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Chen Z, Wang F, Chen B, Wu G, Tian D, Yuan Q, Qiu S, Zhai Y, Chen J, Zheng H, Yan F. Turnip mosaic virus NIb weakens the function of eukaryotic translation initiation factor 6 facilitating viral infection in Nicotiana benthamiana. MOLECULAR PLANT PATHOLOGY 2024; 25:e13434. [PMID: 38388027 PMCID: PMC10883789 DOI: 10.1111/mpp.13434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/24/2024]
Abstract
Viruses rely completely on host translational machinery to produce the proteins encoded by their genes. Controlling translation initiation is important for gaining translational advantage in conflicts between the host and virus. The eukaryotic translation initiation factor 4E (eIF4E) has been reported to be hijacked by potyviruses for virus multiplication. The role of translation regulation in defence and anti-defence between plants and viruses is not well understood. We report that the transcript level of eIF6 was markedly increased in turnip mosaic virus (TuMV)-infected Nicotiana benthamiana. TuMV infection was impaired by overexpression of N. benthamiana eIF6 (NbeIF6) either transiently expressed in leaves or stably expressed in transgenic plants. Polysome profile assays showed that overexpression of NbeIF6 caused the accumulation of 40S and 60S ribosomal subunits, the reduction of polysomes, and also compromised TuMV UTR-mediated translation, indicating a defence role for upregulated NbeIF6 during TuMV infection. However, the polysome profile in TuMV-infected leaves was not identical to that in leaves overexpressing NbeIF6. Further analysis showed that TuMV NIb protein, the RNA-dependent RNA polymerase, interacted with NbeIF6 and interfered with its effect on the ribosomal subunits, suggesting that NIb might have a counterdefence role. The results propose a possible regulatory mechanism at the translation level during plant-virus interaction.
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Affiliation(s)
- Ziqiang Chen
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Biotechnology Research InstituteFujian Academy of Agricultural SciencesFuzhouChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Feng Wang
- Biotechnology Research InstituteFujian Academy of Agricultural SciencesFuzhouChina
| | - Binghua Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Dagang Tian
- Biotechnology Research InstituteFujian Academy of Agricultural SciencesFuzhouChina
| | - Quan Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Shiyou Qiu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Yushan Zhai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Jianping Chen
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐productsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
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Coleman PR, Lay AJ, Ting KK, Zhao Y, Li J, Jarrah S, Vadas MA, Gamble JR. YAP and the RhoC regulator ARHGAP18, are required to mediate flow-dependent endothelial cell alignment. Cell Commun Signal 2020; 18:18. [PMID: 32013974 PMCID: PMC6998144 DOI: 10.1186/s12964-020-0511-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 01/04/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Vascular endothelial cell alignment in the direction of flow is an adaptive response that protects against aortic diseases such as atherosclerosis. The RhoGTPases are known to regulate this alignment. We have shown previously that ARHGAP18 in endothelial cells is a negative regulator of RhoC and its expression is essential in flow-mediated alignment. Depletion of ARHGAP18 inhibits alignment and results in the induction of a pro-inflammatory phenotype. In embryogenesis, ARHGAP18 was identified as a downstream effector of the Yes-associated protein, YAP, which regulates cell shape and size. METHODS We have used siRNA technology to deplete either ARHGAP18 or YAP in human endothelial cells. The in vitro studies were performed under athero-protective, laminar flow conditions. The analysis of YAP activity was also investigated, using high performance confocal imaging, in our ARHGAP18 knockout mutant mice. RESULTS We show here that loss of ARHGAP18, although decreasing the expression of YAP results in its nuclear localisation consistent with activation. We further show that depletion of YAP itself results in its activation as defined by an in increase in its nuclear localisation and an increase in the YAP target gene, CyR61. Depletion of YAP, similar to that observed for ARHGAP18 depletion, results in loss of endothelial cell alignment under high shear stress mediated flow and also in the activation of NFkB, as determined by p65 nuclear localisation. In contrast, ARHGAP18 overexpression results in upregulation of YAP, its phosphorylation, and a decrease in the YAP target gene Cyr61, consistent with YAP inactivation. Finally, in ARHGAP18 deleted mice, in regions where there is a loss of endothelial cell alignment, a situation associated with a priming of the cells to a pro-inflammatory phenotype, YAP shows nuclear localisation. CONCLUSION Our results show that YAP is downstream of ARHGAP18 in mature endothelial cells and that this pathway is involved in the athero-protective alignment of endothelial cells under laminar shear stress. ARHGAP18 depletion leads to a disruption of the junctions as seen by loss of VE-Cadherin localisation to these regions and a concomitant localisation of YAP to the nucleus.
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Affiliation(s)
- Paul R Coleman
- Centre for the Endothelium, Vascular Biology Program, Centenary Institute, The University of Sydney, Locked Bag 6, Newtown, Sydney, 2042, Australia
| | - Angelina J Lay
- Centre for the Endothelium, Vascular Biology Program, Centenary Institute, The University of Sydney, Locked Bag 6, Newtown, Sydney, 2042, Australia
| | - Ka Ka Ting
- Centre for the Endothelium, Vascular Biology Program, Centenary Institute, The University of Sydney, Locked Bag 6, Newtown, Sydney, 2042, Australia
| | - Yang Zhao
- Centre for the Endothelium, Vascular Biology Program, Centenary Institute, The University of Sydney, Locked Bag 6, Newtown, Sydney, 2042, Australia
| | - Jia Li
- Centre for the Endothelium, Vascular Biology Program, Centenary Institute, The University of Sydney, Locked Bag 6, Newtown, Sydney, 2042, Australia
| | - Sorour Jarrah
- Centre for the Endothelium, Vascular Biology Program, Centenary Institute, The University of Sydney, Locked Bag 6, Newtown, Sydney, 2042, Australia
| | - Mathew A Vadas
- Centre for the Endothelium, Vascular Biology Program, Centenary Institute, The University of Sydney, Locked Bag 6, Newtown, Sydney, 2042, Australia
| | - Jennifer R Gamble
- Centre for the Endothelium, Vascular Biology Program, Centenary Institute, The University of Sydney, Locked Bag 6, Newtown, Sydney, 2042, Australia.
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Protective Effects of Scutellarin on Human Cardiac Microvascular Endothelial Cells against Hypoxia-Reoxygenation Injury and Its Possible Target-Related Proteins. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2015; 2015:278014. [PMID: 26557144 PMCID: PMC4628680 DOI: 10.1155/2015/278014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/25/2015] [Accepted: 04/25/2015] [Indexed: 11/17/2022]
Abstract
Scutellarin (SCU) is one of the main components of traditional Chinese medicine plant Erigeron breviscapus (Vant.) Hand.-Mazz. In this paper, we studied the protective effects of SCU on human cardiac microvascular endothelial cells (HCMECs) against hypoxia-reoxygenation (HR) injury and its possible target-related proteins. Results of MTT assay showed that pretreatment of SCU at doses of 1, 5, and 10 μM for 2 h could significantly inhibit the decrease in cell viability of HCMECs induced by HR injury. Subcellular fractions of cells treated with vehicle control, 1 μM SCU, HR injury, or 1 μM SCU + HR injury were separated by ultracentrifugation. The protein expression profiles of cytoplasm and membrane/nuclei fractions were checked using protein two-dimensional electrophoresis (2-DE). Proteins differentially expressed between control and SCU-treated group, control and HR group, or HR and SCU + HR group were identified using mass spectrometry (MS/MS). Possible interaction network of these target-related proteins was predicted using bioinformatic analysis. The influence of SCU on the expression levels of these proteins was confirmed using Western blotting assay. The results indicated that proteins such as p27BBP protein (EIF6), heat shock 60 kDa protein 1 (HSPD1), and chaperonin containing TCP1 subunit 6A isoform (CCT6A) might play important roles in the effects of SCU.
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Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ. Mechanism of eIF6 release from the nascent 60S ribosomal subunit. Nat Struct Mol Biol 2015; 22:914-9. [PMID: 26479198 PMCID: PMC4871238 DOI: 10.1038/nsmb.3112] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/17/2015] [Indexed: 12/20/2022]
Abstract
SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eIF6 from nascent 60S ribosomal subunits. However, the mechanism is completely unknown. Here, we present cryo-EM structures of human SBDS and SBDS-EFL1 bound to Dictyostelium discoideum 60S ribosomal subunits with and without endogenous eIF6. SBDS assesses the integrity of the peptidyl (P) site, bridging uL16 (mutated in T-cell acute lymphoblastic leukemia) with uL11 at the P-stalk base and the sarcin-ricin loop. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit. Our data reveal the conserved mechanism of eIF6 release, which is corrupted in both inherited and sporadic leukemias.
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Affiliation(s)
- Félix Weis
- Cambridge Institute for Medical Research, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Emmanuel Giudice
- Université de Rennes 1, Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 6290, Institut de Génétique et Développement de Rennes, Rennes, France
| | - Mark Churcher
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Li Jin
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Christine Hilcenko
- Cambridge Institute for Medical Research, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Chi C Wong
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - David Traynor
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Robert R Kay
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Alan J Warren
- Cambridge Institute for Medical Research, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
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Michalec-Wawiorka B, Wawiorka L, Derylo K, Krokowski D, Boguszewska A, Molestak E, Szajwaj M, Tchorzewski M. Molecular behavior of human Mrt4 protein, MRTO4, in stress conditions is regulated by its C-terminal region. Int J Biochem Cell Biol 2015; 69:233-40. [PMID: 26494001 DOI: 10.1016/j.biocel.2015.10.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 11/29/2022]
Abstract
Protein Mrt4 is one of trans-acting factors involved in ribosome biogenesis, which in higher eukaryotic cells contains a C-terminal extension similar to the C-terminal part of ribosomal P proteins. We show that human Mrt4 (hMrt4/MRTO4) undergoes phosphorylation in vivo and that serines S229, S233, and S235, placed within its acidic C-termini, have been phosphorylated by CK2 kinase in vitro. Such modification does not alter the subcellular distribution of hMrt4 in standard conditions but affects its molecular behavior during ActD induced nucleolar stress. Thus, we propose a new regulatory element important for the stress response pathway connecting ribosome biogenesis with cellular metabolism.
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Affiliation(s)
- Barbara Michalec-Wawiorka
- Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Leszek Wawiorka
- Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Kamil Derylo
- Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Dawid Krokowski
- Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Aleksandra Boguszewska
- Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Eliza Molestak
- Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Monika Szajwaj
- Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Marek Tchorzewski
- Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland.
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Calligari PA, Calandrini V, Ollivier J, Artero JB, Härtlein M, Johnson M, Kneller GR. Adaptation of Extremophilic Proteins with Temperature and Pressure: Evidence from Initiation Factor 6. J Phys Chem B 2015; 119:7860-73. [PMID: 25996652 DOI: 10.1021/acs.jpcb.5b02034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we study dynamical properties of an extremophilic protein, Initiation Factor 6 (IF6), produced by the archeabacterium Methanocaldococcus jannascii, which thrives close to deep-sea hydrothermal vents where temperatures reach 80 °C and the pressure is up to 750 bar. Molecular dynamics simulations (MD) and quasi-elastic neutron scattering (QENS) measurements give new insights into the dynamical properties of this protein with respect to its eukaryotic and mesophilic homologue. Results obtained by MD are supported by QENS data and are interpreted within the framework of a fractional Brownian dynamics model for the characterization of protein relaxation dynamics. IF6 from M. jannaschii at high temperature and pressure shares similar flexibility with its eukaryotic homologue from S. cerevisieae under ambient conditions. This work shows for the first time, to our knowledge, that the very common pattern of corresponding states for thermophilic protein adaptation can be extended to thermo-barophilic proteins. A detailed analysis of dynamic properties and of local structural fluctuations reveals a complex pattern for "corresponding" structural flexibilities. In particular, in the case of IF6, the latter seems to be strongly related to the entropic contribution given by an additional, C-terminal, 20 amino-acid tail which is evolutionary conserved in all mesophilic IF6s.
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Affiliation(s)
- Paolo A Calligari
- †SISSA, International School for Advanced Studies, via Bonomea 265, 34136 Trieste, Italy
| | - Vania Calandrini
- ‡Computational Biophysics, German Research School for Simulation Sciences, Jülich, Germany
| | - Jacques Ollivier
- §Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble Cedex, France
| | - Jean-Baptiste Artero
- §Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble Cedex, France
| | - Michael Härtlein
- §Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble Cedex, France
| | - Mark Johnson
- §Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble Cedex, France
| | - Gerald R Kneller
- ∥Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, F-45071 Orléans Cedex 2, France.,⊥Synchrotron Soleil, L'Orme de Merisiers, BP 48, 91192 Gif-sur-Yvette, France.,#Université de Orléans, Chateau de la Source-Av. du Parc Floral, 45067 Orléans, France
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Brina D, Miluzio A, Ricciardi S, Biffo S. eIF6 anti-association activity is required for ribosome biogenesis, translational control and tumor progression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:830-5. [PMID: 25252159 DOI: 10.1016/j.bbagrm.2014.09.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/12/2014] [Accepted: 09/14/2014] [Indexed: 12/13/2022]
Abstract
Here we discuss the function of eukaryotic initiation factor 6 (eIF6; Tif6 in yeast). eIF6 binds 60S ribosomal subunits and blocks their joining to 40S. In this context, we propose that eIF6 impedes unproductive 80S formation, namely, the formation of 80S subunits without mRNA. Genetic evidence shows that eIF6 has a dual function: in yeast and mammals, nucleolar eIF6 is necessary for the biogenesis of 60S subunits. In mammals, cytoplasmic eIF6 is required for insulin and growth factor-stimulated translation. In contrast to other translation factors, eIF6 activity is not under mTOR control. The physiological significance of eIF6 impacts on cancer and on inherited Shwachman-Bodian-Diamond syndrome. eIF6 is overexpressed in specific human tumors. In a murine model of lymphomagenesis, eIF6 depletion leads to a striking increase of survival, without adverse effects. Shwachman-Bodian-Diamond syndrome is caused by loss of function of SBDS protein. In yeast, point mutations of Tif6, the yeast homolog of eIF6, rescue the quasi-lethal effect due to the loss of the SBDS homolog, Sdo1. We propose that eIF6 is a node regulator of ribosomal function and predict that prioritizing its pharmacological targeting will be of benefit in cancer and Shwachman-Bodian-Diamond syndrome. This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Daniela Brina
- INGM, "Romeo ed Enrica Invernizzi," Milano 20122, Italy
| | | | - Sara Ricciardi
- INGM, "Romeo ed Enrica Invernizzi," Milano 20122, Italy; DISIT, Alessandria 15100, Italy
| | - Stefano Biffo
- INGM, "Romeo ed Enrica Invernizzi," Milano 20122, Italy; DISIT, Alessandria 15100, Italy.
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8
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Peng X, Yuan S, Tan J, Ma B, Bian X, Xu C, He W, Cao H, Huang Z, Cui Y, Gan C, Wang X, Zhou J, Hu J, Yang S, Luo G, Wu J. Identification of ITGB4BP as a new interaction protein of P311. Life Sci 2012; 90:585-90. [DOI: 10.1016/j.lfs.2012.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 12/21/2011] [Accepted: 02/02/2012] [Indexed: 11/30/2022]
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Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution. J Mol Biol 2012; 418:145-60. [PMID: 22306461 DOI: 10.1016/j.jmb.2012.01.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 01/05/2012] [Accepted: 01/13/2012] [Indexed: 11/20/2022]
Abstract
Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The structure provides detailed architectural insights into the 50S ribosomal subunit from a methanogenic archaeon through identification of the rRNA expansion segments and ribosomal proteins that are shared between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea.
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Tan J, Luo G, Wu J. The biological roles of ITGB4BP and its potential effect on fibrosis. INTERNATIONAL JOURNAL OF BURNS AND TRAUMA 2011; 1:51-5. [PMID: 22928158 PMCID: PMC3415943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Accepted: 08/31/2011] [Indexed: 06/01/2023]
Abstract
Fibrosis is the end result of pathologic wound healing and is characterized by inflammation, excessive proliferation of fibroblasts, and abnormal deposition of extracellular matrix (ECM) proteins. Despite the advanced treatments for the fibrotic diseases, as well as the researches on the fibrosis, pathologic fibrotic diseases remain to be hard cured and the molecular mechanism of fibrosis is still unclear. In our previous studies we found ITGB4BP was involved in the myofibroblast differentiation. However there were no studies about the roles of ITGB4BP in fibrosis. On this background this review explores the basic features and the biological function of ITGB4BP which might imply the underlying cellular and molecular mechanism in the regulation of fibrotic diseases.
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Affiliation(s)
- Jianglin Tan
- Institute of Burn Research, State Key Laboratory for Trauma, Burns and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Southwest Hospital, Third Military Medical University Chongqing 400038, China
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Biswas A, Pasquel D, Tyagi RK, Mani S. Acetylation of pregnane X receptor protein determines selective function independent of ligand activation. Biochem Biophys Res Commun 2011; 406:371-6. [PMID: 21329659 DOI: 10.1016/j.bbrc.2011.02.048] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 02/11/2011] [Indexed: 01/06/2023]
Abstract
Pregnane X receptor (PXR), like other members of its class of nuclear receptors, undergoes post-translational modification [PTM] (e.g., phosphorylation). However, it is unknown if acetylation (a major and common form of protein PTM) is observed on PXR and, if it is, whether it is of functional consequence. PXR has recently emerged as an important regulatory protein with multiple ligand-dependent functions. In the present work we show that PXR is indeed acetylated in vivo. SIRT1 (Sirtuin 1), a NAD-dependent class III histone deacetylase and a member of the sirtuin family of proteins, partially mediates deacetylation of PXR. Most importantly, the acetylation status of PXR regulates its selective function independent of ligand activation.
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Affiliation(s)
- Arunima Biswas
- Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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12
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Biswas A, Mukherjee S, Das S, Shields D, Chow CW, Maitra U. Opposing action of casein kinase 1 and calcineurin in nucleo-cytoplasmic shuttling of mammalian translation initiation factor eIF6. J Biol Chem 2010; 286:3129-38. [PMID: 21084295 DOI: 10.1074/jbc.m110.188565] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic initiation factor 6 (eIF6), a highly conserved protein from yeast to mammals, is essential for 60 S ribosome biogenesis and assembly. Both yeast and mammalian eIF6 are phosphorylated at Ser-174 and Ser-175 by the nuclear isoform of casein kinase 1 (CK1). The molecular basis of eIF6 phosphorylation, however, remains elusive. In the present work, we show that subcellular distribution of eIF6 in the nuclei and the cytoplasm of mammalian cells is mediated by dephosphorylation and phosphorylation, respectively. This nucleo-cytoplasmic shuttling is dependent on the phosphorylation status at Ser-174 and Ser-175 of eIF6. We demonstrate that Ca(2+)-activated calcineurin phosphatase binds to and promotes nuclear localization of eIF6. Increase in intracellular concentration of Ca(2+) leads to rapid translocation of eIF6 from the cytoplasm to the nucleus, an event that is blocked by specific calcineurin inhibitors cyclosporin A or FK520. Nuclear export of eIF6 is regulated by phosphorylation at Ser-174 and Ser-175 by the nuclear isoform of CK1. Mutation of eIF6 at the phosphorylatable Ser-174 and Ser-175 to alanine or treatment of cells with the CK1 inhibitor, D4476 inhibits nuclear export of eIF6 and results in nuclear accumulation of eIF6. Together, these results establish eIF6 as a substrate for calcineurin and suggest a novel paradigm for calcineurin function in 60 S ribosome biogenesis via regulating the nuclear accumulation of eIF6.
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Affiliation(s)
- Arunima Biswas
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Driving ribosome assembly. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:673-83. [DOI: 10.1016/j.bbamcr.2009.10.009] [Citation(s) in RCA: 372] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 10/13/2009] [Accepted: 10/26/2009] [Indexed: 11/19/2022]
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14
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Gartmann M, Blau M, Armache JP, Mielke T, Topf M, Beckmann R. Mechanism of eIF6-mediated inhibition of ribosomal subunit joining. J Biol Chem 2010; 285:14848-14851. [PMID: 20356839 PMCID: PMC2865328 DOI: 10.1074/jbc.c109.096057] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 02/09/2010] [Indexed: 01/25/2023] Open
Abstract
During the process of ribosomal assembly, the essential eukaryotic translation initiation factor 6 (eIF6) is known to act as a ribosomal anti-association factor. However, a molecular understanding of the anti-association activity of eIF6 is still missing. Here we present the cryo-electron microscopy reconstruction of a complex of the large ribosomal subunit with eukaryotic eIF6 from Saccharomyces cerevisiae. The structure reveals that the eIF6 binding site involves mainly rpL23 (L14p in Escherichia coli). Based on our structural data, we propose that the mechanism of the anti-association activity of eIF6 is based on steric hindrance of intersubunit bridge formation around the dynamic bridge B6.
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Affiliation(s)
- Marco Gartmann
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Michael Blau
- Institut für Biochemie der Charité, Humboldt Universität Berlin, Monbijoustrasse 2, 10117 Berlin, Germany
| | - Jean-Paul Armache
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin; Institut für Medizinische Physik und Biophysik, Charité, Ziegelstrasse 5-9, 10098 Berlin, Germany
| | - Maya Topf
- Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Roland Beckmann
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
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15
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Abstract
Ribosome assembly is required for cell growth in all organisms. Classic in vitro work in bacteria has led to a detailed understanding of the biophysical, thermodynamic, and structural basis for the ordered and correct assembly of ribosomal proteins on ribosomal RNA. Furthermore, it has enabled reconstitution of active subunits from ribosomal RNA and proteins in vitro. Nevertheless, recent work has shown that eukaryotic ribosome assembly requires a large macromolecular machinery in vivo. Many of these assembly factors such as ATPases, GTPases, and kinases hydrolyze nucleotide triphosphates. Because these enzymes are likely regulatory proteins, much work to date has focused on understanding their role in the assembly process. Here, we review these factors, as well as other sources of energy, and their roles in the ribosome assembly process. In addition, we propose roles of energy-releasing enzymes in the assembly process, to explain why energy is used for a process that occurs largely spontaneously in bacteria. Finally, we use literature data to suggest testable models for how these enzymes could be used as targets for regulation of ribosome assembly.
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Affiliation(s)
- Bethany S Strunk
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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16
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Benelli D, Marzi S, Mancone C, Alonzi T, la Teana A, Londei P. Function and ribosomal localization of aIF6, a translational regulator shared by archaea and eukarya. Nucleic Acids Res 2008; 37:256-67. [PMID: 19036786 PMCID: PMC2615626 DOI: 10.1093/nar/gkn959] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The translation factor IF6 is shared by the Archaea and the Eukarya, but is not found in Bacteria. The properties of eukaryal IF6 (eIF6) have been extensively studied, but remain somewhat elusive. eIF6 behaves as a ribosome-anti-association factor and is involved in miRNA-mediated gene silencing; however, it also seems to participate in ribosome synthesis and export. Here we have determined the function and ribosomal localization of the archaeal (Sulfolobus solfataricus) IF6 homologue (aIF6). We find that aIF6 binds specifically to the 50S ribosomal subunits, hindering the formation of 70S ribosomes and strongly inhibiting translation. aIF6 is uniformly expressed along the cell cycle, but it is upregulated following both cold- and heat shock. The aIF6 ribosomal binding site lies in the middle of the 30-S interacting surface of the 50S subunit, including a number of critical RNA and protein determinants involved in subunit association. The data suggest that the IF6 protein evolved in the archaeal–eukaryal lineage to modulate translational efficiency under unfavourable environmental conditions, perhaps acquiring additional functions during eukaryotic evolution.
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Affiliation(s)
- Dario Benelli
- Dipartimento Biotecnologie Cellulari ed Ematologia, Policlinico Umberto I, Università di Roma Sapienza, Roma, Italy
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17
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Hong CI, Ruoff P, Loros JJ, Dunlap JC. Closing the circadian negative feedback loop: FRQ-dependent clearance of WC-1 from the nucleus. Genes Dev 2008; 22:3196-204. [PMID: 18997062 DOI: 10.1101/gad.1706908] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In Neurospora crassa, a transcription factor, WCC, activates the transcription of frq. FRQ forms homodimers as well as complexes with an RNA helicase, FRH, and the WCC, and translocates into the nucleus to inactivate the WCC, closing the time-delayed negative feedback loop. The detailed mechanism for closing this loop, however, remains incompletely understood. In particular within the nucleus, the low amount of FRQ compared with that of WC-1 creates a conundrum: How can the nuclear FRQ inactivate the larger amount of WCC? One possibility is that FRQ might function as a catalytic component in phosphorylation-dependent inhibition. However, in silico experiments reveal that stoichiometric noncatalytic binding and inhibition can generate a robust oscillator, even when nuclear FRQ levels are substantially lower than nuclear WCC, so long as there is FRQ-dependent clearance of WC-1 from the nucleus. Based on this model, we can predict and now demonstrate that WC-1 stability cycles, that WC-1 is stable in the absence of FRQ, and that physical binding between FRQ and WCC is essential for closure of the negative feedback loop. Moreover, and consistent with a noncatalytic clearance-based model for inhibition, appreciable amounts of the nuclear FRQ:WCC complex accumulate at some times of day, comprising as much as 10% of the nuclear WC-1.
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Affiliation(s)
- Christian I Hong
- Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
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18
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Ray P, Basu U, Ray A, Majumdar R, Deng H, Maitra U. The Saccharomyces cerevisiae 60 S ribosome biogenesis factor Tif6p is regulated by Hrr25p-mediated phosphorylation. J Biol Chem 2008; 283:9681-91. [PMID: 18256024 DOI: 10.1074/jbc.m710294200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The biosynthesis of 60 S ribosomal subunits in Saccharomyces cerevisiae requires Tif6p, the yeast homologue of mammalian eIF6. This protein is necessary for the formation of 60 S ribosomal subunits because it is essential for the processing of 35 S pre-rRNA to the mature 25 S and 5.8 S rRNAs. In the present work, using molecular genetic and biochemical analyses, we show that Hrr25p, an isoform of yeast casein kinase I, phosphorylates Tif6p both in vitro and in vivo. Tryptic phosphopeptide mapping of in vitro phosphorylated Tif6p by Hrr25p and (32)P-labeled Tif6p isolated from yeast cells followed by mass spectrometric analysis revealed that phosphorylation occurred on a single tryptic peptide at Ser-174. Sucrose gradient fractionation and coimmunoprecipitation experiments demonstrate that a small but significant fraction of Hrr25p is bound to 66 S preribosomal particles that also contain bound Tif6p. Depletion of Hrr25p from a conditional yeast mutant that fails to phosphorylate Tif6p was unable to process pre-rRNAs efficiently, resulting in significant reduction in the formation of 25 S rRNA. These results along with our previous observations that phosphorylatable Ser-174 is required for yeast cell growth and viability, suggest that Hrr25p-mediated phosphorylation of Tif6p plays a critical role in the biogenesis of 60 S ribosomal subunits in yeast cells.
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Affiliation(s)
- Partha Ray
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
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19
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Ji Y, Shah S, Soanes K, Islam MN, Hoxter B, Biffo S, Heslip T, Byers S. Eukaryotic initiation factor 6 selectively regulates Wnt signaling and beta-catenin protein synthesis. Oncogene 2007; 27:755-62. [PMID: 17667944 DOI: 10.1038/sj.onc.1210667] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic initiation factor 6 (eIF6), an essential protein important in ribosome biosynthesis and assembly, was identified as an interacting partner of the beta-catenin C terminus in the yeast two-hybrid assay. Independent studies identified Drosophila eIF6 (DeIF6) in a genetic screen designed to detect new genes involved in the regulation of the Wnt/Wg (wingless) pathway. Ectopic expression of DeIF6 in wing discs results in a Wg phenotype. Expression of eIF6 in adenomatous polyposis coli (APC)-mutant colon cancer cells, which express high levels of active beta-catenin, showed that eIF6 selectively inhibits the Wnt pathway at the level of beta-catenin protein independently of proteasomal degradation. Incorporation of radiolabeled amino acids into beta-catenin was selectively decreased in cells that overexpressed eIF6. A similar inverse relationship of the two proteins was observed in the APC(min/+) mouse intestine, in which beta-catenin levels are very high. Taken together these data reveal a link between eIF6 and Wnt signaling, perhaps at the level of ribosome recycling on beta-catenin mRNA.
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Affiliation(s)
- Y Ji
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC 20057, USA
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20
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Zemp I, Kutay U. Nuclear export and cytoplasmic maturation of ribosomal subunits. FEBS Lett 2007; 581:2783-93. [PMID: 17509569 DOI: 10.1016/j.febslet.2007.05.013] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 05/06/2007] [Indexed: 01/20/2023]
Abstract
Based on the characterization of ribosome precursor particles and associated trans-acting factors, a biogenesis pathway for the 40S and 60S subunits has emerged. After nuclear synthesis and assembly steps, pre-ribosomal subunits are exported through the nuclear pore complex in a Crm1- and RanGTP-dependent manner. Subsequent cytoplasmic biogenesis steps of pre-60S particles include the facilitated release of several non-ribosomal proteins, yielding fully functional 60S subunits. Cytoplasmic maturation of 40S subunit precursors includes rRNA dimethylation and pre-rRNA cleavage, allowing 40S subunits to achieve translation competence. We review current knowledge of nuclear export and cytoplasmic maturation of ribosomal subunits.
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Affiliation(s)
- Ivo Zemp
- Institute of Biochemistry, HPM F11.1, Schafmattstr. 18, ETH Zurich, 8093 Zurich, Switzerland
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21
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Lehmann DM, Galloway CA, MacElrevey C, Sowden MP, Wedekind JE, Smith HC. Functional characterization of APOBEC-1 complementation factor phosphorylation sites. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1773:408-18. [PMID: 17229474 PMCID: PMC1847399 DOI: 10.1016/j.bbamcr.2006.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 11/13/2006] [Accepted: 11/27/2006] [Indexed: 11/17/2022]
Abstract
ApoB mRNA editing involves site-specific deamination of cytidine 6666 producing an in-frame translation stop codon. Editing minimally requires APOBEC-1 and APOBEC-1 complementation factor (ACF). Metabolic stimulation of apoB mRNA editing in hepatocytes is associated with serine phosphorylation of ACF localized to editing competent, nuclear 27S editosomes. We demonstrate that activation of protein kinase C (PKC) stimulated editing and enhanced ACF phosphorylation in rat primary hepatocytes. Conversely, activation of protein kinase A (PKA) had no effect on editing. Recombinant PKC efficiently phosphorylated purified ACF64 protein in vitro, whereas PKA did not. Mutagenesis of predicted PKC phosphorylation sites S154 and S368 to alanine inhibited ethanol-stimulated induction of editing suggesting that these sites function in the metabolic regulation of editing. Consistent with this interpretation, substitution of S154 and S368 with aspartic acid stimulated editing to levels comparable to ethanol treatment in control McArdle RH7777 cells. These data suggest that phosphorylation of ACF by PKC may be a key regulatory mechanism of apoB mRNA editing in rat hepatocytes.
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Affiliation(s)
- David M. Lehmann
- Department of Toxicology, University of Rochester, Rochester, New York 14642
- Environmental Health Sciences Center, University of Rochester, Rochester, New York 14642
| | - Chad A. Galloway
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
| | - Celeste MacElrevey
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
| | - Mark P. Sowden
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, New York 14642
| | - Joseph E. Wedekind
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
| | - Harold C. Smith
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, New York 14642
- Department of Toxicology, University of Rochester, Rochester, New York 14642
- Environmental Health Sciences Center, University of Rochester, Rochester, New York 14642
- James P. Wilmot Cancer Center, University of Rochester, Rochester, New York 14642
- * Corresponding author: Department of Biochemistry and Biophysics, University of Rochester, 601 Elmwood Ave., Rochester, NY 14642 Tel.: 585-275-4267 FAX: 585-275-6007 E-mail:
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22
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Donadini A, Giacopelli F, Ravazzolo R, Gandin V, Marchisio PC, Biffo S. GABP complex regulates transcription of eIF6 (p27BBP), an essential trans-acting factor in ribosome biogenesis. FEBS Lett 2006; 580:1983-7. [PMID: 16530192 DOI: 10.1016/j.febslet.2006.02.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 02/15/2006] [Accepted: 02/26/2006] [Indexed: 10/24/2022]
Abstract
Eukaryotic initiation factor 6 (eIF6, alias p27BBP) is required for the biogenesis of 60S ribosomal subunits. eIF6 expression levels are tightly regulated in vivo, where they correlate with cellular growth. We analyzed how transcriptional regulation of eIF6 is achieved. We show that the human eIF6 promoter contains consensus sites for the GABP (GA-binding protein) transcription factor complex. Functional analysis of GABP consensus sequences by point mutations, EMSA (electrophoretic mobility shift assay) and a dominant negative mutant indicates that GABP is essential for eIF6 promoter activity. These data strengthen the hypothesis that GABP is a global regulator of ribosome synthesis.
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