa-Corona MDP, Sánchez-González VJ, Orozco-Barajas M, Meraz-Ríos MA. The Proteome Profile of Olfactory Ecto-Mesenchymal Stem Cells-Derived from Patients with Familial Alzheimer's Disease Reveals New Insights for AD Study. Int J Mol Sci 2023; 24:12606. [PMID: 37628788 PMCID: PMC10454072 DOI: 10.3390/ijms241612606] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Alzheimer's disease (AD), the most common neurodegenerative disease and the first cause of dementia worldwide, has no effective treatment, and its pathological mechanisms are not yet fully understood. We conducted this study to explore the proteomic differences associated with Familial Alzheimer's Disease (FAD) in olfactory ecto-mesenchymal stem cells (MSCs) derived from PSEN1 (A431E) mutation carriers compared with healthy donors paired by age and gender through two label-free liquid chromatography-mass spectrometry approaches. The first analysis compared carrier 1 (patient with symptoms, P1) and its control (healthy donor, C1), and the second compared carrier 2 (patient with pre-symptoms, P2) with its respective control cells (C2) to evaluate whether the protein alterations presented in the symptomatic carrier were also present in the pre-symptom stages. Finally, we analyzed the differentially expressed proteins (DEPs) for biological and functional enrichment. These proteins showed impaired expression in a stage-dependent manner and are involved in energy metabolism, vesicle transport, actin cytoskeleton, cell proliferation, and proteostasis pathways, in line with previous AD reports. Our study is the first to conduct a proteomic analysis of MSCs from the Jalisco FAD patients in two stages of the disease (symptomatic and presymptomatic), showing these cells as a new and excellent in vitro model for future AD studies.
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Affiliation(s)
- Lory J. Rochín-Hernández
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.A.J.-A.); (M.d.P.F.-C.)
| | - Miguel A. Jiménez-Acosta
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.A.J.-A.); (M.d.P.F.-C.)
| | - Lorena Ramírez-Reyes
- Unidad de Genómica, Proteómica y Metabolómica, Laboratorio Nacional de Servicios Experimentales (LaNSE), Centro de Investigación y de Estudios Avanzados, Ciudad de México 07360, Mexico;
| | - María del Pilar Figueroa-Corona
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.A.J.-A.); (M.d.P.F.-C.)
| | - Víctor J. Sánchez-González
- Centro Universitario de Los Altos, Universidad de Guadalajara, Tepatitlán de Morelos 47620, Mexico; (V.J.S.-G.); (M.O.-B.)
| | - Maribel Orozco-Barajas
- Centro Universitario de Los Altos, Universidad de Guadalajara, Tepatitlán de Morelos 47620, Mexico; (V.J.S.-G.); (M.O.-B.)
| | - Marco A. Meraz-Ríos
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.A.J.-A.); (M.d.P.F.-C.)
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2
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Armas P, Coux G, Weiner AMJ, Calcaterra NB. What's new about CNBP? Divergent functions and activities for a conserved nucleic acid binding protein. Biochim Biophys Acta Gen Subj 2021; 1865:129996. [PMID: 34474118 DOI: 10.1016/j.bbagen.2021.129996] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Cellular nucleic acid binding protein (CNBP) is a conserved single-stranded nucleic acid binding protein present in most eukaryotes, but not in plants. Expansions in the CNBP gene cause myotonic dystrophy type 2. Initially reported as a transcriptional regulator, CNBP was then also identified acting as a translational regulator. SCOPE OF REVIEW The focus of this review was to link the CNBP structural features and newly reported biochemical activities with the recently described biological functions, in the context of its pathological significance. MAJOR CONCLUSIONS Several post-translational modifications affect CNBP subcellular localization and activity. CNBP participates in the transcriptional and translational regulation of a wide range of genes by remodeling single-stranded nucleic acid secondary structures and/or by modulating the activity of trans-acting factors. CNBP is required for proper neural crest and heart development, and plays a role in cell proliferation control. Besides, CNBP has been linked with neurodegenerative, inflammatory, and congenital diseases, as well as with tumor processes. GENERAL SIGNIFICANCE This review provides an insight into the growing functions of CNBP in cell biology. A unique and robust mechanistic or biochemical connection among these roles has yet not been elucidated. However, the ability of CNBP to dynamically integrate signaling pathways and to act as nucleic acid chaperone may explain most of the roles and functions identified so far.
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Affiliation(s)
- Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONIeCET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Esmeralda y Ocampo 531, S2002LRK Rosario, Argentina
| | - Gabriela Coux
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONIeCET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Esmeralda y Ocampo 531, S2002LRK Rosario, Argentina
| | - Andrea M J Weiner
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONIeCET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Esmeralda y Ocampo 531, S2002LRK Rosario, Argentina
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONIeCET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Esmeralda y Ocampo 531, S2002LRK Rosario, Argentina.
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3
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Chen Y, Lei X, Jiang Z, Fitzgerald KA. Cellular nucleic acid-binding protein is essential for type I interferon-mediated immunity to RNA virus infection. Proc Natl Acad Sci U S A 2021; 118:e2100383118. [PMID: 34168080 PMCID: PMC8255963 DOI: 10.1073/pnas.2100383118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Type I interferons (IFNs) are innate immune cytokines required to establish cellular host defense. Precise control of IFN gene expression is crucial to maintaining immune homeostasis. Here, we demonstrated that cellular nucleic acid-binding protein (CNBP) was required for the production of type I IFNs in response to RNA virus infection. CNBP deficiency markedly impaired IFN production in macrophages and dendritic cells that were infected with a panel of RNA viruses or stimulated with synthetic double-stranded RNA. Furthermore, CNBP-deficient mice were more susceptible to influenza virus infection than were wild-type mice. Mechanistically, CNBP was phosphorylated and translocated to the nucleus, where it directly binds to the promoter of IFNb in response to RNA virus infection. Furthermore, CNBP controlled the recruitment of IFN regulatory factor (IRF) 3 and IRF7 to IFN promoters for the maximal induction of IFNb gene expression. These studies reveal a previously unrecognized role for CNBP as a transcriptional regulator of type I IFN genes engaged downstream of RNA virus-mediated innate immune signaling, which provides an additional layer of control for IRF3- and IRF7-dependent type I IFN gene expression and the antiviral innate immune response.
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Affiliation(s)
- Yongzhi Chen
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xuqiu Lei
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Zhaozhao Jiang
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605
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4
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Lee E, Lee TA, Yoo HJ, Lee S, Park B. CNBP controls tumor cell biology by regulating tumor-promoting gene expression. Mol Carcinog 2019; 58:1492-1501. [PMID: 31087358 DOI: 10.1002/mc.23030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/23/2019] [Accepted: 04/15/2019] [Indexed: 12/31/2022]
Abstract
Cellular nucleic acid-binding protein (CNBP) is associated with cell proliferation, and its expression is elevated in human tumors, but the molecular mechanisms of CNBP in tumor cell biology have not been fully elucidated. In this study, we report that CNBP is a transcription factor essential for regulating matrix metalloproteinases mmp-2, mmp-14, and transcription factor e2f2 gene expression by binding to their promoter regions via a sequence-specific manner. Importantly, epidermal growth factor stimulation is required to induce CNBP phosphorylation and nuclear transport, thereby promoting the expression of mmp-2, mmp-14, and e2f2 genes. As a consequence, loss of cnbp attenuates the ability of tumor cell growth, invasion, and migration. Conversely, overexpression of cnbp is associated with tumor cell biology. Collectively, our findings reveal CNBP as a key transcriptional regulator of tumor-promoting target genes to control tumor cell biology.
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Affiliation(s)
- Eunhye Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Taeyun A Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Hye Jin Yoo
- Division of Tumor Immunology, National Cancer Center, Goyang, South Korea
| | - Sungwook Lee
- Division of Tumor Immunology, National Cancer Center, Goyang, South Korea
| | - Boyoun Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
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5
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Chen Y, Sharma S, Assis PA, Jiang Z, Elling R, Olive AJ, Hang S, Bernier J, Huh JR, Sassetti CM, Knipe DM, Gazzinelli RT, Fitzgerald KA. CNBP controls IL-12 gene transcription and Th1 immunity. J Exp Med 2018; 215:3136-3150. [PMID: 30442645 PMCID: PMC6279399 DOI: 10.1084/jem.20181031] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/05/2018] [Accepted: 10/23/2018] [Indexed: 12/22/2022] Open
Abstract
These studies reveal a previously unrecognized role for Cnbp as a novel transcriptional regulator engaged downstream of innate immune receptors controlling the c-Rel–IL-12–Th1 axis, which has important implications for both host defense and inflammatory disease. An inducible program of inflammatory gene expression is a hallmark of antimicrobial defenses. Recently, cellular nucleic acid–binding protein (CNBP) was identified as a regulator of nuclear factor-kappaB (NF-κB)–dependent proinflammatory cytokine gene expression. Here, we generated mice lacking CNBP and found that CNBP regulates a very restricted gene signature that includes IL-12β. CNBP resides in the cytosol of macrophages and translocates to the nucleus in response to diverse microbial pathogens and pathogen-derived products. Cnbp-deficient macrophages induced canonical NF-κB/Rel signaling normally but were impaired in their ability to control the activation of c-Rel, a key driver of IL-12β gene transcription. The nuclear translocation and DNA-binding activity of c-Rel required CNBP. Lastly, Cnbp-deficient mice were more susceptible to acute toxoplasmosis associated with reduced production of IL-12β, as well as a reduced T helper type 1 (Th1) cell IFN-γ response essential to controlling parasite replication. Collectively, these findings identify CNBP as important regulator of c-Rel–dependent IL-12β gene transcription and Th1 immunity.
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Affiliation(s)
- Yongzhi Chen
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Shruti Sharma
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA.,Department of Immunology, Tufts University School of Medicine, Boston, MA
| | - Patricia A Assis
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Zhaozhao Jiang
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Roland Elling
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Andrew J Olive
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA
| | - Saiyu Hang
- Division of Immunology, Department of Microbiology and Immunology, Harvard Medical School, Boston, MA
| | - Jennifer Bernier
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Jun R Huh
- Division of Immunology, Department of Microbiology and Immunology, Harvard Medical School, Boston, MA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA
| | - David M Knipe
- Department of Microbiology and Immunology, Harvard Medical School, Boston, MA
| | - Ricardo T Gazzinelli
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA.,Departamento de Bioquímica e Imunologia, Universidade Federal of Minas Gerais, Belo Horizonte, Brazil.,Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA .,Centre for Molecular Inflammation Research, Department of Cancer Research and Molecular Medicine, Trondheim, Norway
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Lee E, Lee TA, Kim JH, Park A, Ra EA, Kang S, Choi HJ, Choi JL, Huh HD, Lee JE, Lee S, Park B. CNBP acts as a key transcriptional regulator of sustained expression of interleukin-6. Nucleic Acids Res 2017; 45:3280-3296. [PMID: 28168305 PMCID: PMC5389554 DOI: 10.1093/nar/gkx071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/26/2017] [Indexed: 12/17/2022] Open
Abstract
The transcription of inflammatory genes is an essential step in host defense activation. Here, we show that cellular nucleic acid-binding protein (CNBP) acts as a transcription regulator that is required for activating the innate immune response. We identified specific CNBP-binding motifs present in the promoter region of sustained inflammatory cytokines, thus, directly inducing the expression of target genes. In particular, lipopolysaccharide (LPS) induced cnbp expression through an NF-κB-dependent manner and a positive autoregulatory mechanism, which enables prolonged il-6 gene expression. This event depends strictly on LPS-induced CNBP nuclear translocation through phosphorylation-mediated dimerization. Consequently, cnbp-depleted zebrafish are highly susceptible to Shigella flexneri infection in vivo. Collectively, these observations identify CNBP as a key transcriptional regulator required for activating and maintaining the immune response.
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Affiliation(s)
- Eunhye Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
- These authors contributed equally to the paper as first authors
| | - Taeyun A. Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
- These authors contributed equally to the paper as first authors
| | - Ji Hyun Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, South Korea
- These authors contributed equally to the paper as first authors
| | - Areum Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Eun A. Ra
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Sujin Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Hyun jin Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Junhee L. Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Hyunbin D. Huh
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Ji Eun Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, South Korea
- Samsung Genome Institute (SGI), Samsung Medical Center, Seoul 06351, South Korea
- To whom correspondence should be addressed. Tel: +82 2 2123 5655; Fax: +82 2 312 5657; . Correspondence may also be addressed to Ji Eun Lee. Tel: +82 2 3410 6129; Fax: +82 2 3410 0534; . Correspondence may also be addressed to Sungwook Lee. Tel: +82 31 920 2537; Fax: +82 31 920 2542;
| | - Sungwook Lee
- Cancer Immunology Branch, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 10408, South Korea
- To whom correspondence should be addressed. Tel: +82 2 2123 5655; Fax: +82 2 312 5657; . Correspondence may also be addressed to Ji Eun Lee. Tel: +82 2 3410 6129; Fax: +82 2 3410 0534; . Correspondence may also be addressed to Sungwook Lee. Tel: +82 31 920 2537; Fax: +82 31 920 2542;
| | - Boyoun Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
- To whom correspondence should be addressed. Tel: +82 2 2123 5655; Fax: +82 2 312 5657; . Correspondence may also be addressed to Ji Eun Lee. Tel: +82 2 3410 6129; Fax: +82 2 3410 0534; . Correspondence may also be addressed to Sungwook Lee. Tel: +82 31 920 2537; Fax: +82 31 920 2542;
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Holler CJ, Davis PR, Beckett TL, Platt TL, Webb RL, Head E, Murphy MP. Bridging integrator 1 (BIN1) protein expression increases in the Alzheimer's disease brain and correlates with neurofibrillary tangle pathology. J Alzheimers Dis 2015; 42:1221-7. [PMID: 25024306 DOI: 10.3233/jad-132450] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Recent genome wide association studies have implicated bridging integrator 1 (BIN1) as a late-onset Alzheimer's disease (AD) susceptibility gene. There are at least 15 different known isoforms of BIN1, with many being expressed in the brain including the longest isoform (iso1), which is brain-specific and localizes to axon initial segments and nodes of Ranvier. It is currently unknown what role BIN1 plays in AD. We analyzed BIN1 protein expression from a large number (n = 71) of AD cases and controls from five different brain regions (hippocampus, inferior parietal cortex, inferior temporal cortex, frontal cortex (BA9), and superior and middle temporal gyri). We found that the amount of the largest isoform of BIN1 was significantly reduced in the AD brain compared to age-matched controls, and smaller BIN1 isoforms were significantly increased. Further, BIN1 was significantly correlated with the amount of neurofibrillary tangle (NFT) pathology but not with either diffuse or neuritic plaques, or with the amount of amyloid-β peptide. BIN1 is known to be abnormally expressed in another human disease, myotonic dystrophy, which also features prominent NFT pathology. These data suggest that BIN1 is likely involved in AD as a modulator of NFT pathology, and that this role may extend to other human diseases that feature tau pathology.
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Affiliation(s)
- Christopher J Holler
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Paulina R Davis
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, KY, USA
| | - Tina L Beckett
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Thomas L Platt
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Robin L Webb
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Elizabeth Head
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, KY, USA
| | - M Paul Murphy
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA University of Kentucky Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
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Challier E, Lisa MN, Nerli BB, Calcaterra NB, Armas P. Novel high-performance purification protocol of recombinant CNBP suitable for biochemical and biophysical characterization. Protein Expr Purif 2013; 93:23-31. [PMID: 24161561 DOI: 10.1016/j.pep.2013.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/13/2013] [Indexed: 12/21/2022]
Abstract
Cellular nucleic acid binding protein (CNBP) is a highly conserved multi-zinc knuckle protein that enhances c-MYC expression, is related to certain human muscular diseases and is required for proper rostral head development. CNBP binds to single-stranded DNA (ssDNA) and RNA and acts as nucleic acid chaperone. Despite the advances made concerning CNBP biological roles, a full knowledge about the structure-function relationship has not yet been achieved, likely due to difficulty in obtaining pure and tag-free CNBP. Here, we report a fast, simple, reproducible, and high-performance expression and purification protocol that provides recombinant tag-free CNBP from Escherichia coli cultures. We determined that tag-free CNBP binds its molecular targets with higher affinity than tagged-CNBP. Furthermore, fluorescence spectroscopy revealed the presence of a unique and conserved tryptophan, which is exposed to the solvent and involved, directly or indirectly, in nucleic acid binding. Size-exclusion HPLC revealed that CNBP forms homodimers independently of nucleic acid binding and coexist with monomers as non-interconvertible forms or in slow equilibrium. Circular dichroism spectroscopy showed that CNBP has a secondary structure dominated by random-coil and β-sheet coincident with the sequence-predicted repetitive zinc knuckles motifs, which folding is required for CNBP structural stability and biochemical activity. CNBP structural stability increased in the presence of single-stranded nucleic acid targets similar to other unstructured nucleic acid chaperones. Altogether, data suggest that CNBP is a flexible protein with interspersed structured zinc knuckles, and acquires a more rigid structure upon nucleic acid binding.
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Affiliation(s)
- Emilse Challier
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CCT-Rosario, Ocampo y Esmeralda, S2000FHQ Rosario, Argentina
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9
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Armas P, Margarit E, Mouguelar VS, Allende ML, Calcaterra NB. Beyond the binding site: in vivo identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development. PLoS One 2013; 8:e63234. [PMID: 23667590 PMCID: PMC3646763 DOI: 10.1371/journal.pone.0063234] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 04/01/2013] [Indexed: 12/30/2022] Open
Abstract
CNBP is a nucleic acid chaperone implicated in vertebrate craniofacial development, as well as in myotonic dystrophy type 2 (DM2) and sporadic inclusion body myositis (sIBM) human muscle diseases. CNBP is highly conserved among vertebrates and has been implicated in transcriptional regulation; however, its DNA binding sites and molecular targets remain elusive. The main goal of this work was to identify CNBP DNA binding sites that might reveal target genes involved in vertebrate embryonic development. To accomplish this, we used a recently described yeast one-hybrid assay to identify DNA sequences bound in vivo by CNBP. Bioinformatic analyses revealed that these sequences are G-enriched and show high frequency of putative G-quadruplex DNA secondary structure. Moreover, an in silico approach enabled us to establish the CNBP DNA-binding site and to predict CNBP putative targets based on gene ontology terms and synexpression with CNBP. The direct interaction between CNBP and candidate genes was proved by EMSA and ChIP assays. Besides, the role of CNBP upon the identified genes was validated in loss-of-function experiments in developing zebrafish. We successfully confirmed that CNBP up-regulates tbx2b and smarca5, and down-regulates wnt5b gene expression. The highly stringent strategy used in this work allowed us to identify new CNBP target genes functionally important in different contexts of vertebrate embryonic development. Furthermore, it represents a novel approach toward understanding the biological function and regulatory networks involving CNBP in the biology of vertebrates.
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Affiliation(s)
- Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
| | - Ezequiel Margarit
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
| | - Valeria S. Mouguelar
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
| | - Miguel L. Allende
- FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Nora B. Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
- * E-mail:
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10
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Rojas M, Farr GW, Fernandez CF, Lauden L, McCormack JC, Wolin SL. Yeast Gis2 and its human ortholog CNBP are novel components of stress-induced RNP granules. PLoS One 2012; 7:e52824. [PMID: 23285195 PMCID: PMC3528734 DOI: 10.1371/journal.pone.0052824] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 11/23/2012] [Indexed: 11/19/2022] Open
Abstract
Although a CCTG expansion in the gene encoding the zinc knuckle protein CNBP causes a common form of muscular dystrophy, the function of both human CNBP and its putative budding yeast ortholog Gis2 remain poorly understood. Here we report the protein interactions of Gis2 and the subcellular locations of both Gis2 and CNBP. We found that Gis2 exhibits RNA-dependent interactions with two proteins involved in mRNA recognition, the poly(A) binding protein and the translation initiation factor eIF4G. We show that Gis2 is a component of two large RNA-protein granules, processing bodies and stress granules, which contain translationally repressed mRNAs. Consistent with a functional ortholog, CNBP also associates with the poly(A) binding protein and accumulates in stress granules during arsenite treatment of human cells. These results implicate both Gis2 and CNBP in mRNA handling during stress.
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Affiliation(s)
- Marta Rojas
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - George W. Farr
- Department of Genetics and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Cesar F. Fernandez
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Laura Lauden
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - John C. McCormack
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Sandra L. Wolin
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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Calcaterra NB, Armas P, Weiner AMJ, Borgognone M. CNBP: a multifunctional nucleic acid chaperone involved in cell death and proliferation control. IUBMB Life 2011; 62:707-14. [PMID: 20960530 DOI: 10.1002/iub.379] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cellular nucleic acid binding protein (CNBP) has been implicated in vertebrate craniofacial development and in myotonic dystrophy type 2 (DM2) and sporadic inclusion body myositis (sIBM) human diseases. In these seemingly unrelated biological processes, CNBP appears to be involved in controlling cell death and proliferation rates. Low levels of CNBP may reduce rate of global protein synthesis, thereby reducing proliferation and increasing apoptosis. Conversely, CNBP might affect transcription of genes required for cell proliferation. Experimental evidences gathered so far make it difficult to ascertain or rule out any of these possibilities. Moreover, both possibilities may not be mutually exclusive. CNBP is a small and strikingly conserved single-stranded nucleic acid binding protein that is able to bind DNA as well as RNA. CNBP has a broad spectrum of targets, ranging from regulatory sites in gene promoters to translational regulatory elements in mRNA untranslated regions. Biochemical experiments have recently shed light on the possible mechanism of action for CNBP, which may act as a nucleic acid chaperone catalyzing the rearrangement of G-rich nucleic acid secondary structures likely relevant for transcriptional and/or translational gene regulation. This review focuses on the involvement of CNBP in vertebrate craniofacial development and human DM2 and sIBM diseases, as well as on the biochemical and structural features of CNBP and its cellular and molecular mechanism of action.
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Affiliation(s)
- Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas- Área Biología General, Dpto. de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK-Rosario, Argentina.
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