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Wang Y, Xing J, Liang Y, Liang H, Liang N, Li J, Yin G, Li X, Zhang K. The structure and function of multifunctional protein ErbB3 binding protein 1 (Ebp1) and its role in diseases. Cell Biol Int 2024; 48:1069-1079. [PMID: 38884348 DOI: 10.1002/cbin.12196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024]
Abstract
ErbB3-binding protein 1(Ebp1) has two isoforms, p42 Ebp1 and p48 Ebp1, both of which can regulate cell growth and differentiation. But these isoforms often have opposite effects, including contradictory roles in regulation of cell growth in different tissues and cells. P48 Ebp1 belongs to the full-length sequence, while conformational changes in the crystal structure of p42 Ebp1 reveals a lack of an α helix at the amino terminus. Due to the differences in the structures of these two isoforms, they have different binding partners and protein modifications. Ebp1 can function as both an oncogene and a tumor suppressor factor. However, the underlying mechanisms by which these two isoforms exert opposite functions are still not fully understood. In this review, we summarize the genes and the structures of protein of these two isoforms, protein modifications, binding partners and the association of different isoforms with diseases.
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Affiliation(s)
- Ying Wang
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Jianxiao Xing
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Yanyang Liang
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Huifang Liang
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Nannan Liang
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Junqin Li
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Guohua Yin
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Xinhua Li
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Kaiming Zhang
- ShanXi Key Laboratory of Stem Cells for Immunological Dermatosis, State Key Breeding Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
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2
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Marchesini M, Gherli A, Simoncini E, Tor LMD, Montanaro A, Thongon N, Vento F, Liverani C, Cerretani E, D'Antuono A, Pagliaro L, Zamponi R, Spadazzi C, Follini E, Cambò B, Giaimo M, Falco A, Sammarelli G, Todaro G, Bonomini S, Adami V, Piazza S, Corbo C, Lorusso B, Mezzasoma F, Lagrasta CAM, Martelli MP, La Starza R, Cuneo A, Aversa F, Mecucci C, Quaini F, Colla S, Roti G. Orthogonal proteogenomic analysis identifies the druggable PA2G4-MYC axis in 3q26 AML. Nat Commun 2024; 15:4739. [PMID: 38834613 PMCID: PMC11150407 DOI: 10.1038/s41467-024-48953-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/20/2024] [Indexed: 06/06/2024] Open
Abstract
The overexpression of the ecotropic viral integration site-1 gene (EVI1/MECOM) marks the most lethal acute myeloid leukemia (AML) subgroup carrying chromosome 3q26 abnormalities. By taking advantage of the intersectionality of high-throughput cell-based and gene expression screens selective and pan-histone deacetylase inhibitors (HDACis) emerge as potent repressors of EVI1. To understand the mechanism driving on-target anti-leukemia activity of this compound class, here we dissect the expression dynamics of the bone marrow leukemia cells of patients treated with HDACi and reconstitute the EVI1 chromatin-associated co-transcriptional complex merging on the role of proliferation-associated 2G4 (PA2G4) protein. PA2G4 overexpression rescues AML cells from the inhibitory effects of HDACis, while genetic and small molecule inhibition of PA2G4 abrogates EVI1 in 3q26 AML cells, including in patient-derived leukemia xenografts. This study positions PA2G4 at the crosstalk of the EVI1 leukemogenic signal for developing new therapeutics and urges the use of HDACis-based combination therapies in patients with 3q26 AML.
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MESH Headings
- Animals
- Female
- Humans
- Mice
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Proliferation/genetics
- Chromosomes, Human, Pair 3/genetics
- Gene Expression Regulation, Leukemic/drug effects
- Histone Deacetylase Inhibitors/pharmacology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- MDS1 and EVI1 Complex Locus Protein/metabolism
- MDS1 and EVI1 Complex Locus Protein/genetics
- Proteogenomics/methods
- Proto-Oncogene Proteins c-myc/metabolism
- Proto-Oncogene Proteins c-myc/genetics
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Matteo Marchesini
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Andrea Gherli
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
| | - Elisa Simoncini
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
| | - Lucas Moron Dalla Tor
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
| | - Anna Montanaro
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
| | - Natthakan Thongon
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Federica Vento
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
- Department of Medical Science, University of Ferrara, Ferrara, Italy
| | - Chiara Liverani
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Elisa Cerretani
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
- Department of Medical Science, University of Ferrara, Ferrara, Italy
| | - Anna D'Antuono
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
| | - Luca Pagliaro
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Raffaella Zamponi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
| | - Chiara Spadazzi
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Elena Follini
- Hematology and BMT Unit, Azienda USL Piacenza, Piacenza, Italy
| | - Benedetta Cambò
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Mariateresa Giaimo
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Angela Falco
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Gabriella Sammarelli
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Giannalisa Todaro
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Sabrina Bonomini
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Valentina Adami
- High-Throughput Screening Core Facility, CIBIO, University of Trento, Trento, Italy
| | - Silvano Piazza
- High-Throughput Screening Core Facility, CIBIO, University of Trento, Trento, Italy
- Computational Biology group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Claudia Corbo
- University of Milano-Bicocca, Department of Medicine and Surgery, NANOMIB Center, Monza, Italy
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Bruno Lorusso
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Federica Mezzasoma
- Institute of Hematology and Center for Hemato-Oncology Research, University of Perugia and Santa Maria Della Misericordia Hospital, Perugia, Italy
| | | | - Maria Paola Martelli
- Institute of Hematology and Center for Hemato-Oncology Research, University of Perugia and Santa Maria Della Misericordia Hospital, Perugia, Italy
| | - Roberta La Starza
- Institute of Hematology and Center for Hemato-Oncology Research, University of Perugia and Santa Maria Della Misericordia Hospital, Perugia, Italy
| | - Antonio Cuneo
- Department of Medical Science, University of Ferrara, Ferrara, Italy
- Hematology Unit, Azienda Ospedaliera-Universitaria S.ANNA, University of Ferrara, Ferrara, Italy
| | | | - Cristina Mecucci
- Institute of Hematology and Center for Hemato-Oncology Research, University of Perugia and Santa Maria Della Misericordia Hospital, Perugia, Italy
| | - Federico Quaini
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Simona Colla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giovanni Roti
- Department of Medicine and Surgery, University of Parma, Parma, Italy.
- Translational Hematology and Chemogenomics Laboratory, University of Parma, Parma, Italy.
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy.
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Neal SJ, Rajasekaran A, Jusić N, Taylor L, Read M, Alfandari D, Pignoni F, Moody SA. Using Xenopus to discover new candidate genes involved in BOR and other congenital hearing loss syndromes. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:212-240. [PMID: 37830236 PMCID: PMC11014897 DOI: 10.1002/jez.b.23222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/15/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Hearing in infants is essential for brain development, acquisition of verbal language skills, and development of social interactions. Therefore, it is important to diagnose hearing loss soon after birth so that interventions can be provided as early as possible. Most newborns in the United States are screened for hearing deficits and commercially available next-generation sequencing hearing loss panels often can identify the causative gene, which may also identify congenital defects in other organs. One of the most prevalent autosomal dominant congenital hearing loss syndromes is branchio-oto-renal syndrome (BOR), which also presents with defects in craniofacial structures and the kidney. Currently, mutations in three genes, SIX1, SIX5, and EYA1, are known to be causative in about half of the BOR patients that have been tested. To uncover new candidate genes that could be added to congenital hearing loss genetic screens, we have combined the power of Drosophila mutants and protein biochemical assays with the embryological advantages of Xenopus, a key aquatic animal model with a high level of genomic similarity to human, to identify potential Six1 transcriptional targets and interacting proteins that play a role during otic development. We review our transcriptomic, yeast 2-hybrid, and proteomic approaches that have revealed a large number of new candidates. We also discuss how we have begun to identify how Six1 and co-factors interact to direct developmental events necessary for normal otic development.
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Affiliation(s)
- Scott J. Neal
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Anindita Rajasekaran
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Nisveta Jusić
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Louis Taylor
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Mai Read
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Dominique Alfandari
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Francesca Pignoni
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Sally A. Moody
- Department of Anatomy and Cell Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
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Yang Y, Xu L, Lei B, Huang Y, Yu M. Effects of trichlorobisphenol A on the expression of proteins and genes associated with puberty initiation in GT1-7 cells and the relevant molecular mechanism. Food Chem Toxicol 2024; 183:114258. [PMID: 38040238 DOI: 10.1016/j.fct.2023.114258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
This study evaluated the effects of Cl3BPA on kisspeptin-G-protein coupled receptor 54 (GPR54)/gonadotropin-releasing hormone (GnRH) (KGG) signals and analyzed the roles of estrogen receptor alpha (ERɑ) and G-protein coupled estrogen receptor 1 (GPER1) in regulating KGG signals. The results showed that Cl3BPA at 50 μM increased the levels of intracellular reactive oxygen species (ROS) and GnRH, upregulated the protein levels of kisspeptin and the expression of fshr, lhr and gnrh1 genes related to KGG in GT1-7 cells. In addition, 50 μM Cl3BPA significantly upregulated the phosphorylation of extracellular regulated protein kinases 1/2 (Erk1/2), the protein levels of GPER1 and the expression of the gper1 as well as the most target genes associated with mitogen-activated protein kinase (MAPK)/Erk1/2 pathways. Specific signal inhibitor experiments found that Cl3BPA activated KGG signals by activating the GPER1-mediated MAPK/Erk1/2 signaling pathway at the mRNA level. A docking test further confirmed the interactions between Cl3BPA and GPER1. The findings suggest that Cl3BPA might induce precocious puberty by increasing GnRH secretion together with KGG signaling upregulation, which is driven by GPER1-mediated signaling pathway. By comparison, ClxBPAs with fewer chlorine atoms had more obvious effects on the expression of proteins and partial genes related to KGG signals in GT1-7 cells.
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Affiliation(s)
- Yingxin Yang
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, PR China
| | - Lanbing Xu
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, PR China
| | - Bingli Lei
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, PR China.
| | - Yaoyao Huang
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, PR China
| | - Mengjie Yu
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, PR China
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5
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Morovicz AP, Mazloumi Gavgani F, Jacobsen RG, Skuseth Slinning M, Turcu DC, Lewis AE. Phosphoinositide 3-kinase signalling in the nucleolus. Adv Biol Regul 2021; 83:100843. [PMID: 34920983 DOI: 10.1016/j.jbior.2021.100843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 12/26/2022]
Abstract
The phosphoinositide 3-kinase (PI3K) signalling pathway plays key roles in many cellular processes and is altered in many diseases. The function and mode of action of the pathway have mostly been elucidated in the cytoplasm. However, many of the components of the PI3K pathway are also present in the nucleus at specific sub-nuclear sites including nuclear speckles, nuclear lipid islets and the nucleolus. Nucleoli are membrane-less subnuclear structures where ribosome biogenesis occurs. Processes leading to ribosome biogenesis are tightly regulated to maintain protein translation capacity of cells. This review focuses on nucleolar PI3K signalling and how it regulates rRNA synthesis, as well as on the identification of downstream phosphatidylinositol (3,4,5)trisphosphate effector proteins.
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Affiliation(s)
| | | | - Rhîan G Jacobsen
- Department of Biological Sciences, University of Bergen, 5008, Bergen, Norway
| | | | - Diana C Turcu
- Department of Biological Sciences, University of Bergen, 5008, Bergen, Norway
| | - Aurélia E Lewis
- Department of Biological Sciences, University of Bergen, 5008, Bergen, Norway.
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Bregante J, Schönbichler A, Pölöske D, Degenfeld-Schonburg L, Monzó Contreras G, Hadzijusufovic E, de Araujo ED, Valent P, Moriggl R, Orlova A. Efficacy and Synergy of Small Molecule Inhibitors Targeting FLT3-ITD + Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:6181. [PMID: 34944800 PMCID: PMC8699584 DOI: 10.3390/cancers13246181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/22/2022] Open
Abstract
Constitutive activation of FLT3 by ITD mutations is one of the most common genetic aberrations in AML, present in ~1/3 of cases. Patients harboring FLT3-ITD display worse clinical outcomes. The integration and advancement of FLT3 TKI in AML treatment provided significant therapeutic improvement. However, due to the emergence of resistance mechanisms, FLT3-ITD+ AML remains a clinical challenge. We performed an unbiased drug screen to identify 18 compounds as particularly efficacious against FLT3-ITD+ AML. Among these, we characterized two investigational compounds, WS6 and ispinesib, and two approved drugs, ponatinib and cabozantinib, in depth. We found that WS6, although not yet investigated in oncology, shows a similar mechanism and potency as ponatinib and cabozantinib. Interestingly, ispinesib and cabozantinib prevent activation of AXL, a key driver and mechanism of drug resistance in FLT3-ITD+ AML patients. We further investigated synergies between the selected compounds and found that combination treatment with ispinesib and cabozantinib or ponatinib shows high synergy in FLT3-ITD+ AML cell lines and patient samples. Together, we suggest WS6, ispinesib, ponatinib and cabozantinib as novel options for targeting FLT3-ITD+ AML. Whether combinatorial tyrosine kinase and kinesin spindle blockade is effective in eradicating neoplastic (stem) cells in FLT3-ITD+ AML remains to be determined in clinical trials.
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Affiliation(s)
- Javier Bregante
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria; (J.B.); (A.S.); (D.P.); (G.M.C.); (R.M.)
| | - Anna Schönbichler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria; (J.B.); (A.S.); (D.P.); (G.M.C.); (R.M.)
| | - Daniel Pölöske
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria; (J.B.); (A.S.); (D.P.); (G.M.C.); (R.M.)
| | - Lina Degenfeld-Schonburg
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria; (L.D.-S.); (E.H.); (P.V.)
| | - Garazi Monzó Contreras
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria; (J.B.); (A.S.); (D.P.); (G.M.C.); (R.M.)
| | - Emir Hadzijusufovic
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria; (L.D.-S.); (E.H.); (P.V.)
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Clinic for Companion Animals and Horses, University Clinic for Small Animals, Internal Medicine Small Animals, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Elvin D. de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L1C6, Canada;
- Centre for Medicinal Chemistry, University of Toronto Mississauga, Mississauga, ON L5L1C6, Canada
| | - Peter Valent
- Department of Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria; (L.D.-S.); (E.H.); (P.V.)
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, 1090 Vienna, Austria
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria; (J.B.); (A.S.); (D.P.); (G.M.C.); (R.M.)
| | - Anna Orlova
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria; (J.B.); (A.S.); (D.P.); (G.M.C.); (R.M.)
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Birikmen M, Bohnsack KE, Tran V, Somayaji S, Bohnsack MT, Ebersberger I. Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity. Front Microbiol 2021; 12:739000. [PMID: 34603269 PMCID: PMC8481954 DOI: 10.3389/fmicb.2021.739000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/17/2021] [Indexed: 01/23/2023] Open
Abstract
Ribosome assembly is an essential and carefully choreographed cellular process. In eukaryotes, several 100 proteins, distributed across the nucleolus, nucleus, and cytoplasm, co-ordinate the step-wise assembly of four ribosomal RNAs (rRNAs) and approximately 80 ribosomal proteins (RPs) into the mature ribosomal subunits. Due to the inherent complexity of the assembly process, functional studies identifying ribosome biogenesis factors and, more importantly, their precise functions and interplay are confined to a few and very well-established model organisms. Although best characterized in yeast (Saccharomyces cerevisiae), emerging links to disease and the discovery of additional layers of regulation have recently encouraged deeper analysis of the pathway in human cells. In archaea, ribosome biogenesis is less well-understood. However, their simpler sub-cellular structure should allow a less elaborated assembly procedure, potentially providing insights into the functional essentials of ribosome biogenesis that evolved long before the diversification of archaea and eukaryotes. Here, we use a comprehensive phylogenetic profiling setup, integrating targeted ortholog searches with automated scoring of protein domain architecture similarities and an assessment of when search sensitivity becomes limiting, to trace 301 curated eukaryotic ribosome biogenesis factors across 982 taxa spanning the tree of life and including 727 archaea. We show that both factor loss and lineage-specific modifications of factor function modulate ribosome biogenesis, and we highlight that limited sensitivity of the ortholog search can confound evolutionary conclusions. Projecting into the archaeal domain, we find that only few factors are consistently present across the analyzed taxa, and lineage-specific loss is common. While members of the Asgard group are not special with respect to their inventory of ribosome biogenesis factors (RBFs), they unite the highest number of orthologs to eukaryotic RBFs in one taxon. Using large ribosomal subunit maturation as an example, we demonstrate that archaea pursue a simplified version of the corresponding steps in eukaryotes. Much of the complexity of this process evolved on the eukaryotic lineage by the duplication of ribosomal proteins and their subsequent functional diversification into ribosome biogenesis factors. This highlights that studying ribosome biogenesis in archaea provides fundamental information also for understanding the process in eukaryotes.
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Affiliation(s)
- Mehmet Birikmen
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Vinh Tran
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Sharvari Somayaji
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Center (S-BIK-F), Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
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Podvin S, Jones A, Liu Q, Aulston B, Mosier C, Ames J, Winston C, Lietz CB, Jiang Z, O’Donoghue AJ, Ikezu T, Rissman RA, Yuan SH, Hook V. Mutant Presenilin 1 Dysregulates Exosomal Proteome Cargo Produced by Human-Induced Pluripotent Stem Cell Neurons. ACS OMEGA 2021; 6:13033-13056. [PMID: 34056454 PMCID: PMC8158845 DOI: 10.1021/acsomega.1c00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/16/2021] [Indexed: 05/28/2023]
Abstract
The accumulation and propagation of hyperphosphorylated tau (p-Tau) is a neuropathological hallmark occurring with neurodegeneration of Alzheimer's disease (AD). Extracellular vesicles, exosomes, have been shown to initiate tau propagation in the brain. Notably, exosomes from human-induced pluripotent stem cell (iPSC) neurons expressing the AD familial A246E mutant form of presenilin 1 (mPS1) are capable of inducing tau deposits in the mouse brain after in vivo injection. To gain insights into the exosome proteome cargo that participates in propagating tau pathology, this study conducted proteomic analysis of exosomes produced by human iPSC neurons expressing A246E mPS1. Significantly, mPS1 altered the profile of exosome cargo proteins to result in (1) proteins present only in mPS1 exosomes and not in controls, (2) the absence of proteins in the mPS1 exosomes which were present only in controls, and (3) shared proteins which were upregulated or downregulated in the mPS1 exosomes compared to controls. These results show that mPS1 dysregulates the proteome cargo of exosomes to result in the acquisition of proteins involved in the extracellular matrix and protease functions, deletion of proteins involved in RNA and protein translation systems along with proteasome and related functions, combined with the upregulation and downregulation of shared proteins, including the upregulation of amyloid precursor protein. Notably, mPS1 neuron-derived exosomes displayed altered profiles of protein phosphatases and kinases involved in regulating the status of p-tau. The dysregulation of exosome cargo proteins by mPS1 may be associated with the ability of mPS1 neuron-derived exosomes to propagate tau pathology.
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Affiliation(s)
- Sonia Podvin
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Alexander Jones
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Qing Liu
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Brent Aulston
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Charles Mosier
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Janneca Ames
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Charisse Winston
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Christopher B. Lietz
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Zhenze Jiang
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Anthony J. O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Tsuneya Ikezu
- Department
of Pharmacology and Experimental Therapeutics, Department of Neurology,
Alzheimer’s Disease Research Center, Boston University, School of Medicine, Boston 02118, Massachusetts, United States
| | - Robert A. Rissman
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
- Veterans
Affairs San Diego Healthcare System,
La Jolla, San Diego 92161, California, United States
| | - Shauna H. Yuan
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Vivian Hook
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, San Diego 92093, California, United States
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
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9
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Akbar S, Bhakta S, Sengupta J. Structural insights into the interplay of protein biogenesis factors with the 70S ribosome. Structure 2021; 29:755-767.e4. [PMID: 33761323 DOI: 10.1016/j.str.2021.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/16/2021] [Accepted: 03/02/2021] [Indexed: 11/28/2022]
Abstract
Bacterial co-translational N-terminal methionine excision, an early event of nascent polypeptide chain processing, is mediated by two enzymes: peptide deformylase (PDF) and methionine aminopeptidase (MetAP). Trigger factor (TF), the only ribosome-associated bacterial chaperone, offers co-translational chaperoning assistance. Here, we present two high-resolution cryoelectron microscopy structures of tRNA-bound E. coli ribosome complexes showing simultaneous binding of PDF and TF, in the absence (3.4 Å) and presence of MetAP (4.1 Å). These structures establish molecular details of the interactions of the factors with the ribosome, and thereby reveal the structural basis of nascent chain processing. Our results suggest that simultaneous binding of all three factors is not a functionally favorable mechanism of nascent chain processing. Strikingly, an unusual structural distortion of the 70S ribosome, potentially driven by binding of multiple copies of MetAP, is observed when MetAP is incubated with a pre-formed PDF-TF-bound ribosome complex.
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Affiliation(s)
- Shirin Akbar
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Sayan Bhakta
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Jayati Sengupta
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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10
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Hou X, Tang W. Pseudogene PA2G4P4 promotes oncogene PA2G4 expression and nuclear translocation to affect glioblastoma cell viability and apoptosis. Life Sci 2020; 265:118793. [PMID: 33220287 DOI: 10.1016/j.lfs.2020.118793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/02/2020] [Accepted: 11/15/2020] [Indexed: 12/21/2022]
Abstract
Dysregulation of pseudogenes is involved in the progression of various types of cancer, including glioblastoma (GBM). Proliferation associated-2G4 (PA2G4) pseudogene 4 (PA2G4P4) has been shown to play an oncogenic role in bladder cancer development. Our study aimed to explore the role and mechanism of PA2G4P4 in GBM progression. PA2G4P4 and PA2G4 expression in GBM tissues was analyzed using the GEPIA database. Cell viability, apoptosis, and activities of caspase-3 and caspase-9 in GBM cells were explored by CCK-8, flow cytometry analysis, and colorimetric activity assay kits, respectively. GEPIA database showed that PA2G4P4 and PA2G4 were both upregulated in GBM tissues. PA2G4P4 expression was also boosted in GBM cells. Knockdown of PA2G4P4 or PA2G4 inhibited cell viability, induced apoptosis, and increased caspase-3 and caspase-9 activities in GBM cells. Data from UALCAN database showed that among top 15 genes correlated with PA2G4P4, PA2G4 had the highest correlation coefficient. Additionally, knockdown of PA2G4P4 inhibited PA2G4 expression and nuclear translocation in GBM cells. Overexpression of PA2G4 abolished the functions of PA2G4P4 knockdown on viability and apoptosis in GBM cells. Summarily, pseudogene PA2G4P4 promotes oncogene PA2G4 expression and nuclear translocation to affect cell viability and apoptosis in GBM cells.
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Affiliation(s)
- Xiaofeng Hou
- Department of Neurosurgery, The First Affiliated Hospital of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Wenhai Tang
- Department of Neurosurgery, Shanxian Central Hospital, Heze 274300, China.
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11
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Stevenson BW, Gorman MA, Koach J, Cheung BB, Marshall GM, Parker MW, Holien JK. A structural view of PA2G4 isoforms with opposing functions in cancer. J Biol Chem 2020; 295:16100-16112. [PMID: 32952126 DOI: 10.1074/jbc.rev120.014293] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/17/2020] [Indexed: 01/04/2023] Open
Abstract
The role of proliferation-associated protein 2G4 (PA2G4), alternatively known as ErbB3-binding protein 1 (EBP1), in cancer has become apparent over the past 20 years. PA2G4 expression levels are correlated with prognosis in a range of human cancers, including neuroblastoma, cervical, brain, breast, prostate, pancreatic, hepatocellular, and other tumors. There are two PA2G4 isoforms, PA2G4-p42 and PA2G4-p48, and although both isoforms of PA2G4 regulate cellular growth and differentiation, these isoforms often have opposing roles depending on the context. Therefore, PA2G4 can function either as a contextual tumor suppressor or as an oncogene, depending on the tissue being studied. However, it is unclear how distinct structural features of the two PA2G4 isoforms translate into different functional outcomes. In this review, we examine published structures to identify important structural and functional components of PA2G4 and consider how they may explain its crucial role in the malignant phenotype. We will highlight the lysine-rich regions, protein-protein interaction sites, and post-translational modifications of the two PA2G4 isoforms and relate these to the functional cellular role of PA2G4. These data will enable a better understanding of the function and structure relationship of the two PA2G4 isoforms and highlight the care that will need to be undertaken for those who wish to conduct isoform-specific structure-based drug design campaigns.
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Affiliation(s)
| | - Michael A Gorman
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jessica Koach
- Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Belamy B Cheung
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia; School of Women's and Children's Health, University of New South Wales, Randwick, New South Wales, Australia
| | - Glenn M Marshall
- School of Women's and Children's Health, University of New South Wales, Randwick, New South Wales, Australia; Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Michael W Parker
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jessica K Holien
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Surgery, University of Melbourne, Parkville, Victoria, Australia; School of Science, College of Science, Engineering, and Health, RMIT University, Melbourne, Victoria, Australia.
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12
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The roles of multifunctional protein ErbB3 binding protein 1 (EBP1) isoforms from development to disease. Exp Mol Med 2020; 52:1039-1047. [PMID: 32719408 PMCID: PMC8080562 DOI: 10.1038/s12276-020-0476-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022] Open
Abstract
The roles of the two isoforms of ErbB3-binding protein 1 (Ebp1) in cellular function and its regulation in disease and development is a stimulating area in current fields of biology, such as neuroscience, cancer biology, and structural biology. Over the last two decades, a growing body of studies suggests have suggested different functions for the EBP1 isoforms in various cancers, along with their specific binding partners in the ubiquitin-proteasome system. Owing to the specific cellular context or spatial/temporal expression of the EBP1 isoforms, either transcriptional repression or the activation function of EBP1 has been proposed, and epigenetic regulation by p48 EBP1 has also been observed during in the embryo development, including in brain development and neurologic disorders, such as schizophrenia, in using an Ebp1 knockout mouse model. Here, we review recent findings that have shaped our current understanding of the emerging function of EBP1 isoforms in cellular events and gene expression, from development to disease. A pair of proteins that originate from a common gene exert strikingly different effects on embryonic development as well as tumor growth and progression. RNA transcripts generated from the PA2G4 gene can undergo enzymatic processing to yield two different protein products, p42 EB1 and p48 EB1. These proteins differ by the presence or absence of 54 amino acids at one end, and Jee-Yin Ahn at the Sungkyunkwan University School of Medicine, Suwon, South Korea, and colleagues have reviewed current insights into the functional consequences of this difference. The two proteins bind to distinct sets of molecular partners. The p48 form appears to regulate a host of genes involved in brain development, but also appears to drive cancerous growth in various tumors. In contrast, p42 is scarcer during development, and appears to inhibit tumor formation.
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13
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Liang X, Zuo MQ, Zhang Y, Li N, Ma C, Dong MQ, Gao N. Structural snapshots of human pre-60S ribosomal particles before and after nuclear export. Nat Commun 2020; 11:3542. [PMID: 32669547 PMCID: PMC7363849 DOI: 10.1038/s41467-020-17237-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors.
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MESH Headings
- Cell Nucleus/metabolism
- Cryoelectron Microscopy
- Humans
- Models, Molecular
- RNA, Ribosomal, 5S/isolation & purification
- RNA, Ribosomal, 5S/metabolism
- RNA, Ribosomal, 5S/ultrastructure
- RNA-Binding Proteins/isolation & purification
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/ultrastructure
- Ribosomal Proteins/isolation & purification
- Ribosomal Proteins/metabolism
- Ribosomal Proteins/ultrastructure
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Large, Eukaryotic/ultrastructure
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Affiliation(s)
- Xiaomeng Liang
- State Key Laboratory of Membrane Biology, School of Life Science, Tsinghua University, 100084, Beijing, China
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Mei-Qing Zuo
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
- National Institute of Biological Sciences, 102206, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China
| | - Yunyang Zhang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Chengying Ma
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, 102206, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.
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14
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Wells JN, Buschauer R, Mackens-Kiani T, Best K, Kratzat H, Berninghausen O, Becker T, Gilbert W, Cheng J, Beckmann R. Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes. PLoS Biol 2020; 18:e3000780. [PMID: 32687489 PMCID: PMC7392345 DOI: 10.1371/journal.pbio.3000780] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/30/2020] [Accepted: 07/01/2020] [Indexed: 12/20/2022] Open
Abstract
Cells adjust to nutrient deprivation by reversible translational shutdown. This is accompanied by maintaining inactive ribosomes in a hibernation state, in which they are bound by proteins with inhibitory and protective functions. In eukaryotes, such a function was attributed to suppressor of target of Myb protein 1 (Stm1; SERPINE1 mRNA-binding protein 1 [SERBP1] in mammals), and recently, late-annotated short open reading frame 2 (Lso2; coiled-coil domain containing short open reading frame 124 [CCDC124] in mammals) was found to be involved in translational recovery after starvation from stationary phase. Here, we present cryo-electron microscopy (cryo-EM) structures of translationally inactive yeast and human ribosomes. We found Lso2/CCDC124 accumulating on idle ribosomes in the nonrotated state, in contrast to Stm1/SERBP1-bound ribosomes, which display a rotated state. Lso2/CCDC124 bridges the decoding sites of the small with the GTPase activating center (GAC) of the large subunit. This position allows accommodation of the duplication of multilocus region 34 protein (Dom34)-dependent ribosome recycling system, which splits Lso2-containing, but not Stm1-containing, ribosomes. We propose a model in which Lso2 facilitates rapid translation reactivation by stabilizing the recycling-competent state of inactive ribosomes.
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Affiliation(s)
- Jennifer N. Wells
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Robert Buschauer
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Timur Mackens-Kiani
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Katharina Best
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Hanna Kratzat
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Otto Berninghausen
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Thomas Becker
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Wendy Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jingdong Cheng
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
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15
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Osemwenkhae OP, Sakuno T, Hirano Y, Asakawa H, Hayashi-Takanaka Y, Haraguchi T, Hiraoka Y. Human Ebp1 rescues the synthetic lethal growth of fission yeast cells lacking Cdb4 and Nup184. Genes Cells 2020; 25:288-295. [PMID: 32049412 DOI: 10.1111/gtc.12757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 11/29/2022]
Abstract
Cdb4 is a protein with unknown functions that binds to curved DNA in vitro in the fission yeast Schizosaccharomyces pombe. Homologues of Cdb4 were identified in a wide range of eukaryotes, including human Ebp1. Both S. pombe Cdb4 and human Ebp1 are nonpeptidase members of the methionine aminopeptidase family. It has been reported that Ebp1 homologues are involved in cell growth regulation and differentiation. However, opposing functions have also been considered and debated upon, and the precise biological functions of this conserved protein are largely unknown. S. pombe cdb4 is a nonessential gene, and no obvious phenotypes have been detected in cells with cdb4 gene deletion. In this study, we identified nup184, encoding a component of the nuclear pore complex, as a gene responsible for the synthetic lethal phenotype associated with cdb4. Furthermore, the synthetic lethal phenotype of Cdb4 was suppressed by over-expression of human Ebp1, suggesting that it has conserved crucial functions in S. pombe Cdb4 and human Ebp1. This synthetic lethal phenotype associated with Cdb4 and Nup184 provides a molecular genetics tool to study the functions of S. pombe Cdb4 and its conserved members of proteins, including human Ebp1.
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Affiliation(s)
- Osaretin P Osemwenkhae
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Takeshi Sakuno
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yasuhiro Hirano
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | | | - Tokuko Haraguchi
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasushi Hiraoka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
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16
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Han EH, Singh P, Lee IK, Urrutia R, Chi YI. ErbB3-binding protein 1 (EBP1) represses HNF4α-mediated transcription and insulin secretion in pancreatic β-cells. J Biol Chem 2019; 294:13983-13994. [PMID: 31362984 DOI: 10.1074/jbc.ra119.009558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/18/2019] [Indexed: 12/13/2022] Open
Abstract
HNF4α (hepatocyte nuclear factor 4α) is one of the master regulators of pancreatic β-cell development and function, and mutations in the HNF4α gene are well-known monogenic causes of diabetes. As a member of the nuclear receptor family, HNF4α exerts its gene regulatory function through various molecular interactions; however, there is a paucity of knowledge of the different functional complexes in which HNF4α participates. Here, to find HNF4α-binding proteins in pancreatic β-cells, we used yeast two-hybrid screening, a mammalian two-hybrid assay, and glutathione S-transferase pulldown approaches, which identified EBP1 (ErbB3-binding protein 1) as a factor that binds HNF4α in a LXXLL motif-mediated manner. In the β-cells, EBP1 suppressed the expression of HNF4α target genes that are implicated in insulin secretion, which is impaired in HNF4α mutation-driven diabetes. The crystal structure of the HNF4α ligand-binding domain in complex with a peptide harboring the EBP1 LXXLL motif at 3.15Å resolution hinted at the molecular basis of the repression. The details of the structure suggested that EBP1's LXXLL motif competes with HNF4α coactivators for the same binding pocket and thereby prevents recruitment of additional transcriptional coactivators. These findings provide further evidence that EBP1 plays multiple cellular roles and is involved in nuclear receptor-mediated gene regulation. Selective disruption of the HNF4α-EBP1 interaction or tissue-specific EBP1 inactivation can enhance HNF4α activities and thereby improve insulin secretion in β-cells, potentially representing a new strategy for managing diabetes and related metabolic disorders.
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Affiliation(s)
- Eun Hee Han
- Section of Structural Biology, Hormel Institute, University of Minnesota, Austin, Minnesota 55912.,Drug & Disease Target Group, Division of Life Science, Korea Basic Science Institute, Cheongju 28119, Republic of Korea
| | - Puja Singh
- Section of Structural Biology, Hormel Institute, University of Minnesota, Austin, Minnesota 55912
| | - In-Kyu Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, Republic of Korea
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Young-In Chi
- Section of Structural Biology, Hormel Institute, University of Minnesota, Austin, Minnesota 55912 .,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
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17
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Investigating the role of Ebp1 in Chandipura virus infection. J Biosci 2019. [DOI: 10.1007/s12038-019-9847-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Miao M, Yu F, Wang D, Tong Y, Yang L, Xu J, Qiu Y, Zhou X, Zhao X. Proteomics Profiling of Host Cell Response via Protein Expression and Phosphorylation upon Dengue Virus Infection. Virol Sin 2019; 34:549-562. [PMID: 31134586 DOI: 10.1007/s12250-019-00131-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022] Open
Abstract
Dengue virus (DENV) infection is a worldwide public health threat. To date, the knowledge about the pathogenesis and progression of DENV infection is still limited. Combining global profiling based on proteomic analysis together with functional verification analysis is a powerful strategy to investigate the interplay between the virus and host cells. In the present study, quantitative proteomics has been applied to evaluate host responses (as indicated by altered proteins and modifications) in human cells (using K562 cell line) upon DENV-2 infection, as DENV-2 spreads most widely among all DENV serotypes. Comparative analysis was performed to define differentially expressed proteins in the infected cells compared to the mock-control, and it revealed critical pathogen-induced changes covering a broad spectrum of host cellular compartments and processes. We also discovered more dramatic changes (> 20%, 160 regulated phosphoproteins) in protein phosphorylation compared to protein expression (14%, 321 regulated proteins). Most of these proteins/phosphoproteins were involved in transcription regulation, RNA splicing and processing, immune system, cellular response to stimulus, and macromolecule biosynthesis. Western blot analysis was also performed to confirm the proteomic data. Potential roles of these altered proteins were discussed. The present study provides valuable large-scale protein-related information for elucidating the functional emphasis of host cell proteins and their post-translational modifications in virus infection, and also provides insight and protein evidence for understanding the general pathogenesis and pathology of DENV.
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Affiliation(s)
- Meng Miao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fei Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Danya Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongjia Tong
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Liuting Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiuyue Xu
- Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China
| | - Yang Qiu
- Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China
| | - Xi Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China. .,Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China.
| | - Xiaolu Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China. .,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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19
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Ahmad Z, Magyar Z, Bögre L, Papdi C. Cell cycle control by the target of rapamycin signalling pathway in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2275-2284. [PMID: 30918972 DOI: 10.1093/jxb/erz140] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Cells need to ensure a sufficient nutrient and energy supply before committing to proliferate. In response to positive mitogenic signals, such as light, sugar availability, and hormones, the target of rapamycin (TOR) signalling pathway promotes cell growth that connects to the entry and passage through the cell division cycle via multiple signalling mechanisms. Here, we summarize current understanding of cell cycle regulation by the RBR-E2F regulatory hub and the DREAM-like complexes, and highlight possible functional relationships between these regulators and TOR signalling. A genetic screen recently uncovered a downstream signalling component to TOR that regulates cell proliferation, YAK1, a member of the dual specificity tyrosine phosphorylation-regulated kinase (DYRK) family. YAK1 activates the plant-specific SIAMESE-RELATED (SMR) cyclin-dependent kinase inhibitors and therefore could be important to regulate both the CDKA-RBR-E2F pathway to control the G1/S transition and the mitotic CDKB1;1 to control the G2/M transition. TOR, as a master regulator of both protein synthesis-driven cell growth and cell proliferation is also central for cell size homeostasis. We conclude the review by briefly highlighting the potential applications of combining TOR and cell cycle knowledge in the context of ensuring future food security.
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Affiliation(s)
- Zaki Ahmad
- School of Biological Sciences, Bourne Laboratory. Royal Holloway, University of London, Egham, Surrey, UK
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences Szeged, Hungary
| | - László Bögre
- School of Biological Sciences, Bourne Laboratory. Royal Holloway, University of London, Egham, Surrey, UK
| | - Csaba Papdi
- School of Biological Sciences, Bourne Laboratory. Royal Holloway, University of London, Egham, Surrey, UK
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20
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Stegmann M. EBP1: A crucial growth regulator downstream of receptor kinases across kingdoms. PLoS Biol 2018; 16:e3000056. [PMID: 30403659 PMCID: PMC6242329 DOI: 10.1371/journal.pbio.3000056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/19/2018] [Indexed: 11/20/2022] Open
Abstract
Controlling organ growth and development is crucial for all multicellular organisms and is controlled by plasma membrane localized receptor kinases (RKs) across kingdoms, including animals and plants. A central RK in plants is FERONIA (FER), which perceives endogenous rapid alkalinization factor (RALF) peptides to regulate a plethora of biological responses, including growth and development. However, it remained largely unknown how RALF sensing by FER at the plasma membrane is translated into a nuclear response. A key step forward is presented by Li and colleagues, who show that FER increases ERBB3 binding protein 1 (EBP1) mRNA translation and directly phosphorylates EBP1 to shift its subcellular localization from the cytoplasm to the nucleus where it controls growth and development through its regulation of transcription. Importantly, EBP1 is described as a transcriptional and translational regulator in mammals by acting downstream of epidermal growth factor receptor (EGFR) signaling, suggesting that animals and plants use similar conserved pathways to fine-tune growth and development. Furthermore, this work highlights the importance of protein translation as a direct output of RK signaling, a mechanism that is largely unknown in plants. This Primer discusses the recent demonstration that EBP1 is a major transcriptional and translational regulator across kingdoms, acting downstream of EGFR signalling in animals and the central receptor kinase FERONIA in plants.
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Affiliation(s)
- Martin Stegmann
- Phytopathology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- * E-mail:
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21
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Zhang J, Wang Q, Abdul-Aziz D, Mattiacio J, Edge ASB, White PM. ERBB2 signaling drives supporting cell proliferation in vitro and apparent supernumerary hair cell formation in vivo in the neonatal mouse cochlea. Eur J Neurosci 2018; 48:3299-3316. [PMID: 30270571 DOI: 10.1111/ejn.14183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/07/2018] [Accepted: 09/03/2018] [Indexed: 12/29/2022]
Abstract
In mammals, cochlear hair cells are not regenerated once they are lost, leading to permanent hearing deficits. In other vertebrates, the adjacent supporting cells act as a stem cell compartment, in that they both proliferate and differentiate into de novo auditory hair cells. Although there is evidence that mammalian cochlear supporting cells can differentiate into new hair cells, the signals that regulate this process are poorly characterized. We hypothesize that signaling from the epidermal growth factor receptor (EGFR) family may play a role in cochlear regeneration. We focus on one such member, ERBB2, and report the effects of expressing a constitutively active ERBB2 receptor in neonatal mouse cochlear supporting cells, using viruses and transgenic expression. Lineage tracing with fluorescent reporter proteins was used to determine the relationships between cells with active ERBB2 signaling and cells that divided or differentiated into hair cells. In vitro, individual supporting cells harbouring a constitutively active ERBB2 receptor appeared to signal to their neighbouring supporting cells, inducing them to down-regulate a supporting cell marker and to proliferate. In vivo, we found supernumerary hair cell-like cells near supporting cells that expressed ERBB2 receptors. Both supporting cell proliferation and hair cell differentiation were largely reproduced in vitro using small molecules that we show also activate ERBB2. Our data suggest that signaling from the receptor tyrosine kinase ERBB2 can drive the activation of secondary signaling pathways to regulate regeneration, suggesting a new model where an interplay of cell signaling regulates regeneration by endogenous stem-like cells.
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Affiliation(s)
- Jingyuan Zhang
- Department of Biology, School of Arts and Sciences, University of Rochester, Rochester, New York
| | - Quan Wang
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts
| | - Dunia Abdul-Aziz
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts
| | - Jonelle Mattiacio
- Department of Microbiology and Immunology, University of Rochester School of Medicine, Rochester, New York
| | - Albert S B Edge
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear, Boston, Massachusetts.,Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, Massachusetts.,Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Patricia M White
- Department of Neuroscience, The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine, Rochester, New York
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22
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Li C, Liu X, Qiang X, Li X, Li X, Zhu S, Wang L, Wang Y, Liao H, Luan S, Yu F. EBP1 nuclear accumulation negatively feeds back on FERONIA-mediated RALF1 signaling. PLoS Biol 2018; 16:e2006340. [PMID: 30339663 PMCID: PMC6195255 DOI: 10.1371/journal.pbio.2006340] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/28/2018] [Indexed: 12/22/2022] Open
Abstract
FERONIA (FER), a plasma membrane receptor-like kinase, is a central regulator of cell growth that integrates environmental and endogenous signals. A peptide ligand rapid alkalinization factor 1 (RALF1) binds to FER and triggers a series of downstream events, including inhibition of Arabidopsis H+-ATPase 2 activity at the cell surface and regulation of gene expression in the nucleus. We report here that, upon RALF1 binding, FER first promotes ErbB3-binding protein 1 (EBP1) mRNA translation and then interacts with and phosphorylates the EBP1 protein, leading to EBP1 accumulation in the nucleus. There, EBP1 associates with the promoters of previously identified RALF1-regulated genes, such as CML38, and regulates gene transcription in response to RALF1 signaling. EBP1 appears to inhibit the RALF1 peptide response, thus forming a transcription-translation feedback loop (TTFL) similar to that found in circadian rhythm control. The plant RALF1-FER-EBP1 axis is reminiscent of animal epidermal growth factor receptor (EGFR) signaling, in which EGF peptide induces EGFR to interact with and phosphorylate EBP1, promoting EBP1 nuclear accumulation to control cell growth. Thus, we suggest that in response to peptide signals, plant FER and animal EGFR use the conserved key regulator EBP1 to control cell growth in the nucleus.
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Affiliation(s)
- Chiyu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, People’s Republic of China
| | - Xuanming Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, People’s Republic of China
| | - Xiaonan Qiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, People’s Republic of China
| | - Xiaoyan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, People’s Republic of China
| | - Xiushan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, People’s Republic of China
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, People’s Republic of China
| | - Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, People’s Republic of China
| | - Yuan Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Hongdong Liao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, People’s Republic of China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, People’s Republic of China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- * E-mail:
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23
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Nguyen DQ, Hoang DH, Nguyen Vo TT, Huynh V, Ghoda L, Marcucci G, Nguyen LXT. The role of ErbB3 binding protein 1 in cancer: Friend or foe? J Cell Physiol 2018; 233:9110-9120. [PMID: 30076717 DOI: 10.1002/jcp.26951] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 06/12/2018] [Indexed: 12/20/2022]
Abstract
ErbB3, a member of the epidermal growth factor receptor family, reportedly plays an essential role in the regulation of cancer progression and therapeutic resistance. Numerous studies have indicated that ErbB3 binding protein 1 (Ebp1), a binding partner for ErbB3, plays an important regulatory role in the expression and function of ErbB3, but there is no agreement as to whether Ebp1 also has an ErbB3-independent function in cancer and how it might contribute to tumorigenesis. In this review, we will discuss the different functions of the two Ebp1 isoforms, p48 and p42, that may be responsible for the potentially dual role of Ebp1 in cancer growth.
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Affiliation(s)
- Dang Quan Nguyen
- Department of Medical Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Dinh Hoa Hoang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, California
| | - Thanh Thao Nguyen Vo
- Department of Medical Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Vu Huynh
- Department of Medical Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Lucy Ghoda
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, California
| | - Guido Marcucci
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, California
| | - Le Xuan Truong Nguyen
- Department of Medical Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam.,Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, California
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24
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Somanath P, Bush KM, Knoepfler PS. ERBB3-Binding Protein 1 (EBP1) Is a Novel Developmental Pluripotency-Associated-4 (DPPA4) Cofactor in Human Pluripotent Cells. Stem Cells 2018; 36:671-682. [PMID: 29327467 DOI: 10.1002/stem.2776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 12/04/2017] [Accepted: 12/09/2017] [Indexed: 12/31/2022]
Abstract
Developmental Pluripotency-Associated-4 (DPPA4) is one of the few core pluripotency genes lacking clearly defined molecular and cellular functions. Here, we used a proteomics screening approach of human embryonic stem cell (hESC) nuclear extract to determine DPPA4 molecular functions through identification of novel cofactors. Unexpectedly, the signaling molecule ERBB3-binding protein 1 (EBP1) was the strongest candidate binding partner for DPPA4 in hESC. EBP1 is a growth factor signaling mediator present in two isoforms, p48 and p42. The two isoforms generally have opposing functions, however their roles in pluripotent cells have not been established. We found that DPPA4 preferentially binds p48 in pluripotent and NTERA-2 cells, but this interaction is largely absent in non-pluripotent cells and is reduced with differentiation. The DPPA4-EBP1 interaction is mediated at least in part in DPPA4 by the highly conserved SAF-A/B, Acinus and PIAS (SAP) domain. Functionally, we found that DPPA4 transcriptional repressive function in reporter assays is significantly increased by specific p48 knockdown, an effect that was abolished with an interaction-deficient DPPA4 ΔSAP mutant. Thus, DPPA4 and EBP1 may cooperate in transcriptional functions through their physical association in a pluripotent cell specific context. Our study identifies EBP1 as a novel pluripotency cofactor and provides insight into potential mechanisms used by DPPA4 in regulating pluripotency through its association with EBP1. Stem Cells 2018;36:671-682.
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Affiliation(s)
- Priyanka Somanath
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, California, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
| | - Kelly M Bush
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, California, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
| | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, California, USA.,Institute of Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
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25
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Rogell B, Fischer B, Rettel M, Krijgsveld J, Castello A, Hentze MW. Specific RNP capture with antisense LNA/DNA mixmers. RNA (NEW YORK, N.Y.) 2017; 23:1290-1302. [PMID: 28476952 PMCID: PMC5513073 DOI: 10.1261/rna.060798.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/25/2017] [Indexed: 05/07/2023]
Abstract
RNA-binding proteins (RBPs) play essential roles in RNA biology, responding to cellular and environmental stimuli to regulate gene expression. Important advances have helped to determine the (near) complete repertoires of cellular RBPs. However, identification of RBPs associated with specific transcripts remains a challenge. Here, we describe "specific ribonucleoprotein (RNP) capture," a versatile method for the determination of the proteins bound to specific transcripts in vitro and in cellular systems. Specific RNP capture uses UV irradiation to covalently stabilize protein-RNA interactions taking place at "zero distance." Proteins bound to the target RNA are captured by hybridization with antisense locked nucleic acid (LNA)/DNA oligonucleotides covalently coupled to a magnetic resin. After stringent washing, interacting proteins are identified by quantitative mass spectrometry. Applied to in vitro extracts, specific RNP capture identifies the RBPs bound to a reporter mRNA containing the Sex-lethal (Sxl) binding motifs, revealing that the Sxl homolog sister of Sex lethal (Ssx) displays similar binding preferences. This method also revealed the repertoire of RBPs binding to 18S or 28S rRNAs in HeLa cells, including previously unknown rRNA-binding proteins.
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Affiliation(s)
- Birgit Rogell
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Bernd Fischer
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jeroen Krijgsveld
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alfredo Castello
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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26
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Yu M, Wang H, Liu Z, Lu Y, Yu D, Li D, Du W. Ebp1 regulates myogenic differentiation of myoblast cells via SMAD2/3 signaling pathway. Dev Growth Differ 2017; 59:540-551. [PMID: 28707296 DOI: 10.1111/dgd.12380] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 12/25/2022]
Abstract
Regulation of skeletal muscle development requires many of the regulatory networks that are fundamental to developmental myogenesis. ErbB3 binding protein-1 (Ebp1) is involved in the control of myoblasts development in chicken. However, the expression and biological functions of Ebp1 in the progress of myogenesis are unclear. This study focused on determining the effect of Ebp1 on myogenic proliferation and differentiation using a primary myoblasts culture model. Ebp1 was found to upregulate in proliferating myoblasts and decrease at the early stage of myogenic differentiation. The level of endogenous Ebp1 increased from E9 to E20 chicken leg muscles. Knockdown of Ebp1 had no effect on myoblasts proliferation. However, myogenic differentiation into multinucleated myotubes was significantly reduced. The mRNA and protein expression of MRFs was decreased when Ebp1 was knocked down. Downregulation of Ebp1, accompanied by elevated levels of pSMAD2/3, suggests that Ebp1 is involved in regulating myogenic differentiation via SMAD2/3 inhibition. The phosphorylation of SMAD2/3 was activated and the expression of MYOD and MYOG was reduced in Ebp1 knockdown myoblasts, but addition of LY2109761 (an inhibitor specified to SMAD2/3) blocked these effects. Collectively, these results indicate that Ebp1 promotes myoblast differentiation by inhibition of SMAD2/3 signaling pathway during chicken myogenesis. These data provide new insights into the biological role of Ebp1 in embryonic chicken skeletal muscle development.
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Affiliation(s)
- Minli Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Huan Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Zhen Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Yinglin Lu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Debing Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Dongfeng Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Wenxing Du
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
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27
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Neilson KM, Abbruzzesse G, Kenyon K, Bartolo V, Krohn P, Alfandari D, Moody SA. Pa2G4 is a novel Six1 co-factor that is required for neural crest and otic development. Dev Biol 2017; 421:171-182. [PMID: 27940157 PMCID: PMC5221411 DOI: 10.1016/j.ydbio.2016.11.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/15/2016] [Accepted: 11/28/2016] [Indexed: 11/29/2022]
Abstract
Mutations in SIX1 and in its co-factor, EYA1, underlie Branchiootorenal Spectrum disorder (BOS), which is characterized by variable branchial arch, otic and kidney malformations. However, mutations in these two genes are identified in only half of patients. We screened for other potential co-factors, and herein characterize one of them, Pa2G4 (aka Ebp1/Plfap). In human embryonic kidney cells, Pa2G4 binds to Six1 and interferes with the Six1-Eya1 complex. In Xenopus embryos, knock-down of Pa2G4 leads to down-regulation of neural border zone, neural crest and cranial placode genes, and concomitant expansion of neural plate genes. Gain-of-function leads to a broader neural border zone, expanded neural crest and altered cranial placode domains. In loss-of-function assays, the later developing otocyst is reduced in size, which impacts gene expression. In contrast, the size of the otocyst in gain-of-function assays is not changed but the expression domains of several otocyst genes are reduced. Together these findings establish an interaction between Pa2G4 and Six1, and demonstrate that it has an important role in the development of tissues affected in BOS. Thereby, we suggest that pa2g4 is a potential candidate gene for BOS.
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Affiliation(s)
- Karen M Neilson
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Genevieve Abbruzzesse
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Kristy Kenyon
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, USA
| | - Vanessa Bartolo
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Patrick Krohn
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Dominique Alfandari
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Sally A Moody
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA.
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28
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Mishra P, Dixit U, Pandey AK, Upadhyay A, Pandey VN. Modulation of HCV replication and translation by ErbB3 binding protein1 isoforms. Virology 2016; 500:35-49. [PMID: 27770702 DOI: 10.1016/j.virol.2016.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/30/2016] [Accepted: 10/06/2016] [Indexed: 01/01/2023]
Abstract
We recently identified a cell-factor, ErbB3 binding protein 1 (Ebp-1), which specifically interacts with the viral RNA genome and modulates HCV replication and translation. Ebp1 has two isoforms, p48, and p42, that result from differential splicing. We found that both isoforms interact with HCV proteins NS5A and NS5B, as well as cell-factor PKR. The p48 isoform, which localizes in the cytoplasm and nuclei, promoted HCV replication, whereas the shorter p42 isoform, which resides exclusively in the cytoplasm, strongly inhibited HCV replication. Transient expression of individual isoforms in Ebp1-knockdown MH14 cells confirmed that the p48 isoform promotes HCV replication, while the p42 isoform inhibits it. We found that Ebp1-p42 significantly enhanced autophosphorylation of PKR, while Ebp1-p48 isoform strongly inhibited it. We propose that modulation of autophosphorylation of PKR by p48 isoform is an important mechanism whereby the HCV virus escapes innate antiviral immune responses by circumventing p42-mediated inhibition of its replication.
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Affiliation(s)
- Priya Mishra
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Updesh Dixit
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Ashutosh K Pandey
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Alok Upadhyay
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Virendra N Pandey
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA.
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29
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Vuong NQ, Goegan P, Mohottalage S, Breznan D, Ariganello M, Williams A, Elisma F, Karthikeyan S, Vincent R, Kumarathasan P. Proteomic changes in human lung epithelial cells (A549) in response to carbon black and titanium dioxide exposures. J Proteomics 2016; 149:53-63. [DOI: 10.1016/j.jprot.2016.03.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/12/2016] [Accepted: 03/26/2016] [Indexed: 01/16/2023]
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30
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Nelissen H, Gonzalez N, Inzé D. Leaf growth in dicots and monocots: so different yet so alike. CURRENT OPINION IN PLANT BIOLOGY 2016; 33:72-76. [PMID: 27344391 DOI: 10.1016/j.pbi.2016.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/02/2016] [Accepted: 06/09/2016] [Indexed: 05/22/2023]
Abstract
In plants, most organs grow post-embryonically through cell division and cell expansion. The coordination of these two growth processes is generally considered to be different between dicots and monocots. In dicot plants, such as the model plant Arabidopsis, leaf growth is most often described as being temporally regulated with cell division ceasing earlier at the tip and continuing longer at the base of the leaf. Conversely, in monocot leaves, the organization of the growth processes is rather viewed as spatially regulated with dividing cells at the base of the leaf, followed by expanding cells and finally mature cells at the tip. As our understanding of the leaf growth processes in the two major classes of flowering plants expands, it becomes increasingly clear that the regulation of the growth processes is to a great extent conserved between dicots and monocots. In this review, we highlight how the temporal and spatial organization of cell division and cell expansion takes place in both dicot and monocot leaves. We also show that there are similarities in the molecular wiring that coordinates these two processes during leaf development.
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Affiliation(s)
- Hilde Nelissen
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium.
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Lee J, Ahn E, Park WK, Park S. Phosphoproteome Profiling of SH-SY5y Neuroblastoma Cells Treated with Anesthetics: Sevoflurane and Isoflurane Affect the Phosphorylation of Proteins Involved in Cytoskeletal Regulation. PLoS One 2016; 11:e0162214. [PMID: 27611435 PMCID: PMC5017685 DOI: 10.1371/journal.pone.0162214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/18/2016] [Indexed: 12/11/2022] Open
Abstract
Inhalation anesthetics are used to decrease the spinal cord transmission of painful stimuli. However, the molecular or biochemical processes within cells that regulate anesthetic-induced responses at the cellular level are largely unknown. Here, we report the phosphoproteome profile of SH-SY5y human neuroblastoma cells treated with sevoflurane, a clinically used anesthetic. Phosphoproteins were isolated from cell lysates and analyzed using two-dimensional gel electrophoresis. The phosphorylation of putative anesthetic-responsive marker proteins was validated using western blot analysis in cells treated with both sevoflurane and isoflurane. A total of 25 phosphoproteins were identified as differentially phosphorylated proteins. These included key regulators that signal cytoskeletal remodeling steps in pathways related to vesicle trafficking, axonal growth, and cell migration. These proteins included the Rho GTPase, Ras-GAP SH3 binding protein, Rho GTPase activating protein, actin-related protein, and actin. Sevoflurane and isoflurane also resulted in the dissolution of F-actin fibers in SH-SY5y cells. Our results show that anesthetics affect the phosphorylation of proteins involved in cytoskeletal remodeling pathways.
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Affiliation(s)
- Joomin Lee
- Department of Food and Nutrition, Chosun University, Gwangju 61452, Korea
| | - Eunsook Ahn
- Department of Applied Chemistry, Dongduk Women’s University, Seoul 02748, Korea
| | - Wyun Kon Park
- Department of Anesthesia and Pain, College of Medicine, Department of Anesthesia and Pain, Yonsei University, Seoul 03722, Korea
| | - Seyeon Park
- Department of Applied Chemistry, Dongduk Women’s University, Seoul 02748, Korea
- * E-mail:
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Tummala H, Walne A, Williams M, Bockett N, Collopy L, Cardoso S, Ellison A, Wynn R, Leblanc T, Fitzgibbon J, Kelsell D, van Heel D, Payne E, Plagnol V, Dokal I, Vulliamy T. DNAJC21 Mutations Link a Cancer-Prone Bone Marrow Failure Syndrome to Corruption in 60S Ribosome Subunit Maturation. Am J Hum Genet 2016; 99:115-24. [PMID: 27346687 DOI: 10.1016/j.ajhg.2016.05.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/03/2016] [Indexed: 10/21/2022] Open
Abstract
A substantial number of individuals with bone marrow failure (BMF) present with one or more extra-hematopoietic abnormality. This suggests a constitutional or inherited basis, and yet many of them do not fit the diagnostic criteria of the known BMF syndromes. Through exome sequencing, we have now identified a subgroup of these individuals, defined by germline biallelic mutations in DNAJC21 (DNAJ homolog subfamily C member 21). They present with global BMF, and one individual developed a hematological cancer (acute myeloid leukemia) in childhood. We show that the encoded protein associates with rRNA and plays a highly conserved role in the maturation of the 60S ribosomal subunit. Lymphoblastoid cells obtained from an affected individual exhibit increased sensitivity to the transcriptional inhibitor actinomycin D and reduced amounts of rRNA. Characterization of mutations revealed impairment in interactions with cofactors (PA2G4, HSPA8, and ZNF622) involved in 60S maturation. DNAJC21 deficiency resulted in cytoplasmic accumulation of the 60S nuclear export factor PA2G4, aberrant ribosome profiles, and increased cell death. Collectively, these findings demonstrate that mutations in DNAJC21 cause a cancer-prone BMF syndrome due to corruption of early nuclear rRNA biogenesis and late cytoplasmic maturation of the 60S subunit.
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Li J, Yu G, Sun X, Zhang X, Liu J, Pan H. AcEBP1, an ErbB3-Binding Protein (EBP1) from halophyte Atriplex canescens, negatively regulates cell growth and stress responses in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 248:64-74. [PMID: 27181948 DOI: 10.1016/j.plantsci.2016.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 03/13/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
An ErbB-3-binding protein gene AcEBP1, also known as proliferation-associated 2G4 gene (PA2G4s) belonging to the M24 superfamily, was obtained from the saltbush Atriplex canescens. Subcellular localization imaging showed the fusion protein AcEBP1-eGFP was located in the nucleus of epidermal cells in Nicotiana benthamiana. The AcEBP1 gene expression levels were up-regulated under salt, osmotic stress, and hormones treatment as revealed by qRT-PCR. Overexpression of AcEBP1 in Arabidopsis demonstrated that AcEBP1 was involved in root cell growth and stress responses (NaCl, osmotic stress, ABA, low temperature, and drought). These phenotypic data were correlated with the expression patterns of stress responsive genes and PR genes. The AcEBP1 transgenic Arabidopsis plants also displayed increased sensitivity under low temperature and evaluated resistance to drought stress. Together, these results demonstrate that AcEBP1 negatively affects cell growth and is a regulator under stress conditions.
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Affiliation(s)
- Jingtao Li
- College of Plant Science, Jilin University, Changchun, 130062 Jilin, China.
| | - Gang Yu
- College of Plant Science, Jilin University, Changchun, 130062 Jilin, China.
| | - Xinhua Sun
- College of Plant Science, Jilin University, Changchun, 130062 Jilin, China.
| | - Xianghui Zhang
- College of Plant Science, Jilin University, Changchun, 130062 Jilin, China.
| | - Jinliang Liu
- College of Plant Science, Jilin University, Changchun, 130062 Jilin, China.
| | - Hongyu Pan
- College of Plant Science, Jilin University, Changchun, 130062 Jilin, China.
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Xing L, Martyniuk CJ, Esau C, Da Fonte DF, Trudeau VL. Proteomic profiling reveals dopaminergic regulation of progenitor cell functions of goldfish radial glial cells in vitro. J Proteomics 2016; 144:123-32. [DOI: 10.1016/j.jprot.2016.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 04/26/2016] [Accepted: 05/02/2016] [Indexed: 01/03/2023]
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Ko HR, Chang YS, Park WS, Ahn JY. Opposing roles of the two isoforms of ErbB3 binding protein 1 in human cancer cells. Int J Cancer 2016; 139:1202-8. [DOI: 10.1002/ijc.30165] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 04/25/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Hyo Rim Ko
- Department of Molecular Cell Biology; Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine; Suwon Korea
| | - Yun Sil Chang
- Department of Pediatrics; Samsung Medical Center, Sungkyunkwan University School of Medicine; Seoul Korea
| | - Won Soon Park
- Department of Pediatrics; Samsung Medical Center, Sungkyunkwan University School of Medicine; Seoul Korea
| | - Jee-Yin Ahn
- Department of Molecular Cell Biology; Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine; Suwon Korea
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36
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A polybasic motif in ErbB3-binding protein 1 (EBP1) has key functions in nucleolar localization and polyphosphoinositide interaction. Biochem J 2016; 473:2033-47. [PMID: 27118868 PMCID: PMC4941749 DOI: 10.1042/bcj20160274] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/26/2016] [Indexed: 12/29/2022]
Abstract
We reveal the identification of a polybasic motif necessary for polyphosphoinositide interaction and nucleolar targeting of ErbB3 binding protein 1 (EBP1). EBP1 interacts directly with phosphatidylinositol(3,4,5)-triphosphate and their association is detected in the nucleolus, implying regulatory roles of nucleolar processes. Polyphosphoinositides (PPIns) are present in the nucleus where they participate in crucial nuclear processes, such as chromatin remodelling, transcription and mRNA processing. In a previous interactomics study, aimed to gain further insight into nuclear PPIns functions, we identified ErbB3 binding protein 1 (EBP1) as a potential nuclear PPIn-binding protein in a lipid pull-down screen. EBP1 is a ubiquitous and conserved protein, located in both the cytoplasm and nucleolus, and associated with cell proliferation and survival. In the present study, we show that EBP1 binds directly to several PPIns via two distinct PPIn-binding sites consisting of clusters of lysine residues and positioned at the N- and C-termini of the protein. Using interaction mutants, we show that the C-terminal PPIn-binding motif contributes the most to the localization of EBP1 in the nucleolus. Importantly, a K372N point mutation, located within the C-terminal motif and found in endometrial tumours, is sufficient to alter the nucleolar targeting of EBP1. Our study reveals also the presence of the class I phosphoinositide 3-kinase (PI3K) catalytic subunit p110β and its product PtdIns(3,4,5)P3 together with EBP1 in the nucleolus. Using NMR, we further demonstrate an association between EBP1 and PtdIns(3,4,5)P3 via both electrostatic and hydrophobic interactions. Taken together, these results show that EBP1 interacts directly with PPIns and associate with PtdIns(3,4,5)P3 in the nucleolus. The presence of p110β and PtdIns(3,4,5)P3 in the nucleolus indicates their potential role in regulating nucleolar processes, at least via EBP1.
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Wang T, Sui Z, Liu X, Li Y, Li H, Xing J, Song F, Zhang Y, Sun Q, Ni Z. Ectopic expression of a maize hybrid up-regulated gene, ErbB-3 binding Protein 1 (ZmEBP1), increases organ size by promoting cell proliferation in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 243:23-34. [PMID: 26795148 DOI: 10.1016/j.plantsci.2015.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 05/21/2023]
Abstract
The alteration of gene expression in hybrids may be an important factor promoting phenotypic variation and plasticity. To provide insight into the underlying molecular basis of maize heterosis in terms of the kernel number per ear, we established DGE profiles for the immature ears of maize hybrid Zong3/87-1 and its parental lines at the floral organ differentiation stage. Among 4,337 identified differentially expressed genes, 4,021 (92%) exhibited nonadditive expression patterns in the hybrid. Notably, the maize homolog of Arabidopsis EBP1, designated ZmEBP1, displayed an overdominant expression pattern in the Zong3/87-1 hybrid. Moreover, the results of qRT-PCR revealed that the ZmEBP1 gene was upregulated in the immature ears of the reciprocal hybrids Zong3/87-1 and 87-1/Zong3 at different developmental stages. Additionally, ectopic expression of ZmEBP1 in Arabidopsis increased organ size, which was mainly attributed to an increase in cell numbers, rather than cell size. Considering all of these findings together, we speculate that upregulation of ZmEBP1 in maize hybrids may accelerate cell proliferation and promote ear development.
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Affiliation(s)
- Tianya Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Yangyang Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Hongjian Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Fangwei Song
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Yirong Zhang
- National Maize Improvement Centre of China, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China.
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Nguyen LXT, Zhu L, Lee Y, Ta L, Mitchell BS. Expression and Role of the ErbB3-Binding Protein 1 in Acute Myelogenous Leukemic Cells. Clin Cancer Res 2016; 22:3320-7. [PMID: 26813358 DOI: 10.1158/1078-0432.ccr-15-2282] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/21/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE The ErbB3-binding protein 1 (Ebp1) has been implicated in diverse cancers as having either oncogenic or tumor suppressor activities. The present study was undertaken to determine the effects of Ebp1 expression in AML cells and to determine the mechanisms by which Ebp1 promotes cell proliferation in these cells. EXPERIMENTAL DESIGN The expression of Ebp1 was studied in mononuclear cells obtained from the peripheral blood of 54 patients with AML by Western blot analysis. The effects of Ebp1 expression on proliferating cell nuclear antigen (PCNA) expression and cell proliferation was measured using Western blot analysis, immunoprecipitation, in vitro ubiquitination, and colony-forming assays. The role of Ebp1 in promoting rRNA synthesis and cell proliferation was evaluated by measuring the level of pre-rRNA and the recruitment of Pol I to rDNA. RESULTS Ebp1 is highly expressed in acute myelogenous leukemia (AML) cells and regulates the level of ribosomal RNA (rRNA) synthesis by binding to RNA Polymerase I (Pol I) and enhancing the formation of the Pol I initiation complex. Ebp1 also increases the stability of PCNA protein by preventing its interaction with Mdm2, for which it is a substrate. CONCLUSIONS These results demonstrate an important role of Ebp1 in promoting cell proliferation in AML cells through the regulation of both rRNA synthesis and PCNA expression. Clin Cancer Res; 22(13); 3320-7. ©2016 AACR.
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Affiliation(s)
- Le Xuan Truong Nguyen
- Departments of Medicine and Chemical and Systems Biology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Li Zhu
- Departments of Medicine and Chemical and Systems Biology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Yunqin Lee
- Departments of Medicine and Chemical and Systems Biology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Lynn Ta
- Departments of Medicine and Chemical and Systems Biology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Beverly S Mitchell
- Departments of Medicine and Chemical and Systems Biology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California.
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Cheng H, Chen X, Zhu J, Huang H. Overexpression of a Hevea brasiliensis ErbB-3 Binding protein 1 Gene Increases Drought Tolerance and Organ Size in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2016; 7:1703. [PMID: 27895658 PMCID: PMC5107689 DOI: 10.3389/fpls.2016.01703] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/28/2016] [Indexed: 05/04/2023]
Abstract
Rubber trees are economically important tropical tree species and the major source of natural rubber, which is an essential industrial material. This tropical perennial tree is susceptible to cold stress and other abiotic stresses, especially in the marginal northern tropics. Recent years, the genome sequencing and RNA-seq projects produced huge amount of sequence data, which greatly facilitated the functional genomics study. However, the characterization of individual functional gene is in urgent demands, especially for those involved in stress resistance. Here we identified and characterized the rubber tree gene ErbB-3 binding protein 1, which undergoes changes in expression in response to cold, drought stress and ABA treatment. HbEBP1 overexpression (OE) in Arabidopsis increased organ size, facilitated root growth and increased adult leaf number by delaying the vegetative-to-reproductive transition. In addition, HbEBP1 OE enhanced the resistance of the Arabidopsis plants to freezing and drought stress, demonstrating that this gene participates in the regulation of abiotic stress resistance. RD29a, RD22 and CYCD3;1 expression was also greatly enhanced by HbEBP1 OE, which explains its regulatory roles in organ size and stress resistance. The regulation of drought stress resistance is a novel function identified in plant EBP1 genes, which expands our understanding of the roles of EBP1 gene in response to the environment. Our results provide information that may lead to the use of HbEBP1 in genetically engineered crops to increase both biomass and abiotic stress resistance.
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Affiliation(s)
- Han Cheng
- *Correspondence: Han Cheng, Huasun Huang,
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40
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Moody SA, Neilson KM, Kenyon KL, Alfandari D, Pignoni F. Using Xenopus to discover new genes involved in branchiootorenal spectrum disorders. Comp Biochem Physiol C Toxicol Pharmacol 2015; 178:16-24. [PMID: 26117063 PMCID: PMC4662879 DOI: 10.1016/j.cbpc.2015.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 12/14/2022]
Abstract
Congenital hearing loss is an important clinical problem because, without early intervention, affected children do not properly acquire language and consequently have difficulties developing social skills. Although most newborns in the US are screened for hearing deficits, even earlier diagnosis can be made with prenatal genetic screening. Genetic screening that identifies the relevant mutated gene can also warn about potential congenital defects in organs not related to hearing. We will discuss efforts to identify new candidate genes that underlie the Branchiootorenal spectrum disorders in which affected children have hearing deficits and are also at risk for kidney defects. Mutations in two genes, SIX1 and EYA1, have been identified in about half of the patients tested. To uncover new candidate genes, we have used the aquatic animal model, Xenopus laevis, to identify genes that are part of the developmental genetic pathway of Six1 during otic and kidney development. We have already identified a large number of potential Six1 transcriptional targets and candidate co-factor proteins that are expressed at the right time and in the correct tissues to interact with Six1 during development. We discuss the advantages of using this system for gene discovery in a human congenital hearing loss syndrome.
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Affiliation(s)
- Sally A Moody
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA.
| | - Karen M Neilson
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Kristy L Kenyon
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, USA
| | - Dominique Alfandari
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Francesca Pignoni
- Department of Ophthalmology, Upstate Medical University, Syracuse, NY, USA
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Abstract
To achieve optimal functionality, plant organs like leaves and petals have to grow to a certain size. Beginning with a limited number of undifferentiated cells, the final size of an organ is attained by a complex interplay of cell proliferation and subsequent cell expansion. Regulatory mechanisms that integrate intrinsic growth signals and environmental cues are required to enable optimal leaf and flower development. This review focuses on plant-specific principles of growth reaching from the cellular to the organ level. The currently known genetic pathways underlying these principles are summarized and network connections are highlighted. Putative non-cell autonomously acting mechanisms that might coordinate plant-cell growth are discussed.
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Affiliation(s)
- Hjördis Czesnick
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
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42
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TIF-IA and Ebp1 regulate RNA synthesis in T cells. Blood 2015; 125:2456-7. [PMID: 25883228 DOI: 10.1182/blood-2015-03-630780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this issue of Blood, Nguyen et al show that mycophenolic acid (MPA) induces GTP depletion, which inhibits the function of transcription initiation factor I (TIF-IA) and impacts the interaction of TIF-IA with ErbB3-binding protein 1 (Ebp1), a key in regulating proliferating cell nuclear antigen (PCNA) expression and ribosomal RNA (rRNA) synthesis in T cells during activation.
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43
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Pisapia L, Barba P, Cortese A, Cicatiello V, Morelli F, Del Pozzo G. EBP1 protein modulates the expression of human MHC class II molecules in non-hematopoietic cancer cells. Int J Oncol 2015; 47:481-9. [PMID: 26081906 PMCID: PMC4501648 DOI: 10.3892/ijo.2015.3051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/04/2015] [Indexed: 12/11/2022] Open
Abstract
Many solid tumours including melanoma, glioblastoma, and breast carcinomas express MHC class II molecules (MHC II). The surface expression of these molecules confers to non-hematopoietic tumour cells the role of non-professional antigen presenting cells and the ability to potentially stimulate tumour-specific CD4+ T cell response. We studied EBP1, an ErbB3 binding protein, and the effects of p48 and p42 isoforms on the MHC II expression in U87 glioblastoma, M14 melanoma and MCF7 mammary carcinoma cell lines. We found that overexpression of p48 increases MHC II transcription in U87 and M14, through upregulation of CIITA transactivator and STAT1 phosphorylation. In addition, p48 protein influences MHC II expression by increasing mRNA stability. In melanoma and glioblastoma cell lines, p48 isoform functions as oncogene promoting tumour growth, while p42 isoform, that does not affect MHC II expression, acts as a tumour suppressor by blocking cell growth and inducing apoptosis. In contrast, p48 seems to act as tumour suppressor in breast carcinoma inhibiting proliferation, favouring apoptosis, and inducing a slight increase of MHC II expression similar to p42. Our data highlight the tissue specificity function of EBP1 isoforms and demonstrate that only the oncogene p48 activates MHC II expression in human solid tumours, via STAT1 phosphorylation, in order to affect tumour progression by triggering specific immune response.
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Affiliation(s)
- Laura Pisapia
- Institute of Genetics and Biophysics 'Adriano Buzzati Traverso'-CNR, 80131 Naples, Italy
| | - Pasquale Barba
- Institute of Genetics and Biophysics 'Adriano Buzzati Traverso'-CNR, 80131 Naples, Italy
| | - Angela Cortese
- Institute of Genetics and Biophysics 'Adriano Buzzati Traverso'-CNR, 80131 Naples, Italy
| | - Valeria Cicatiello
- Institute of Genetics and Biophysics 'Adriano Buzzati Traverso'-CNR, 80131 Naples, Italy
| | - Franco Morelli
- Institute of Genetics and Biophysics 'Adriano Buzzati Traverso'-CNR, 80131 Naples, Italy
| | - Giovanna Del Pozzo
- Institute of Genetics and Biophysics 'Adriano Buzzati Traverso'-CNR, 80131 Naples, Italy
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Nguyen LXT, Lee Y, Urbani L, Utz PJ, Hamburger AW, Sunwoo JB, Mitchell BS. Regulation of ribosomal RNA synthesis in T cells: requirement for GTP and Ebp1. Blood 2015; 125:2519-29. [PMID: 25691158 PMCID: PMC4400289 DOI: 10.1182/blood-2014-12-616433] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/04/2015] [Indexed: 11/20/2022] Open
Abstract
Mycophenolic acid (MPA) is the active metabolite of mycophenolate mofetil, an effective immunosuppressive drug. Both MPA and mycophenolate mofetil are highly specific inhibitors of guanine nucleotide synthesis and of T-cell activation. However, the mechanism by which guanine nucleotide depletion suppresses T-cell activation is unknown. Depletion of GTP inhibits ribosomal RNA synthesis in T cells by inhibiting transcription initiation factor I (TIF-IA), a GTP-binding protein that recruits RNA polymerase I to the ribosomal DNA promoter. TIF-IA-GTP binds the ErbB3-binding protein 1, and together they enhance the transcription of proliferating cell nuclear antigen (PCNA). GTP binding by TIF-IA and ErbB3-binding protein 1 phosphorylation by protein kinase C δ are both required for optimal PCNA expression. The protein kinase C inhibitor sotrastaurin markedly potentiates the inhibition of ribosomal RNA synthesis, PCNA expression, and T-cell activation induced by MPA, suggesting that the combination of the two agents are more highly effective than either alone in inducing immunosuppression.
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Affiliation(s)
| | - Yunqin Lee
- Department of Otolaryngology (Head and Neck Surgery), Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Lenore Urbani
- Departments of Medicine and Chemical and Systems Biology, and
| | - Paul J Utz
- Division of Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford CA; and
| | - Anne W Hamburger
- Department of Pathology and Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD
| | - John B Sunwoo
- Department of Otolaryngology (Head and Neck Surgery), Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
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Henriques R, Bögre L, Horváth B, Magyar Z. Balancing act: matching growth with environment by the TOR signalling pathway. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2691-701. [PMID: 24567496 DOI: 10.1093/jxb/eru049] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
One of the most fundamental aspects of growth in plants is its plasticity in relation to fluctuating environmental conditions. Growth of meristematic cells relies predominantly on protein synthesis, one of the most energy-consuming activities in cells, and thus is tightly regulated in accordance with the available nutrient and energy supplies. The Target of Rapamycin (TOR) signalling pathway takes a central position in this regulation. The core of the TOR signalling pathway is conserved throughout evolution, and can be traced back to the last eukaryotic common ancestor. In plants, a single complex constitutes the TOR signalling pathway. Manipulating the components of the TOR complex in Arabidopsis highlighted its common role as a major regulator of protein synthesis and metabolism, that is also involved in other biological functions such as cell-wall integrity, regulation of cell proliferation, and cell size. TOR, as an integral part of the auxin signalling pathway, connects hormonal and nutrient pathways. Downstream of TOR, S6 kinase and the ribosomal S6 protein have been shown to mediate several of these responses, although there is evidence of other complex non-linear TOR signalling pathway structures.
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Affiliation(s)
- Rossana Henriques
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca UAB, Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - László Bögre
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey TW20 0EX, UK
| | - Beátrix Horváth
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey TW20 0EX, UK
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Temesvári kru. 62, POB 521, H-6701, Szeged, Hungary
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Chevalier C, Bourdon M, Pirrello J, Cheniclet C, Gévaudant F, Frangne N. Endoreduplication and fruit growth in tomato: evidence in favour of the karyoplasmic ratio theory. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2731-46. [PMID: 24187421 DOI: 10.1093/jxb/ert366] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The growth of a plant organ depends upon the developmental processes of cell division and cell expansion. The activity of cell divisions sets the number of cells that will make up the organ; the cell expansion activity then determines its final size. Among the various mechanisms that may influence the determination of cell size, endopolyploidy by means of endoreduplication appears to be of great importance in plants. Endoreduplication is widespread in plants and supports the process of differentiation of cells and organs. Its functional role in plant cells is not fully understood, although it is commonly associated with ploidy-dependent cell expansion. During the development of tomato fruit, cells from the (fleshy) pericarp tissue become highly polyploid, reaching a DNA content barely encountered in other plant species (between 2C and 512C). Recent investigations using tomato fruit development as a model provided new data in favour of the long-standing karyoplasmic ratio theory, stating that cells tend to adjust their cytoplasmic volume to the nuclear DNA content. By establishing a highly structured cellular system where multiple physiological functions are integrated, endoreduplication does act as a morphogenetic factor supporting cell growth during tomato fruit development.
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Affiliation(s)
- Christian Chevalier
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
| | - Matthieu Bourdon
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
| | - Julien Pirrello
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
| | - Catherine Cheniclet
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France CNRS, Bordeaux Imaging Center, UMS 3420, F-33000 Bordeaux, France
| | - Frédéric Gévaudant
- University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
| | - Nathalie Frangne
- University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
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Upregulated expression of ebp1 contributes to schwann cell differentiation and migration after sciatic nerve crush. J Mol Neurosci 2014; 54:602-13. [PMID: 24878627 DOI: 10.1007/s12031-014-0331-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 05/13/2014] [Indexed: 12/15/2022]
Abstract
Ebp1, an ErbB3-binding protein, is the human homologue of the cell cycle-regulated mouse protein p38-2G4. Ebp1 was reported to inhibit the proliferation and induce the differentiation of human cancer cells. Its p48 isoform contributes to neuronal differentiation and growth factor specificity. However, the expression and role of Ebp1 in peripheral system lesions and repair are still unknown. Herein, we investigated the spatiotemporal pattern of Ebp1 expression following sciatic nerve crush. After crush, the level of Ebp1 protein was elevated gradually, peaked at day 5, and then declined to the normal at 4 weeks, which was similar to the expression of Oct-6. Furthermore, using double immunofluorescent staining, we found Ebp1 had a colocalization with S100 and Oct-6 in 5-day injured tissues. In vitro, we observed enhanced expression of Ebp1 during the process of cyclic adenosine monophosphate (cAMP)-induced Schwann cells differentiation. Interestingly, Ebp1-depleted SCs did not show significant morphologic change after the treatment of cAMP. Also, we observed a colocalization between Ebp1 and Cyclin D1 and that Ebp1-specific siRNA-transfected SCs had a decreased migration. Taken together, we speculated that Ebp1 was upregulated in the sciatic nerve after crush, which was involved in the differentiation and migration of Schwann cells.
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Proteomic Identification of Nrf2-Mediated Phase II Enzymes Critical for Protection of Tao Hong Si Wu Decoction against Oxygen Glucose Deprivation Injury in PC12 Cells. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 2014:945814. [PMID: 24949080 PMCID: PMC4037622 DOI: 10.1155/2014/945814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 03/27/2014] [Accepted: 04/07/2014] [Indexed: 02/02/2023]
Abstract
Chinese herbal medicine formula Tao Hong Si Wu decoction (THSWD) is traditionally used in China for cerebrovascular diseases. However, the molecular mechanisms of THSWD associated with the cerebral ischemia reperfusion injury are largely unknown. The current study applied the two-dimensional gel electrophoresis-based proteomics to investigate the different protein profiles in PC12 cells with and without the treatment of THSWD. Twenty-six proteins affected by THSWD were identified by MALDI-TOF mass spectrometry. Gene ontology analysis showed that those proteins participated in several important biological processes and exhibited diverse molecular functions. In particular, six of them were found to be phase II antioxidant enzymes, which were regulated by NF-E2-related factor-2 (Nrf2). Quantitative PCR further confirmed a dose-dependent induction of the six phase II enzymes by THSWD at the transcription level. Moreover, the individual ingredients of THSWD were discovered to synergistically contribute to the induction of phase II enzymes. Importantly, THSWD's protection against oxygen-glucose deprivation-reperfusion (OGD-Rep) induced cell death was significantly attenuated by antioxidant response element (ARE) decoy oligonucleotides, suggesting the protection of THSWD may be likely regulated at least in part by Nrf2-mediated phase II enzymes. Thus, our data will help to elucidate the molecular mechanisms underlying the neuroprotective effect of THSWD.
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Silva A, Luís D, Santos S, Silva J, Mendo AS, Coito L, Silva TFS, da Silva MFCG, Martins LMDRS, Pombeiro AJL, Borralho PM, Rodrigues CMP, Cabral MG, Videira PA, Monteiro C, Fernandes AR. Biological characterization of the antiproliferative potential of Co(II) and Sn(IV) coordination compounds in human cancer cell lines: a comparative proteomic approach. ACTA ACUST UNITED AC 2014; 28:167-76. [PMID: 23800656 DOI: 10.1515/dmdi-2013-0015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/29/2013] [Indexed: 11/15/2022]
Abstract
BACKGROUND The discovery of cisplatin's antitumor activity led to a great interest in the potential application of coordination compounds as chemotherapeutic agents. It is essential to identify new compounds that selectively inhibit tumor proliferation, evading secondary effects and resistance associated with chemotherapeutics. METHODS The in vitro antiproliferative potential of an organotin(IV) compound was evaluated using colorectal and hepatocellular carcinoma, mammary gland adenocarcinoma cell lines, and human fibroblasts. Tumor cell death was evaluated by fluorescence microscopy and flow cytometry for the Sn(IV) compound and also for a Co(II) compound bearing 1,10-phenanthroline-5,6-dione as ligand. Comparative proteomic analysis for both compounds was assessed in the colorectal cancer cell line. RESULTS The Sn(IV) compound presented a high cytotoxic effect in colorectal and hepatocellular carcinoma cell lines (IC50 of 0.238 ± 0.011 μM, 0.199 ± 0.003 μM, respectively), and a lower cytotoxicity in human fibroblasts. Both compounds induced cell apoptosis and promoted the overexpression of oxidative stress-related enzyme superoxide dismutase [Cu-Zn] (SODC). The Co(II) compound induced a decreased expression of anti-apoptotic proteins (translationally-controlled tumor protein and endoplasmin), and the Sn(IV) compound decreased expression of proteins involved in microtubule stabilization, TCTP, and cofilin-1. CONCLUSIONS Our data reveals a high in vitro antiproliferative potential against cancer cell lines and a moderate selectivity promoted by the Sn(IV) compound. Proteomic analysis of Sn(IV) and Co(II) compounds in the colorectal cancer cell line allowed an insight to their mechanisms of action, particularly by affecting the expression of proteins typically deregulated in cancer, and also suggesting a promising therapeutic potential for both compounds.
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Vetere A, Choudhary A, Burns SM, Wagner BK. Targeting the pancreatic β-cell to treat diabetes. Nat Rev Drug Discov 2014; 13:278-89. [PMID: 24525781 DOI: 10.1038/nrd4231] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Diabetes is a leading cause of morbidity and mortality worldwide, and predicted to affect over 500 million people by 2030. However, this growing burden of disease has not been met with a comparable expansion in therapeutic options. The appreciation of the pancreatic β-cell as a central player in the pathogenesis of both type 1 and type 2 diabetes has renewed focus on ways to improve glucose homeostasis by preserving, expanding and improving the function of this key cell type. Here, we provide an overview of the latest developments in this field, with an emphasis on the most promising strategies identified to date for treating diabetes by targeting the β-cell.
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Affiliation(s)
- Amedeo Vetere
- Chemical Biology Program, Center for the Science of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Amit Choudhary
- 1] Chemical Biology Program, Center for the Science of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. [2] Society of Fellows, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Sean M Burns
- Medical & Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Bridget K Wagner
- Chemical Biology Program, Center for the Science of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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