1
|
Yuan Y, Fan Y, Tang W, Sun H, Sun J, Su H, Fan H. Identification of ALYREF in pan cancer as a novel cancer prognostic biomarker and potential regulatory mechanism in gastric cancer. Sci Rep 2024; 14:6270. [PMID: 38491127 PMCID: PMC10942997 DOI: 10.1038/s41598-024-56895-5] [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: 10/07/2023] [Accepted: 03/12/2024] [Indexed: 03/18/2024] Open
Abstract
ALYREF is considered as a specific mRNA m5C-binding protein which recognizes m5C sites in RNA and facilitates the export of RNA from the nucleus to the cytoplasm. Expressed in various tissues and highly involved in the transcriptional regulation, ALYREF has the potential to become a novel diagnostic marker and therapeutic target for cancer patients. However, few studies focused on its function during carcinogenesis and progress. In order to explore the role of ALYREF on tumorigenesis, TCGA and GTEx databases were used to investigate the relationship of ALYREF to pan-cancer. We found that ALYREF was highly expressed in majority of cancer types and that elevated expression level was positively associated with poor prognosis in many cancers. GO and KEGG analysis showed that ALYREF to be essential in regulating the cell cycle and gene mismatch repair in tumor progression. The correlation analysis of tumor heterogeneity indicated that ALYREF could be specially correlated to the tumor stemness in stomach adenocarcinoma (STAD). Furthermore, we investigate the potential function of ALYREF on gastric carcinogenesis. Prognostic analysis of different molecular subtypes of gastric cancer (GC) unfolded that high ALYREF expression leads to poor prognosis in certain subtypes of GC. Finally, enrichment analysis revealed that ALYREF-related genes possess the function of regulating cell cycle and apoptosis that cause further influences in GC tumor progression. For further verification, we knocked down the expression of ALYREF by siRNA in GC cell line AGS. Knockdown of ALYREF distinctly contributed to inhibition of GC cell proliferation. Moreover, it is observed that knocked-down of ALYREF induced AGS cells arrested in G1 phase and increased cell apoptosis. Our findings highlighted the essential function of ALYREF in tumorigenesis and revealed the specific contribution of ALYREF to gastric carcinogenesis through pan-cancer analysis and biological experiments.
Collapse
Affiliation(s)
- Yujie Yuan
- The Key Laboratory of Developmental Genes and Human Diseases, Department of Medical Genetics and Developmental Biology, School of Medicine, Ministry of Education, Southeast University, Nanjing, 210009, China
| | - Yiyang Fan
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Wenqing Tang
- School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Hui Sun
- School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Jinghan Sun
- School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Hongmeng Su
- The Key Laboratory of Developmental Genes and Human Diseases, Department of Medical Genetics and Developmental Biology, School of Medicine, Ministry of Education, Southeast University, Nanjing, 210009, China
| | - Hong Fan
- The Key Laboratory of Developmental Genes and Human Diseases, Department of Medical Genetics and Developmental Biology, School of Medicine, Ministry of Education, Southeast University, Nanjing, 210009, China.
| |
Collapse
|
2
|
Goswami N, Singh A, Bharadwaj S, Sahoo AK, Singh IK. Targeting neuroblastoma by small-molecule inhibitors of human ALYREF protein: mechanistic insights using molecular dynamics simulations. J Biomol Struct Dyn 2024; 42:1352-1367. [PMID: 37158061 DOI: 10.1080/07391102.2023.2204376] [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: 11/16/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
Neuroblastoma is a tumour of the sympathetic nervous system mainly prevalent in children. Many strategies have been employed to target several drug-targetable proteins for the clinical management of neuroblastoma. However, the heterogeneous nature of neuroblastoma presents serious challenges in drug development for its treatment. Albeit numerous medications have been developed to target various signalling pathways in neuroblastoma, the redundant nature of the tumour pathways makes its suppression unsuccessful. Recently, the quest for neuroblastoma therapy resulted in the identification of human ALYREF, a nuclear protein that plays an essential role in tumour growth and progression. Therefore, this study used the structure-based drug discovery method to identify the putative inhibitors targeting ALYREF for the Neuroblastoma treatment. Herein, a library of 119 blood-brain barrier crossing small molecules from the ChEMBL database was downloaded and docked against the predicted binding pocket of the human ALYREF protein. Based on docking scores, the top four compounds were considered for intermolecular interactions and molecular dynamics simulation analysis, which revealed CHEMBL3752986 and CHEMBL3753744 with substantial affinity and stability with the ALYREF. These results were further supported by binding free energies and essential dynamics analysis of the respective complexes. Hence, this study advocates the sorted compounds targeting ALYREF for further in vitro and in vivo assessment to develop a drug against neuroblastoma.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Nidhi Goswami
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
- Neuropharmacology and Drug Delivery Laboratory, Department of Zoology, Daulat Ram College, University of Delhi, Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, Uttar Pradesh, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
- Delhi School of Public Health, Institute of Eminence, University of Delhi, Delhi, India
| |
Collapse
|
3
|
Zhao Y, Xing C, Peng H. ALYREF (Aly/REF export factor): A potential biomarker for predicting cancer occurrence and therapeutic efficacy. Life Sci 2024; 338:122372. [PMID: 38135116 DOI: 10.1016/j.lfs.2023.122372] [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: 10/04/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
5-Methylcytosine (m5C) methylation is present in almost all types of RNA as an essential epigenetic modification. It is dynamically modulated by its associated enzymes, including m5C methyltransferases (NSUN, DNMT and TRDMT family members), demethylases (TET family and ALKBH1) and binding proteins (YTHDF2, ALYREF and YBX1). Among them, aberrant expression of the RNA-binding protein ALYREF can facilitate a variety of malignant phenotypes such as maintenance of proliferation, malignant heterogeneity, metastasis, and drug resistance to cell death through different regulatory mechanisms, including pre-mRNA processing, mRNA stability, and nuclear-cytoplasmic shuttling. The induction of these cellular processes by ALYREF results in treatment resistance and poor outcomes for patients. However, there are currently few reports of clinical applications or drug trials related to ALYREF. In addition, the looming observations on the role of ALYREF in the mechanisms of carcinogenesis and disease prognosis have triggered considerable interest, but critical evidence is not available. For example, animal experiments and ALYREF small molecule inhibitor trials. In this review, we, therefore, revisit the literature on ALYREF and highlight its importance as a prognostic biomarker for early prevention and as a therapeutic target.
Collapse
Affiliation(s)
- Yan Zhao
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Cheng Xing
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Changsha, Hunan 410011, China; Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan 410011, China.
| |
Collapse
|
4
|
Mihaylov SR, Castelli LM, Lin YH, Gül A, Soni N, Hastings C, Flynn HR, Păun O, Dickman MJ, Snijders AP, Goldstone R, Bandmann O, Shelkovnikova TA, Mortiboys H, Ultanir SK, Hautbergue GM. The master energy homeostasis regulator PGC-1α exhibits an mRNA nuclear export function. Nat Commun 2023; 14:5496. [PMID: 37679383 PMCID: PMC10485026 DOI: 10.1038/s41467-023-41304-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
PGC-1α plays a central role in maintaining mitochondrial and energy metabolism homeostasis, linking external stimuli to transcriptional co-activation of genes involved in adaptive and age-related pathways. The carboxyl-terminus encodes a serine/arginine-rich (RS) region and an RNA recognition motif, however the RNA-processing function(s) were poorly investigated over the past 20 years. Here, we show that the RS domain of human PGC-1α directly interacts with RNA and the nuclear RNA export receptor NXF1. Inducible depletion of PGC-1α and expression of RNAi-resistant RS-deleted PGC-1α further demonstrate that its RNA/NXF1-binding activity is required for the nuclear export of some canonical mitochondrial-related mRNAs and mitochondrial homeostasis. Genome-wide investigations reveal that the nuclear export function is not strictly linked to promoter-binding, identifying in turn novel regulatory targets of PGC-1α in non-homologous end-joining and nucleocytoplasmic transport. These findings provide new directions to further elucidate the roles of PGC-1α in gene expression, metabolic disorders, aging and neurodegeneration.
Collapse
Affiliation(s)
- Simeon R Mihaylov
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Aytac Gül
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Nikita Soni
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Christopher Hastings
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Helen R Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oana Păun
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Sir Robert Hadfield Building, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Life Science Mass Spectrometry, Bruker Daltonics, Banner Lane, Coventry, CV4 9GH, UK
| | - Robert Goldstone
- Bioinformatics and Biostatistics Science and Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oliver Bandmann
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| |
Collapse
|
5
|
Klec C, Knutsen E, Schwarzenbacher D, Jonas K, Pasculli B, Heitzer E, Rinner B, Krajina K, Prinz F, Gottschalk B, Ulz P, Deutsch A, Prokesch A, Jahn SW, Lellahi SM, Perander M, Barbano R, Graier WF, Parrella P, Calin GA, Pichler M. ALYREF, a novel factor involved in breast carcinogenesis, acts through transcriptional and post-transcriptional mechanisms selectively regulating the short NEAT1 isoform. Cell Mol Life Sci 2022; 79:391. [PMID: 35776213 PMCID: PMC9249705 DOI: 10.1007/s00018-022-04402-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/15/2022] [Accepted: 05/25/2022] [Indexed: 12/15/2022]
Abstract
The RNA-binding protein ALYREF (THOC4) is involved in transcriptional regulation and nuclear mRNA export, though its role and molecular mode of action in breast carcinogenesis are completely unknown. Here, we identified high ALYREF expression as a factor for poor survival in breast cancer patients. ALYREF significantly influenced cellular growth, apoptosis and mitochondrial energy metabolism in breast cancer cells as well as breast tumorigenesis in orthotopic mouse models. Transcriptional profiling, phenocopy and rescue experiments identified the short isoform of the lncRNA NEAT1 as a molecular trigger for ALYREF effects in breast cancer. Mechanistically, we found that ALYREF binds to the NEAT1 promoter region to enhance the global NEAT1 transcriptional activity. Importantly, by stabilizing CPSF6, a protein that selectively activates the post-transcriptional generation of the short isoform of NEAT1, as well as by direct binding and stabilization of the short isoform of NEAT1, ALYREF selectively fine-tunes the expression of the short NEAT1 isoform. Overall, our study describes ALYREF as a novel factor contributing to breast carcinogenesis and identifies novel molecular mechanisms of regulation the two isoforms of NEAT1.
Collapse
Affiliation(s)
- Christiane Klec
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Medical Biology, Faculty of Health Sciences, UiT-the Arctic University of Norway, Tromsö, Norway
| | - Daniela Schwarzenbacher
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Katharina Jonas
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Barbara Pasculli
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz (MUG), Graz, Austria
| | - Beate Rinner
- Biomedical Research, Medical University of Graz (MUG), Graz, Austria
| | - Katarina Krajina
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Felix Prinz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Benjamin Gottschalk
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cellular Signaling, Metabolism and Aging, Medical University of Graz (MUG), Graz, Austria
| | - Peter Ulz
- Institute of Human Genetics, Medical University of Graz (MUG), Graz, Austria
| | - Alexander Deutsch
- Division of Hematology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Andreas Prokesch
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
| | - Stephan W Jahn
- Institute of Pathology, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - S Mohammad Lellahi
- Department of Medical Biology, Faculty of Health Sciences, UiT-the Arctic University of Norway, Tromsö, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, UiT-the Arctic University of Norway, Tromsö, Norway
| | - Raffaela Barbano
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - Wolfgang F Graier
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cellular Signaling, Metabolism and Aging, Medical University of Graz (MUG), Graz, Austria
| | - Paola Parrella
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - George Adrian Calin
- Department of Translational Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria.
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria.
| |
Collapse
|
6
|
Byron A, Griffith BGC, Herrero A, Loftus AEP, Koeleman ES, Kogerman L, Dawson JC, McGivern N, Culley J, Grimes GR, Serrels B, von Kriegsheim A, Brunton VG, Frame MC. Characterisation of a nucleo-adhesome. Nat Commun 2022; 13:3053. [PMID: 35650196 PMCID: PMC9160004 DOI: 10.1038/s41467-022-30556-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 05/02/2022] [Indexed: 11/09/2022] Open
Abstract
In addition to central functions in cell adhesion signalling, integrin-associated proteins have wider roles at sites distal to adhesion receptors. In experimentally defined adhesomes, we noticed that there is clear enrichment of proteins that localise to the nucleus, and conversely, we now report that nuclear proteomes contain a class of adhesome components that localise to the nucleus. We here define a nucleo-adhesome, providing experimental evidence for a remarkable scale of nuclear localisation of adhesion proteins, establishing a framework for interrogating nuclear adhesion protein functions. Adding to nuclear FAK's known roles in regulating transcription, we now show that nuclear FAK regulates expression of many adhesion-related proteins that localise to the nucleus and that nuclear FAK binds to the adhesome component and nuclear protein Hic-5. FAK and Hic-5 work together in the nucleus, co-regulating a subset of genes transcriptionally. We demonstrate the principle that there are subcomplexes of nuclear adhesion proteins that cooperate to control transcription.
Collapse
Affiliation(s)
- Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK.
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK.
| | - Billie G C Griffith
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Ana Herrero
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, 39011, Santander, Spain
| | - Alexander E P Loftus
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Emma S Koeleman
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120, Heidelberg, Germany
| | - Linda Kogerman
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - John C Dawson
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Niamh McGivern
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Almac Diagnostic Services, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Jayne Culley
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Graeme R Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Bryan Serrels
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- NanoString Technologies, Inc., Seattle, WA, 98109, USA
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Valerie G Brunton
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Margaret C Frame
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| |
Collapse
|
7
|
Chen X, Zhou W, Song RH, Liu S, Wang S, Chen Y, Gao C, He C, Xiao J, Zhang L, Wang T, Liu P, Duan K, Cheng Z, Zhang C, Zhang J, Sun Y, Jackson F, Lan F, Liu Y, Xu Y, Wong JJL, Wang P, Yang H, Xiong Y, Chen T, Li Y, Ye D. Tumor suppressor CEBPA interacts with and inhibits DNMT3A activity. SCIENCE ADVANCES 2022; 8:eabl5220. [PMID: 35080973 PMCID: PMC8791617 DOI: 10.1126/sciadv.abl5220] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
DNA methyltransferases (DNMTs) catalyze DNA methylation, and their functions in mammalian embryonic development and diseases including cancer have been extensively studied. However, regulation of DNMTs remains under study. Here, we show that CCAAT/enhancer binding protein α (CEBPA) interacts with the long splice isoform DNMT3A, but not the short isoform DNMT3A2. CEBPA, by interacting with DNMT3A N-terminus, blocks DNMT3A from accessing DNA substrate and thereby inhibits its activity. Recurrent tumor-associated CEBPA mutations, such as preleukemic CEBPAN321D mutation, which is particularly potent in causing AML with high mortality, disrupt DNMT3A association and cause aberrant DNA methylation, notably hypermethylation of PRC2 target genes. Consequently, leukemia cells with the CEBPAN321D mutation are hypersensitive to hypomethylation agents. Our results provide insights into the functional difference between DNMT3A isoforms and the regulation of de novo DNA methylation at specific loci in the genome. Our study also suggests a therapeutic strategy for the treatment of CEBPA-mutated leukemia with DNA-hypomethylating agents.
Collapse
Affiliation(s)
- Xiufei Chen
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Target Discovery Institute, NDM Research Building, Oxford Ludwig Institute of Cancer Research, Oxford University, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Wenjie Zhou
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ren-Hua Song
- Epigenetics and RNA Biology Program, Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Shuang Liu
- MOE Key Laboratory of Model Animals for Disease Study, Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Chemistry and Biomedicine Innovation Center (ChemBIC), Model Animal Research Center, Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Shu Wang
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yujia Chen
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chao Gao
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chenxi He
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jianxiong Xiao
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lei Zhang
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Tianxiang Wang
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Peng Liu
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kunlong Duan
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhouli Cheng
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chen Zhang
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jinye Zhang
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yiping Sun
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Felix Jackson
- Department of Computer Science, University of Oxford, 15 Parks Rd, Oxford OX1 3QD, UK
| | - Fei Lan
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanhui Xu
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Justin Jong-Leong Wong
- Epigenetics and RNA Biology Program, Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Pu Wang
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hui Yang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Tong Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
- Corresponding author. (T.C.); (Yan Li); (D.Y.)
| | - Yan Li
- MOE Key Laboratory of Model Animals for Disease Study, Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Chemistry and Biomedicine Innovation Center (ChemBIC), Model Animal Research Center, Nanjing University Medical School, Nanjing University, Nanjing, China
- Corresponding author. (T.C.); (Yan Li); (D.Y.)
| | - Dan Ye
- Huashan Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), and Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Corresponding author. (T.C.); (Yan Li); (D.Y.)
| |
Collapse
|
8
|
Nagy Z, Seneviratne JA, Kanikevich M, Chang W, Mayoh C, Venkat P, Du Y, Jiang C, Salib A, Koach J, Carter DR, Mittra R, Liu T, Parker MW, Cheung BB, Marshall GM. An ALYREF-MYCN coactivator complex drives neuroblastoma tumorigenesis through effects on USP3 and MYCN stability. Nat Commun 2021; 12:1881. [PMID: 33767157 PMCID: PMC7994381 DOI: 10.1038/s41467-021-22143-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 02/23/2021] [Indexed: 02/03/2023] Open
Abstract
To achieve the very high oncoprotein levels required to drive the malignant state cancer cells utilise the ubiquitin proteasome system to upregulate transcription factor levels. Here our analyses identify ALYREF, expressed from the most common genetic copy number variation in neuroblastoma, chromosome 17q21-ter gain as a key regulator of MYCN protein turnover. We show strong co-operativity between ALYREF and MYCN from transgenic models of neuroblastoma in vitro and in vivo. The two proteins form a nuclear coactivator complex which stimulates transcription of the ubiquitin specific peptidase 3, USP3. We show that increased USP3 levels reduce K-48- and K-63-linked ubiquitination of MYCN, thus driving up MYCN protein stability. In the MYCN-ALYREF-USP3 signal, ALYREF is required for MYCN effects on the malignant phenotype and that of USP3 on MYCN stability. This data defines a MYCN oncoprotein dependency state which provides a rationale for future pharmacological studies. Neuroblastoma (NB) is often driven by MYCN amplification. Here, the authors show that the most frequent genetic lesion, gain of 17q21-ter in NB leads to overexpression of ALYREF, which forms a complex with MYCN, regulating MYCN stability via the deubiquitinating enzyme, USP3.
Collapse
Affiliation(s)
- Zsuzsanna Nagy
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Randwick, NSW, Australia
| | - Janith A Seneviratne
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Maxwell Kanikevich
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - William Chang
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Randwick, NSW, Australia
| | - Pooja Venkat
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Yanhua Du
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Cizhong Jiang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Alice Salib
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Jessica Koach
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Daniel R Carter
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia.,School of Women's and Children's Health, UNSW Sydney, Randwick, NSW, Australia.,School of Biomedical Engineering, University of Technology, Sydney, NSW, Australia
| | - Rituparna Mittra
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.,ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Belamy B Cheung
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia. .,School of Women's and Children's Health, UNSW Sydney, Randwick, NSW, Australia. .,School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Glenn M Marshall
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia. .,School of Women's and Children's Health, UNSW Sydney, Randwick, NSW, Australia. .,Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia.
| |
Collapse
|
9
|
Fujita T, Kubo S, Shioda T, Tokumura A, Minami S, Tsuchiya M, Isaka Y, Ogawa H, Hamasaki M, Yu L, Yoshimori T, Nakamura S. THOC4 regulates energy homeostasis by stabilizing TFEB mRNA during prolonged starvation. J Cell Sci 2021; 134:jcs.248203. [PMID: 33589500 DOI: 10.1242/jcs.248203] [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: 04/30/2020] [Accepted: 02/03/2021] [Indexed: 11/20/2022] Open
Abstract
TFEB, a basic helix-loop-helix transcription factor, is a master regulator of autophagy, lysosome biogenesis and lipid catabolism. Compared to posttranslational regulation of TFEB, the regulation of TFEB mRNA stability remains relatively uncharacterized. In this study, we identified the mRNA-binding protein THOC4 as a novel regulator of TFEB. In mammalian cells, siRNA-mediated knockdown of THOC4 decreased the level of TFEB protein to a greater extent than other bHLH transcription factors. THOC4 bound to TFEB mRNA and stabilized it after transcription by maintaining poly(A) tail length. We further found that this mode of regulation was conserved in Caenorhabditis elegans and was essential for TFEB-mediated lipid breakdown, which becomes over-represented during prolonged starvation. Taken together, our findings reveal the presence of an additional layer of TFEB regulation by THOC4 and provide novel insights into the function of TFEB in mediating autophagy and lipid metabolism.
Collapse
Affiliation(s)
- Toshiharu Fujita
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Sayaka Kubo
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Tatsuya Shioda
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Ayaka Tokumura
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Satoshi Minami
- Department of Nephrology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Megumi Tsuchiya
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Hidesato Ogawa
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Maho Hamasaki
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan.,Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Li Yu
- Department of Biological Science and Biotechnology, Tsinghua University, 100084 Beijing, China
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan .,Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Shuhei Nakamura
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan .,Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan.,Institute for Advanced Co-Creation Studies, Osaka University, Osaka 565-0871, Japan
| |
Collapse
|
10
|
Into the basket and beyond: the journey of mRNA through the nuclear pore complex. Biochem J 2020; 477:23-44. [DOI: 10.1042/bcj20190132] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/28/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023]
Abstract
The genetic information encoded in nuclear mRNA destined to reach the cytoplasm requires the interaction of the mRNA molecule with the nuclear pore complex (NPC) for the process of mRNA export. Numerous proteins have important roles in the transport of mRNA out of the nucleus. The NPC embedded in the nuclear envelope is the port of exit for mRNA and is composed of ∼30 unique proteins, nucleoporins, forming the distinct structures of the nuclear basket, the pore channel and cytoplasmic filaments. Together, they serve as a rather stationary complex engaged in mRNA export, while a variety of soluble protein factors dynamically assemble on the mRNA and mediate the interactions of the mRNA with the NPC. mRNA export factors are recruited to and dissociate from the mRNA at the site of transcription on the gene, during the journey through the nucleoplasm and at the nuclear pore at the final stages of export. In this review, we present the current knowledge derived from biochemical, molecular, structural and imaging studies, to develop a high-resolution picture of the many events that culminate in the successful passage of the mRNA out of the nucleus.
Collapse
|
11
|
Infantino V, Stutz F. The functional complexity of the RNA-binding protein Yra1: mRNA biogenesis, genome stability and DSB repair. Curr Genet 2019; 66:63-71. [PMID: 31292684 DOI: 10.1007/s00294-019-01011-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/21/2022]
Abstract
The mRNA export adaptor Yra1 is essential in S. cerevisiae, and conserved from yeast to human (ALY/REF). It is well characterized for its function during transcription elongation, 3' processing and mRNA export. Recently, different studies linked Yra1 to genome stability showing that Yra1 overexpression causes DNA Double Strand Breaks through DNA:RNA hybrids stabilization, and that Yra1 depletion affects DSB repair. However, the mechanisms through which Yra1 contributes to genome stability maintenance are not fully understood. Interestingly, our results showed that the Yra1 C-box domain is required for Yra1 recruitment to an HO-induced irreparable DSB following extensive resection, and that it is essential to repair an HO-induced reparable DSB. Furthermore, we defined that the C-box domain of Yra1 plays a crucial role in DSB repair through homologous recombination but not through non-homologous end joining. Future studies aim at deciphering the mechanism by which Yra1 contributes to DSB repair by searching for Yra1 partners important for this process. This review focuses on the functional complexity of the Yra1 protein, not only summarizing its role in mRNA biogenesis but also emphasizing its auto-regulation and implication in genome integrity either through DNA:RNA hybrids stabilization or DNA double strand break repair in S. cerevisiae.
Collapse
Affiliation(s)
- Valentina Infantino
- Department of Cell Biology, University of Geneva, 30 Quai E. Ansermet, 1211, Geneva, Switzerland
| | - Françoise Stutz
- Department of Cell Biology, University of Geneva, 30 Quai E. Ansermet, 1211, Geneva, Switzerland.
| |
Collapse
|
12
|
Berson A, Goodman LD, Sartoris AN, Otte CG, Aykit JA, Lee VMY, Trojanowski JQ, Bonini NM. Drosophila Ref1/ALYREF regulates transcription and toxicity associated with ALS/FTD disease etiologies. Acta Neuropathol Commun 2019; 7:65. [PMID: 31036086 PMCID: PMC6487524 DOI: 10.1186/s40478-019-0710-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/25/2019] [Indexed: 12/11/2022] Open
Abstract
RNA-binding proteins (RBPs) are associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), but the underlying disease mechanisms remain unclear. In an unbiased screen in Drosophila for RBPs that genetically interact with TDP-43, we found that downregulation of the mRNA export factor Ref1 (fly orthologue to human ALYREF) mitigated TDP-43 induced toxicity. Further, Ref1 depletion also reduced toxicity caused by expression of the C9orf72 GGGGCC repeat expansion. Ref1 knockdown lowered the mRNA levels for these related disease genes and reduced the encoded proteins with no effect on a wild-type Tau disease transgene or a control transgene. Interestingly, expression of TDP-43 or the GGGGCC repeat expansion increased endogenous Ref1 mRNA levels in the fly brain. Further, the human orthologue ALYREF was upregulated by immunohistochemistry in ALS motor neurons, with the strongest upregulation occurring in ALS cases harboring the GGGGCC expansion in C9orf72. These data support ALYREF as a contributor to ALS/FTD and highlight its downregulation as a potential therapeutic target that may affect co-existing disease etiologies.
Collapse
Affiliation(s)
- Amit Berson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lindsey D Goodman
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ashley N Sartoris
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Charlton G Otte
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James A Aykit
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Virginia M-Y Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
13
|
Zhang H, Fu Y, Guo H, Zhang L, Wang C, Song W, Yan Z, Wang Y, Ji W. Transcriptome and Proteome-Based Network Analysis Reveals a Model of Gene Activation in Wheat Resistance to Stripe Rust. Int J Mol Sci 2019; 20:ijms20051106. [PMID: 30836695 PMCID: PMC6429138 DOI: 10.3390/ijms20051106] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/24/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
Stripe rust, caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is an important fungal foliar disease of wheat (Triticum aestivum). To study the mechanism underlying the defense of wheat to Pst, we used the next-generation sequencing and isobaric tags for relative and absolute quantification (iTRAQ) technologies to generate transcriptomic and proteomic profiles of seedling leaves at different stages under conditions of pathogen stress. By conducting comparative proteomic analysis using iTRAQ, we identified 2050, 2190, and 2258 differentially accumulated protein species at 24, 48, and 72 h post-inoculation (hpi). Using pairwise comparisons and weighted gene co-expression network analysis (WGCNA) of the transcriptome, we identified a stress stage-specific module enriching in transcription regulator genes. The homologs of several regulators, including splicing and transcription factors, were similarly identified as hub genes operating in the Pst-induced response network. Moreover, the Hsp70 protein were predicted as a key point in protein–protein interaction (PPI) networks from STRING database. Taking the genetics resistance gene locus into consideration, we identified 32 induced proteins in chromosome 1BS as potential candidates involved in Pst resistance. This study indicated that the transcriptional regulation model plays an important role in activating resistance-related genes in wheat responding to Pst stress.
Collapse
Affiliation(s)
- Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Ying Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Huan Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Weining Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
- Shaanxi Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shaanxi 712100, China.
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Shaanxi 712100, China.
- Shaanxi Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Shaanxi 712100, China.
| |
Collapse
|
14
|
Abstract
TRanscription and EXport (TREX) is a conserved multisubunit complex essential for embryogenesis, organogenesis and cellular differentiation throughout life. By linking transcription, mRNA processing and export together, it exerts a physiologically vital role in the gene expression pathway. In addition, this complex prevents DNA damage and regulates the cell cycle by ensuring optimal gene expression. As the extent of TREX activity in viral infections, amyotrophic lateral sclerosis and cancer emerges, the need for a greater understanding of TREX function becomes evident. A complete elucidation of the composition, function and interactions of the complex will provide the framework for understanding the molecular basis for a variety of diseases. This review details the known composition of TREX, how it is regulated and its cellular functions with an emphasis on mammalian systems.
Collapse
|
15
|
Shaikhali J. GIP1 protein is a novel cofactor that regulates DNA-binding affinity of redox-regulated members of bZIP transcription factors involved in the early stages of Arabidopsis development. PROTOPLASMA 2015; 252:867-883. [PMID: 25387999 DOI: 10.1007/s00709-014-0726-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/28/2014] [Indexed: 06/04/2023]
Abstract
In response to environmental light signals, gene expression adjustments play an important role in regulation of photomorphogenesis. LHCB2.4 is among the genes responsive to light signals, and its expression is regulated by redox-regulated members of G-group bZIP transcription factors. The biochemical interrelations of GBF1-interacting protein 1 (GIP1) and the G-group bZIP transcription factors have been investigated. GIP1, previously shown to enhance DNA-binding activities of maize GBF1 and Arabidopsis GBF3, is a plant specific protein that reduces DNA-binding activity of AtbZIP16, AtbZIP68, and AtGBF1 under non-reducing conditions through direct physical interaction shown by the yeast two-hybrid and pull-down assays. Fluorescence microscopy studies using cyan fluorescent protein (CFP)-fusion protein indicate that GIP1 is exclusively localized in the nucleus. Under non- reducing conditions, GIP1 exhibits predominantly high molecular weight forms, whereas it predominates in low molecular weight monomers under reducing conditions. While reduced GIP1 induced formation of DNA-protein complexes of G-group bZIPs, oxidized GIP1 decreased the amount of those complexes and instead induced its chaperone function suggesting functional switching from redox to chaperone activity. Finally analysis of transgenic plants overexpressing GIP1 revealed that GIP1 is a negative co-regulator in red and blue light mediated hypocotyl elongation. By regulating the repression effect by bZIP16 and the activation effect by bZIP68 and GBF1 on LHCB2.4 expression, GIP1 functions to promote hypocotyl elongation during the early stages of Arabidopsis seedling development.
Collapse
Affiliation(s)
- Jehad Shaikhali
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences SLU, 901 83, Umeå, Sweden,
| |
Collapse
|
16
|
Stability of structured Kaposi's sarcoma-associated herpesvirus ORF57 protein is regulated by protein phosphorylation and homodimerization. J Virol 2015; 89:3256-74. [PMID: 25568207 DOI: 10.1128/jvi.03721-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 plays an essential role in KSHV lytic infection by promoting viral gene expression at the posttranscriptional level. Using bioinformatic and biochemical approaches, we determined that ORF57 contains two structurally and functionally distinct domains: a disordered nonstructural N-terminal domain (amino acids [aa] 1 to 152) and a structured α-helix-rich C-terminal domain (aa 153 to 455). The N-terminal domain mediates ORF57 interaction with several RNA-protein complexes essential for ORF57 to function. The N-terminal phosphorylation by cellular casein kinase II (CKII) at S21, T32, and S43, and other cellular kinases at S95 and S97 residues in proximity of the caspase-7 cleavage site, 30-DETD-33, inhibits caspase-7 digestion of ORF57. The structured C-terminal domain mediates homodimerization of ORF57, and the critical region for this function was mapped carefully to α-helices 7 to 9. Introduction of point mutations into α-helix 7 at ORF57 aa 280 to 299, a region highly conserved among ORF57 homologues from other herpesviruses, inhibited ORF57 homodimerization and led to proteasome-mediated degradation of ORF57 protein. Thus, homodimerization of ORF57 via its C terminus prevents ORF57 from degrading and allows two structure-free N termini of the dimerized ORF57 to work coordinately for host factor interactions, leading to productive KSHV lytic infection and pathogenesis. IMPORTANCE KSHV is a human oncogenic virus linked to the development of several malignancies. KSHV-mediated oncogenesis requires both latent and lytic infection. The KSHV ORF57 protein is essential for KSHV lytic replication, as it regulates the expression of viral lytic genes at the posttranscriptional level. This report provides evidence that the structural conformation of the ORF57 protein plays a critical role in regulation of ORF57 stability. Phosphorylation by CKII on the identified serine/threonine residues at the N-terminal unstructured domain of ORF57 prevents its digestion by caspase-7. The C-terminal domain of ORF57, which is rich in α-helices, contributes to homodimerization of ORF57 to prevent proteasome-mediated protein degradation. Elucidation of the ORF57 structure not only enables us to better understand ORF57 stability and functions but also provides an important tool for us to modulate ORF57's activity with the aim to inhibit KSHV lytic replication.
Collapse
|
17
|
Stubbs SH, Conrad NK. Depletion of REF/Aly alters gene expression and reduces RNA polymerase II occupancy. Nucleic Acids Res 2014; 43:504-19. [PMID: 25477387 PMCID: PMC4288173 DOI: 10.1093/nar/gku1278] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pre-mRNA processing is mechanistically linked to transcription with RNA pol II serving as a platform to recruit RNA processing factors to nascent transcripts. The TREX complex member, REF/Aly, has been suggested to play roles in transcription and nuclear RNA stability in addition to its more broadly characterized role in mRNA export. We employed RNA-seq to identify a subset of transcripts with decreased expression in both nuclear and cytoplasmic fractions upon REF/Aly knockdown, which implies that REF/Aly affects their expression upstream of its role in mRNA export. Transcription inhibition experiments and metabolic labeling assays argue that REF/Aly does not affect stability of selected candidate transcripts. Instead, ChIP assays and nuclear run-on analysis reveal that REF/Aly depletion diminishes the transcription of these candidate genes. Furthermore, we determined that REF/Aly binds directly to candidate transcripts, supporting a direct effect of REF/Aly on candidate gene transcription. Taken together, our data suggest that the importance of REF/Aly is not limited to RNA export, but that REF/Aly is also critical for gene expression at the level of transcription. Our data are consistent with the model that REF/Aly is involved in linking splicing with transcription efficiency.
Collapse
Affiliation(s)
- Sarah H Stubbs
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9048, USA
| | - Nicholas K Conrad
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9048, USA
| |
Collapse
|
18
|
Fagone P, Muthumani K, Mangano K, Magro G, Meroni PL, Kim JJ, Sardesai NY, Weiner DB, Nicoletti F. VGX-1027 modulates genes involved in lipopolysaccharide-induced Toll-like receptor 4 activation and in a murine model of systemic lupus erythematosus. Immunology 2014; 142:594-602. [PMID: 24527796 DOI: 10.1111/imm.12267] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/04/2014] [Indexed: 01/12/2023] Open
Abstract
VGX-1027 [(S,R)-3-phenyl-4,5-dihydro-5-isoxasole acetic acid] is a small molecule compound with immunomodulatory properties, which favourably influences the development of immuno-inflammatory and autoimmune diseases in different animal models such as type 1 diabetes mellitus, pleurisy, rheumatoid arthritis and inflammatory bowel disease. However, the precise mechanism of action of VGX-1027 remains to be ascertained. With this aim, we have studied the immunomodulatory effects of VGX-1027 in vitro, using a genome-wide oligonucleotide microarray approach, and in vivo, using the NZB/NZW F1 model of systemic lupus erythematosus. Microarray data revealed that the administration of VGX-1027 profoundly affected the immune response to exogenous antigens, by modulating the expression of genes that are primarily involved in antigen processing and presentation as well as genes that regulate immune activation. When administered in vivo VGX-1027 ameliorated the course of the disease in the NZB/NZW F1 mice, which correlated with higher per cent survival and improved clinical and histopathological signs. The data presented herein support the theory that VGX-1027 modulates immunity, probably by inhibiting inflammatory antigen presentation and so limiting immune cell expansion.
Collapse
Affiliation(s)
- Paolo Fagone
- Department of Bio-Medical Sciences, University of Catania, Catania, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
TREX is a conserved multiprotein complex that is necessary for efficient mRNA export to the cytoplasm. In Saccharomyces cerevisiae, the TREX complex is additionally implicated in RNA quality control pathways, but it is unclear whether this function is conserved in mammalian cells. The Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 protein binds and recruits the TREX component REF/Aly to viral mRNAs. Here, we demonstrate that REF/Aly is recruited to the KSHV noncoding polyadenylated nuclear (PAN) RNA by ORF57. This recruitment correlates with ORF57-mediated stabilization of PAN RNA, suggesting that REF/Aly promotes nuclear RNA stability. Further supporting this idea, tethering REF/Aly to PAN RNA is sufficient to increase the nuclear abundance and half-life of PAN RNA but is not sufficient to promote its export. Interestingly, REF/Aly appears to protect the poly(A) tail from deadenylation, and REF/Aly-stabilized transcripts are further adenylated over time, consistent with previous reports linking poly(A) tail length with nuclear RNA surveillance. These studies show that REF/Aly can stabilize nuclear RNAs independently of their export and support a broader conservation of RNA quality control mechanisms from yeast to humans.
Collapse
|
20
|
Funnell APW, Crossley M. Homo- and Heterodimerization in Transcriptional Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 747:105-21. [DOI: 10.1007/978-1-4614-3229-6_7] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
21
|
Johnson SA, Kim H, Erickson B, Bentley DL. The export factor Yra1 modulates mRNA 3' end processing. Nat Struct Mol Biol 2011; 18:1164-71. [PMID: 21947206 PMCID: PMC3307051 DOI: 10.1038/nsmb.2126] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Accepted: 07/20/2011] [Indexed: 11/09/2022]
Abstract
The Saccharomyces cerevisiae mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A that links export to 3' end formation. We found that an unexpected consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit Clp1 for binding to Pcf11, and excess Yra1 inhibits 3' processing in vitro. Release of Yra1 at the 3' ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit; instead, Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice, particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A 3' processing factor.
Collapse
Affiliation(s)
- Sara A Johnson
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | | | | |
Collapse
|
22
|
Sengel C, Gavarini S, Sharma N, Ozelius LJ, Bragg DC. Dimerization of the DYT6 dystonia protein, THAP1, requires residues within the coiled-coil domain. J Neurochem 2011; 118:1087-100. [PMID: 21752024 DOI: 10.1111/j.1471-4159.2011.07386.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thanatos-associated [THAP] domain-containing apoptosis-associated protein 1 (THAP1) is a DNA-binding protein that has been recently associated with DYT6 dystonia, a hereditary movement disorder involving sustained, involuntary muscle contractions. A large number of dystonia-related mutations have been identified in THAP1 in diverse patient populations worldwide. Previous reports have suggested that THAP1 oligomerizes with itself via a C-terminal coiled-coil domain, raising the possibility that DYT6 mutations in this region might affect this interaction. In this study, we examined the ability of wild-type THAP1 to bind itself and the effects on this interaction of the following disease mutations: C54Y, F81L, ΔF132, T142A, I149T, Q154fs180X, and A166T. The results confirmed that wild-type THAP1 associated with itself and most of the DYT6 mutants tested, except for the Q154fs180X variant, which loses most of the coiled-coil domain because of a frameshift at position 154. However, deletion of C-terminal residues after position 166 produced a truncated variant of THAP1 that was able to bind the wild-type protein. The interaction of THAP1 with itself therefore required residues within a 13-amino acid region (aa 154-166) of the coiled-coil domain. Further inspection of this sequence revealed elements highly consistent with previous descriptions of leucine zippers, which serve as dimerization domains in other transcription factor families. Based on this similarity, a structural model was generated to predict how hydrophobic residues in this region may mediate dimerization. These observations offer additional insight into the role of the coiled-coil domain in THAP1, which may facilitate future analyses of DYT6 mutations in this region.
Collapse
Affiliation(s)
- Cem Sengel
- Neuroscience Center, Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | | | | | | | | |
Collapse
|
23
|
Hafez EE, Moustafa MF. Differential expression of cytochrome oxidase and ALY-family genes in resistant and susceptible tomato cultivars (Solanum lycopersicum) inoculated with Tomato bushy stunt virus. J Genet Eng Biotechnol 2011. [DOI: 10.1016/j.jgeb.2011.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
24
|
Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. ACTA ACUST UNITED AC 2010; 189:739-54. [PMID: 20479470 PMCID: PMC2872919 DOI: 10.1083/jcb.200911091] [Citation(s) in RCA: 351] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
QUBIC, a specific and highly sensitive method for detection of protein–protein interactions, is used to identify new partners for the mitotic spindle components pericentrin and TACC3. Protein interactions are involved in all cellular processes. Their efficient and reliable characterization is therefore essential for understanding biological mechanisms. In this study, we show that combining bacterial artificial chromosome (BAC) TransgeneOmics with quantitative interaction proteomics, which we call quantitative BAC–green fluorescent protein interactomics (QUBIC), allows specific and highly sensitive detection of interactions using rapid, generic, and quantitative procedures with minimal material. We applied this approach to identify known and novel components of well-studied complexes such as the anaphase-promoting complex. Furthermore, we demonstrate second generation interaction proteomics by incorporating directed mutational transgene modification and drug perturbation into QUBIC. These methods identified domain/isoform-specific interactors of pericentrin- and phosphorylation-specific interactors of TACC3, which are necessary for its recruitment to mitotic spindles. The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome.
Collapse
Affiliation(s)
- Nina C Hubner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol 2010. [DOI: 10.1083/jcb.200911091 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Protein interactions are involved in all cellular processes. Their efficient and reliable characterization is therefore essential for understanding biological mechanisms. In this study, we show that combining bacterial artificial chromosome (BAC) TransgeneOmics with quantitative interaction proteomics, which we call quantitative BAC–green fluorescent protein interactomics (QUBIC), allows specific and highly sensitive detection of interactions using rapid, generic, and quantitative procedures with minimal material. We applied this approach to identify known and novel components of well-studied complexes such as the anaphase-promoting complex. Furthermore, we demonstrate second generation interaction proteomics by incorporating directed mutational transgene modification and drug perturbation into QUBIC. These methods identified domain/isoform-specific interactors of pericentrin- and phosphorylation-specific interactors of TACC3, which are necessary for its recruitment to mitotic spindles. The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome.
Collapse
Affiliation(s)
- Nina C. Hubner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alexander W. Bird
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bianca Splettstoesser
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Peter Bandilla
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anthony Hyman
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
26
|
Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol 2010. [DOI: 10.1083/jcb.200911091 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Protein interactions are involved in all cellular processes. Their efficient and reliable characterization is therefore essential for understanding biological mechanisms. In this study, we show that combining bacterial artificial chromosome (BAC) TransgeneOmics with quantitative interaction proteomics, which we call quantitative BAC–green fluorescent protein interactomics (QUBIC), allows specific and highly sensitive detection of interactions using rapid, generic, and quantitative procedures with minimal material. We applied this approach to identify known and novel components of well-studied complexes such as the anaphase-promoting complex. Furthermore, we demonstrate second generation interaction proteomics by incorporating directed mutational transgene modification and drug perturbation into QUBIC. These methods identified domain/isoform-specific interactors of pericentrin- and phosphorylation-specific interactors of TACC3, which are necessary for its recruitment to mitotic spindles. The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome.
Collapse
Affiliation(s)
- Nina C. Hubner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alexander W. Bird
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bianca Splettstoesser
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Peter Bandilla
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anthony Hyman
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
27
|
Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Biophys Biochem Cytol 2010. [DOI: 10.1083/jcb.200911091 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Protein interactions are involved in all cellular processes. Their efficient and reliable characterization is therefore essential for understanding biological mechanisms. In this study, we show that combining bacterial artificial chromosome (BAC) TransgeneOmics with quantitative interaction proteomics, which we call quantitative BAC–green fluorescent protein interactomics (QUBIC), allows specific and highly sensitive detection of interactions using rapid, generic, and quantitative procedures with minimal material. We applied this approach to identify known and novel components of well-studied complexes such as the anaphase-promoting complex. Furthermore, we demonstrate second generation interaction proteomics by incorporating directed mutational transgene modification and drug perturbation into QUBIC. These methods identified domain/isoform-specific interactors of pericentrin- and phosphorylation-specific interactors of TACC3, which are necessary for its recruitment to mitotic spindles. The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome.
Collapse
Affiliation(s)
- Nina C. Hubner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alexander W. Bird
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bianca Splettstoesser
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Peter Bandilla
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anthony Hyman
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
28
|
Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol 2010. [DOI: 10.1083/jcb.200911091 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Protein interactions are involved in all cellular processes. Their efficient and reliable characterization is therefore essential for understanding biological mechanisms. In this study, we show that combining bacterial artificial chromosome (BAC) TransgeneOmics with quantitative interaction proteomics, which we call quantitative BAC–green fluorescent protein interactomics (QUBIC), allows specific and highly sensitive detection of interactions using rapid, generic, and quantitative procedures with minimal material. We applied this approach to identify known and novel components of well-studied complexes such as the anaphase-promoting complex. Furthermore, we demonstrate second generation interaction proteomics by incorporating directed mutational transgene modification and drug perturbation into QUBIC. These methods identified domain/isoform-specific interactors of pericentrin- and phosphorylation-specific interactors of TACC3, which are necessary for its recruitment to mitotic spindles. The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome.
Collapse
Affiliation(s)
- Nina C. Hubner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alexander W. Bird
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bianca Splettstoesser
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Peter Bandilla
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anthony Hyman
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
29
|
Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Biophys Biochem Cytol 2010. [DOI: 10.1083/jcb.200911091 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Protein interactions are involved in all cellular processes. Their efficient and reliable characterization is therefore essential for understanding biological mechanisms. In this study, we show that combining bacterial artificial chromosome (BAC) TransgeneOmics with quantitative interaction proteomics, which we call quantitative BAC–green fluorescent protein interactomics (QUBIC), allows specific and highly sensitive detection of interactions using rapid, generic, and quantitative procedures with minimal material. We applied this approach to identify known and novel components of well-studied complexes such as the anaphase-promoting complex. Furthermore, we demonstrate second generation interaction proteomics by incorporating directed mutational transgene modification and drug perturbation into QUBIC. These methods identified domain/isoform-specific interactors of pericentrin- and phosphorylation-specific interactors of TACC3, which are necessary for its recruitment to mitotic spindles. The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome.
Collapse
Affiliation(s)
- Nina C. Hubner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alexander W. Bird
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bianca Splettstoesser
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Peter Bandilla
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anthony Hyman
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
30
|
Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol 2010. [DOI: 10.1083/jcb.200911091 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Protein interactions are involved in all cellular processes. Their efficient and reliable characterization is therefore essential for understanding biological mechanisms. In this study, we show that combining bacterial artificial chromosome (BAC) TransgeneOmics with quantitative interaction proteomics, which we call quantitative BAC–green fluorescent protein interactomics (QUBIC), allows specific and highly sensitive detection of interactions using rapid, generic, and quantitative procedures with minimal material. We applied this approach to identify known and novel components of well-studied complexes such as the anaphase-promoting complex. Furthermore, we demonstrate second generation interaction proteomics by incorporating directed mutational transgene modification and drug perturbation into QUBIC. These methods identified domain/isoform-specific interactors of pericentrin- and phosphorylation-specific interactors of TACC3, which are necessary for its recruitment to mitotic spindles. The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome.
Collapse
Affiliation(s)
- Nina C. Hubner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alexander W. Bird
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bianca Splettstoesser
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Peter Bandilla
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anthony Hyman
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
31
|
Hubner NC, Bird AW, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Biophys Biochem Cytol 2010. [DOI: 10.1083/jcb.200911091 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Protein interactions are involved in all cellular processes. Their efficient and reliable characterization is therefore essential for understanding biological mechanisms. In this study, we show that combining bacterial artificial chromosome (BAC) TransgeneOmics with quantitative interaction proteomics, which we call quantitative BAC–green fluorescent protein interactomics (QUBIC), allows specific and highly sensitive detection of interactions using rapid, generic, and quantitative procedures with minimal material. We applied this approach to identify known and novel components of well-studied complexes such as the anaphase-promoting complex. Furthermore, we demonstrate second generation interaction proteomics by incorporating directed mutational transgene modification and drug perturbation into QUBIC. These methods identified domain/isoform-specific interactors of pericentrin- and phosphorylation-specific interactors of TACC3, which are necessary for its recruitment to mitotic spindles. The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome.
Collapse
Affiliation(s)
- Nina C. Hubner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alexander W. Bird
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bianca Splettstoesser
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Peter Bandilla
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ina Poser
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anthony Hyman
- Department of Microtubules and Cell Division, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
32
|
Abstract
Nuclear factor κB (NF-κB) is an inducible transcription factor that tightly regulates the expression of a large cohort of genes. As a key component of the cellular machinery NF-κB is involved in a wide range of biological processes including innate and adaptive immunity, inflammation, cellular stress responses, cell adhesion, apoptosis and proliferation. Appropriate regulation of NF-κB is critical for the proper function and survival of the cell. Aberrant NF-κB activity has now been implicated in the pathogenesis of several diseases ranging from inflammatory bowel disease to autoimmune conditions such as rheumatoid arthritis. Systems governing NF-κB activity are complex and there is an increased understanding of the importance of nuclear events in regulating NF-κB's activities as a transcription factor. A number of novel nuclear regulators of NF-κB such as IκB-ζ and PDZ and LIM domain 2 (PDLIM2) have now been identified, adding another layer to the mechanics of NF-κB regulation. Further insight into the functions of these molecules raises the prospect for better understanding and rational design of therapeutics for several important diseases.
Collapse
Affiliation(s)
- Arun K Mankan
- Department of Clinical Medicine and Institute of Molecular Medicine, Trinity College, Dublin, Ireland.
| | | | | | | | | |
Collapse
|
33
|
Corley SM, Gready JE. Identification of the RGG box motif in Shadoo: RNA-binding and signaling roles? Bioinform Biol Insights 2008; 2:383-400. [PMID: 19812790 PMCID: PMC2735946 DOI: 10.4137/bbi.s1075] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Using comparative genomics and in-silico analyses, we previously identified a new member of the prion-protein (PrP) family, the gene SPRN, encoding the protein Shadoo (Sho), and suggested its functions might overlap with those of PrP. Extended bioinformatics and conceptual biology studies to elucidate Sho’s functions now reveal Sho has a conserved RGG-box motif, a well-known RNA-binding motif characterized in proteins such as FragileX Mental Retardation Protein. We report a systematic comparative analysis of RGG-box containing proteins which highlights the motif’s functional versatility and supports the suggestion that Sho plays a dual role in cell signaling and RNA binding in brain. These findings provide a further link to PrP, which has well-characterized RNA-binding properties.
Collapse
Affiliation(s)
- Susan M Corley
- Computational Proteomics and Therapy Design Group, Division of Molecular Bioscience, John Curtin School of Medical Research, Australian National University, PO Box 334, Canberra ACT 2601, Australia
| | | |
Collapse
|
34
|
Iglesias N, Stutz F. Regulation of mRNP dynamics along the export pathway. FEBS Lett 2008; 582:1987-96. [PMID: 18394429 DOI: 10.1016/j.febslet.2008.03.038] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Revised: 03/25/2008] [Accepted: 03/26/2008] [Indexed: 02/02/2023]
Abstract
The transcription of mRNA is tightly coupled to the concomitant recruitment of mRNA processing and export factors, resulting in the formation of mature and export competent mRNP complexes. This interconnection in gene expression implies extensive spatio-temporal control of mRNP dynamics to prevent mRNA export factors bound to pre-mRNA from functioning at the incorrect time and exporting nascent or incompletely processed pre-mRNAs. Recent discoveries provide molecular understanding of how a broad range of post-translational modifications together with RNA-dependent ATPases coordinate proteins acting at different steps and regulate mRNP assembly and export.
Collapse
Affiliation(s)
- Nahid Iglesias
- Department of Cell Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva 4, Switzerland
| | | |
Collapse
|
35
|
Sun S, Tang Y, Lou X, Zhu L, Yang K, Zhang B, Shi H, Wang C. UXT is a novel and essential cofactor in the NF-kappaB transcriptional enhanceosome. ACTA ACUST UNITED AC 2007; 178:231-44. [PMID: 17620405 PMCID: PMC2064443 DOI: 10.1083/jcb.200611081] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
As a latent transcription factor, nuclear factor κB (NF-κB) translocates from the cytoplasm into the nucleus upon stimulation and mediates the expression of genes that are important in immunity, inflammation, and development. However, little is known about how it is regulated inside the nucleus. By a two-hybrid approach, we identify a prefoldin-like protein, ubiquitously expressed transcript (UXT), that is expressed predominantly and interacts specifically with NF-κB inside the nucleus. RNA interference knockdown of UXT leads to impaired NF-κB activity and dramatically attenuates the expression of NF-κB–dependent genes. This interference also sensitizes cells to apoptosis by tumor necrosis factor-α. Furthermore, UXT forms a dynamic complex with NF-κB and is recruited to the NF-κB enhanceosome upon stimulation. Interestingly, the UXT protein level correlates with constitutive NF-κB activity in human prostate cancer cell lines. The presence of NF-κB within the nucleus of stimulated or constitutively active cells is considerably diminished with decreased endogenous UXT levels. Our results reveal that UXT is an integral component of the NF-κB enhanceosome and is essential for its nuclear function, which uncovers a new mechanism of NF-κB regulation.
Collapse
Affiliation(s)
- Shaogang Sun
- Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Golovanov AP, Hautbergue GM, Tintaru AM, Lian LY, Wilson SA. The solution structure of REF2-I reveals interdomain interactions and regions involved in binding mRNA export factors and RNA. RNA (NEW YORK, N.Y.) 2006; 12:1933-48. [PMID: 17000901 PMCID: PMC1624900 DOI: 10.1261/rna.212106] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The RNA binding and export factor (REF) family of mRNA export adaptors are found in several nuclear protein complexes including the spliceosome, TREX, and exon junction complexes. They bind RNA, interact with the helicase UAP56/DDX39, and are thought to bridge the interaction between the export factor TAP/NXF1 and mRNA. REF2-I consists of three domains, with the RNA recognition motif (RRM) domain positioned in the middle. Here we dissect the interdomain interactions of REF2-I and present the solution structure of a functionally competent double domain (NM; residues 1-155). The N-terminal domain comprises a transient helix (N-helix) linked to the RRM by a flexible arm that includes an Arg-rich region. The N-helix, which is required for REF2-I function in vivo, overlaps the highly conserved REF-N motif and, together with the adjacent Arg-rich region, interacts transiently with the RRM. RNA interacts with REF2-I through arginine-rich regions in its N- and C-terminal domains, but we show that it also interacts weakly with the RRM. The mode of interaction is unusual for an RRM since it involves loops L1 and L5. NMR signal mapping and biochemical analysis with NM indicate that DDX39 and TAP interact with both the N and RRM domains of REF2-I and show that binding of these proteins and RNA will favor an open conformation for the two domains. The proximity of the RNA, TAP, and DDX39 binding sites on REF2-I suggests their binding may be mutually exclusive, which would lead to successive ligand binding events in the course of mRNA export.
Collapse
Affiliation(s)
- Alexander P Golovanov
- Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, UK.
| | | | | | | | | |
Collapse
|
37
|
Zhang W, Walker E, Tamplin OJ, Rossant J, Stanford WL, Hughes TR. Zfp206 regulates ES cell gene expression and differentiation. Nucleic Acids Res 2006; 34:4780-90. [PMID: 16971461 PMCID: PMC1635278 DOI: 10.1093/nar/gkl631] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding transcriptional regulation in early developmental stages is fundamental to understanding mammalian development and embryonic stem (ES) cell properties. Expression surveys suggest that the putative SCAN-Zinc finger transcription factor Zfp206 is expressed specifically in ES cells [Zhang,W., Morris,Q.D., Chang,R., Shai,O., Bakowski,M.A., Mitsakakis,N., Mohammad,N., Robinson,M.D., Zirngibl,R., Somogyi,E. et al., (2004) J. Biol., 3, 21; Brandenberger,R., Wei,H., Zhang,S., Lei,S., Murage,J., Fisk,G.J., Li,Y., Xu,C., Fang,R., Guegler,K. et al., (2004) Nat. Biotechnol., 22, 707-716]. Here, we confirm this observation, and we show that ZFP206 expression decreases rapidly upon differentiation of cultured mouse ES cells, and during development of mouse embryos. We find that there are at least six isoforms of the ZFP206 transcript, the longest being predominant. Overexpression and depletion experiments show that Zfp206 promotes formation of undifferentiated ES cell clones, and positively regulates abundance of a very small set of transcripts whose expression is also specific to ES cells and the two- to four-cell stages of preimplantation embryos. This set includes members of the Zscan4, Thoc4, Tcstv1 and eIF-1A gene families, none of which have been functionally characterized in vivo but whose members include apparent transcription factors, RNA-binding proteins and translation factors. Together, these data indicate that Zfp206 is a regulator of ES cell differentiation that controls a set of genes expressed very early in development, most of which themselves appear to be regulators.
Collapse
Affiliation(s)
- Wen Zhang
- Department of Molecular and Medical Genetics, University of Toronto#4388 Medical Sciences Building, 1 King's College Circle, Toronto, ON M5S 1A8 Canada
| | - Emily Walker
- Institute for Biomaterials and Biomedical Engineering164 College Street Room 407, Toronto, ON M5S 3G9 Canada
| | - Owen J. Tamplin
- Department of Molecular and Medical Genetics, University of Toronto#4388 Medical Sciences Building, 1 King's College Circle, Toronto, ON M5S 1A8 Canada
- The Hospital for Sick Children101 College Street Room 13-305, Toronto, ON M5G 1L7 Canada
| | - Janet Rossant
- Department of Molecular and Medical Genetics, University of Toronto#4388 Medical Sciences Building, 1 King's College Circle, Toronto, ON M5S 1A8 Canada
- The Hospital for Sick Children101 College Street Room 13-305, Toronto, ON M5G 1L7 Canada
| | - William L. Stanford
- Institute for Biomaterials and Biomedical Engineering164 College Street Room 407, Toronto, ON M5S 3G9 Canada
| | - Timothy R. Hughes
- Department of Molecular and Medical Genetics, University of Toronto#4388 Medical Sciences Building, 1 King's College Circle, Toronto, ON M5S 1A8 Canada
- Banting and Best Department of Medical Research, University of Toronto112 College Street, Toronto, ON M5G 1L6 Canada
- To whom correspondence should be addressed. Tel: 416 946 8260; Fax: 416 978 8528;
| |
Collapse
|
38
|
Canto T, Uhrig JF, Swanson M, Wright KM, MacFarlane SA. Translocation of Tomato bushy stunt virus P19 protein into the nucleus by ALY proteins compromises its silencing suppressor activity. J Virol 2006; 80:9064-72. [PMID: 16940518 PMCID: PMC1563904 DOI: 10.1128/jvi.00953-06] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Accepted: 06/30/2006] [Indexed: 11/20/2022] Open
Abstract
The P19 protein of Tomato bushy stunt virus is a potent suppressor of RNA silencing and, depending on the host species, is required for short- and long-distance virus movement and symptom production. P19 interacts with plant ALY proteins and relocalizes a subset of these proteins from the nucleus to the cytoplasm. Here we showed that coexpression by agroinfiltration in Nicotiana benthamiana of P19 and the subset of ALY proteins that are not relocalized from the nucleus interfered with the ability of P19 to suppress RNA silencing. We demonstrated that this interference correlates with the relocation of P19 from the cytoplasm into the nucleus, and by constructing and analyzing chimeric ALY genes, we showed that the C-terminal part of the central, RNA recognition motif of ALY is responsible for interaction with P19, relocalization or nonrelocalization of ALY, and inhibition of silencing suppression by P19. We studied the interaction of ALY and P19 by using the technique of bimolecular fluorescence complementation to show that these proteins associate physically in the nucleus but not detectably in the cytoplasm, and we present a model to explain the dynamics of this interaction.
Collapse
Affiliation(s)
- Tomas Canto
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | | | | | | | | |
Collapse
|
39
|
Preker PJ, Guthrie C. Autoregulation of the mRNA export factor Yra1p requires inefficient splicing of its pre-mRNA. RNA (NEW YORK, N.Y.) 2006; 12:994-1006. [PMID: 16618971 PMCID: PMC1464842 DOI: 10.1261/rna.6706] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Yra1p is an essential RNA-binding protein that couples transcription to export. The YRA1 gene is one of only approximately 5% of genes that undergo splicing in budding yeast, and its intron is unusual in several respects, including its large size and anomalous branchpoint sequence. We showed previously that the intron is required for autogenous regulation of Yra1p levels, which cause a dominant negative growth phenotype when elevated. The mechanism of this regulation, however, remains unknown. Here we demonstrate that growth is inversely correlated with splicing efficiency. Substitution of a canonical branchpoint moderately improves splicing but compromises autoregulation. Shortening the intron from 766 to approximately 350 nt significantly improves splicing but abolishes autoregulation. Notably, proper regulation can be restored by insertion of unrelated sequences into the shortened intron. In that the current paradigm for regulated splicing involves the binding of protein factors to specific elements in the pre-mRNA, the regulation of YRA1 expression appears to occur by a novel mechanism. We propose that appropriate levels of Yra1p are maintained by inefficient cotranscriptional splicing.
Collapse
Affiliation(s)
- Pascal J Preker
- Department of Biochemistry and Biophysics, University of California, San Francisco, 94143, USA
| | | |
Collapse
|
40
|
Vinson C, Acharya A, Taparowsky EJ. Deciphering B-ZIP transcription factor interactions in vitro and in vivo. ACTA ACUST UNITED AC 2006; 1759:4-12. [PMID: 16580748 DOI: 10.1016/j.bbaexp.2005.12.005] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2004] [Revised: 12/22/2005] [Accepted: 12/27/2005] [Indexed: 10/25/2022]
Abstract
Over the last 15 years, numerous studies have addressed the structural rules that regulate dimerization stability and dimerization specificity of the leucine zipper, a dimeric parallel coiled-coil domain that can either homodimerize or heterodimerize. Initially, these studies were performed with a limited set of B-ZIP proteins, sequence-specific DNA binding proteins that dimerize using the leucine zipper domain to bind DNA. A global analysis of B-ZIP leucine zipper dimerization properties can be rationalized using a limited number of structural rules [J.R. Newman, A.E. Keating, Comprehensive identification of human bZIP interactions with coiled-coil arrays, Science 300 (2003) 2097-2101]. Today, however, access to the genomic sequences of many different organisms has made possible the annotation of all B-ZIP proteins from several species and has generated a bank of data that can be used to refine, and potentially expand, these rules. Already, a comparative analysis of the B-ZIP proteins from Arabidopsis thaliana and Homo sapiens has revealed that the same amino acids are used in different patterns to generate diverse B-ZIP dimerization patterns [C.D. Deppmann, A. Acharya, V. Rishi, B. Wobbes, S. Smeekens, E.J. Taparowsky, C. Vinson, Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs, Nucleic Acids Res. 32 (2004) 3435-3445]. The challenge ahead is to investigate the biological significance of different B-ZIP protein-protein interactions. Gaining insight at this level will rely on ongoing investigations to (a) define the role of target DNA on modulating B-ZIP dimerization partners, (b) characterize the B-ZIP transcriptome in various cells and tissues through mRNA microarray analysis, (c) identify the genomic localization of B-ZIP binding at a genomic level using the chromatin immunoprecipitation assay, and (d) develop more sophisticated imaging technologies to visualize dimer dynamics in single cells and whole organisms. Studies of B-ZIP family leucine zipper dimerization and the regulatory mechanisms that control their biological activities could serve as a paradigm for deciphering the biophysical and biological parameters governing other well-characterized protein-protein interaction motifs. This review will focus on the dimerization specificity of coiled-coil proteins, particularly the human B-ZIP transcription family that consists of 53 proteins that use the leucine zipper coiled-coil as a dimerization motif.
Collapse
Affiliation(s)
- Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | | |
Collapse
|
41
|
Wang Q, He J, Lynn B, Rymond BC. Interactions of the yeast SF3b splicing factor. Mol Cell Biol 2005; 25:10745-54. [PMID: 16314500 PMCID: PMC1316957 DOI: 10.1128/mcb.25.24.10745-10754.2005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Revised: 07/12/2005] [Accepted: 09/21/2005] [Indexed: 11/20/2022] Open
Abstract
The U2 snRNP promotes prespliceosome assembly through interactions that minimally involve the branchpoint binding protein, Mud2p, and the pre-mRNA. We previously showed that seven proteins copurify with the yeast (Saccharomyces cerevisiae) SF3b U2 subcomplex that associates with the pre-mRNA branchpoint region: Rse1p, Hsh155p, Hsh49p, Cus1p, and Rds3p and unidentified subunits p10 and p17. Here proteomic and genetic studies identify Rcp10p as p10 and show that it contributes to SF3b stability and is necessary for normal cellular Cus1p accumulation and for U2 snRNP recruitment in splicing. Remarkably, only the final 53 amino acids of Rcp10p are essential. p17 is shown to be composed of two accessory splicing factors, Bud31p and Ist3p, the latter of which independently associates with the RES complex implicated in the nuclear pre-mRNA retention. A directed two-hybrid screen reveals a network of prospective interactions that includes previously unreported intra-SF3b contacts and SF3b interactions with the RES subunit Bud13p, the Prp5p DExD/H-box protein, Mud2p, and the late-acting nineteen complex. These data establish the concordance of yeast and mammalian SF3b complexes, implicate accessory splicing factors in U2 snRNP function, and support SF3b contribution from early pre-mRNP recognition to late steps in splicing.
Collapse
Affiliation(s)
- Qiang Wang
- Department of Biology, University of Kentucky, Lexington, 40506, USA
| | | | | | | |
Collapse
|
42
|
Rosonina E, Ip JYY, Calarco JA, Bakowski MA, Emili A, McCracken S, Tucker P, Ingles CJ, Blencowe BJ. Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol Cell Biol 2005; 25:6734-46. [PMID: 16024807 PMCID: PMC1190332 DOI: 10.1128/mcb.25.15.6734-6746.2005] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Revised: 03/23/2005] [Accepted: 05/10/2005] [Indexed: 11/20/2022] Open
Abstract
In a recent study, we provided evidence that strong promoter-bound transcriptional activators result in higher levels of splicing and 3'-end cleavage of nascent pre-mRNA than do weak promoter-bound activators and that this effect of strong activators requires the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II). In the present study, we have investigated the mechanism of activator- and CTD-mediated stimulation of pre-mRNA processing. Affinity chromatography experiments reveal that two factors previously implicated in the coupling of transcription and pre-mRNA processing, PSF and p54(nrb)/NonO, preferentially bind a strong rather than a weak activation domain. Elevated expression in human 293 cells of PSF bypasses the requirement for a strong activator to promote efficient splicing and 3'-end cleavage. Truncation of the pol II CTD, which consists of 52 repeats of the consensus heptapeptide sequence YSPTSPS, to 15 heptapeptide repeats prevents PSF-dependent stimulation of splicing and 3'-end cleavage. Moreover, PSF and p54(nrb)/NonO bind in vitro to the wild-type CTD but not to the truncated 15-repeat CTD, and domains in PSF that are required for binding to activators and to the CTD are also important for the stimulation of pre-mRNA processing. Interestingly, activator- and CTD-dependent stimulation of splicing mediated by PSF appears to primarily affect the removal of first introns. Collectively, these results suggest that the recruitment of PSF to activated promoters and the pol II CTD provides a mechanism by which transcription and pre-mRNA processing are coordinated within the cell.
Collapse
Affiliation(s)
- Emanuel Rosonina
- Banting and Best Department of Medical Research, C. H. Best Institute, 112 College Street, Toronto, Ontario M5G 1L6, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Sehnke PC, Laughner BJ, Lyerly Linebarger CR, Gurley WB, Ferl RJ. Identification and characterization of GIP1, an Arabidopsis thaliana protein that enhances the DNA binding affinity and reduces the oligomeric state of G-box binding factors. Cell Res 2005; 15:567-75. [PMID: 16117846 DOI: 10.1038/sj.cr.7290326] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Environmental control of the alcohol dehydrogenase (Adh) and other stress response genes in plants is in part brought about by transcriptional regulation involving the G-box cis-acting DNA element and bZIP G-box Binding Factors (GBFs). The mechanisms of GBF regulation and requirements for additional factors in this control process are not well understood. In an effort to identify potential GBF binding and control partners, maize GBF1 was used as bait in a yeast two-hybrid screen of an A. thaliana cDNA library. GBF Interacting Protein 1 (GIP1) arose from the screen as a 496 amino acid protein with a predicted molecular weight of 53,748 kDa that strongly interacts with GBFs. Northern analysis of A. thaliana tissue suggests a 1.8-1.9 kb GIP1 transcript, predominantly in roots. Immunolocalization studies indicate that GIP1 protein is mainly localized to the nucleus. In vitro electrophoretic mobility shift assays using an Adh G-box DNA probe and recombinant A. thaliana GBF3 or maize GBF1, showed that the presence of GIP1 resulted in a tenfold increase in GBF DNA binding activity without altering the migration, suggesting a transient association between GIP1 and GBF. Addition of GIP1 to intentionally aggregated GBF converted GBF to lower molecular weight macromolecular complexes and GIP1 also refolded denatured rhodanese in the absence of ATP. These data suggest GIP1 functions to enhance GBF DNA binding activity by acting as a potent nuclear chaperone or crowbar, and potentially regulates the multimeric state of GBFs, thereby contributing to bZIP-mediated gene regulation.
Collapse
Affiliation(s)
- Paul C Sehnke
- Program in Plant Cellular and Molecular Biology, Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | | | | | | | | |
Collapse
|
44
|
Schrem H, Klempnauer J, Borlak J. Liver-enriched transcription factors in liver function and development. Part II: the C/EBPs and D site-binding protein in cell cycle control, carcinogenesis, circadian gene regulation, liver regeneration, apoptosis, and liver-specific gene regulation. Pharmacol Rev 2004; 56:291-330. [PMID: 15169930 DOI: 10.1124/pr.56.2.5] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In the first part of our review (see Pharmacol Rev 2002;54:129-158), we discussed the basic principles of gene transcription and the complex interactions within the network of hepatocyte nuclear factors, coactivators, ligands, and corepressors in targeted liver-specific gene expression. Now we summarize the role of basic region/leucine zipper protein family members and particularly the albumin D site-binding protein (DBP) and the CAAT/enhancer-binding proteins (C/EBPs) for their importance in liver-specific gene expression and their role in liver function and development. Specifically, regulatory networks and molecular interactions were examined in detail, and the experimental findings summarized in this review point to pivotal roles of DBP and C/EBPs in cell cycle control, carcinogenesis, circadian gene regulation, liver regeneration, apoptosis, and liver-specific gene regulation. These regulatory proteins are therefore of great importance in liver physiology, liver disease, and liver development. Furthermore, interpretation of the vast data generated by novel genomic platform technologies requires a thorough understanding of regulatory networks and particularly the hierarchies that govern transcription and translation of proteins as well as intracellular protein modifications. Thus, this review aims to stimulate discussions on directions of future research and particularly the identification of molecular targets for pharmacological intervention of liver disease.
Collapse
Affiliation(s)
- Harald Schrem
- Center for Drug Research and Medical Biotechnology, Fraunhofer Institut für Toxikologie und Experimentelle Medizin, Nicolai Fuchs Str. 1, 30625 Hannover, Germany
| | | | | |
Collapse
|
45
|
Shao BM, Dai H, Xu W, Lin ZB, Gao XM. Immune receptors for polysaccharides from Ganoderma lucidum. Biochem Biophys Res Commun 2004; 323:133-41. [PMID: 15351712 DOI: 10.1016/j.bbrc.2004.08.069] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Indexed: 10/26/2022]
Abstract
This study was designed to identify and characterize the immune receptors for polysaccharides from Ganoderma lucidum, a Chinese medicinal fungus that exhibits anti-tumor activities via enhancing host immunity. We herein demonstrate that G. lucidum polysaccharides (GLPS) activated BALB/c mouse B cells and macrophages, but not T cells, in vitro. However, GLPS was unable to activate splenic B cells from C3H/HeJ mice that have a mutated TLR4 molecule (incapable of signal transduction) in proliferation assays. Rat anti-mouse TLR4 monoclonal antibody (Ab) inhibited the proliferation of BALB/c mouse B cells under GLPS stimulation. Combination of Abs against mouse TLR4 and immunoglobulin (Ig) achieved almost complete inhibition of GLPS-induced B cell proliferation, implying that both membrane Ig and TLR4 are required for GLPS-mediated B cell activation. In addition, GLPS significantly inhibited the binding of mouse peritoneal macrophages with polysaccharides from Astragalus membranaceus, which is known to bind directly with TLR4 on macrophage surface. Moreover, GLPS induced IL-1beta production by peritoneal macrophages from BALB/c, but not C3H/HeJ, mice, suggesting that TLR4 is also involved in GLPS-mediated macrophage activation. We Further identified a unique 31 kDa serum protein and two intracellular proteins (ribosomal protein S7 and a transcriptional coactivator) capable of binding with GLPS in co-precipitation experiments. Our results may have important implications for our understanding on the molecular mechanisms of immunopotentiating polysaccharides from traditional Chinese medicine.
Collapse
Affiliation(s)
- Bao-Mei Shao
- Department of Immunology, Peking University Health Science Center, School of Basic Medical Sciences, Beijing, China
| | | | | | | | | |
Collapse
|
46
|
Uhrig JF, Canto T, Marshall D, MacFarlane SA. Relocalization of nuclear ALY proteins to the cytoplasm by the tomato bushy stunt virus P19 pathogenicity protein. PLANT PHYSIOLOGY 2004; 135:2411-23. [PMID: 15299117 PMCID: PMC520808 DOI: 10.1104/pp.104.046086] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The P19 protein of tomato bushy stunt virus (TBSV) is a multifunctional pathogenicity determinant involved in suppression of posttranscriptional gene silencing, virus movement, and symptom induction. Here, we report that P19 interacts with the conserved RNA-binding domain of an as yet uncharacterized family of plant ALY proteins that, in animals, are involved in export of RNAs from the nucleus and transcriptional coactivation. We show that the four ALY proteins encoded by the Arabidopsis genome and two ALY proteins from Nicotiana benthamiana are localized to the nucleus. Moreover, and in contrast to animal ALY, all but one of the proteins are also in the nucleolus, with distinct subnuclear localizations. Infection of plants by TBSV or expression of P19 from Agrobacterium results in relocation of three of the six ALY proteins from the nucleus to the cytoplasm demonstrating specific targeting of the ALY proteins by P19. The differential effects on subcellular localization indicate that, in plants, the various ALY proteins may have different functions. Interaction with and relocalization of ALY is prevented by mutation of P19 at residues previously shown to be important for P19 function in plants. Down-regulation of expression of two N. benthamiana ALY genes by virus-induced gene silencing did not interfere with posttranscriptional gene silencing. Targeting of ALY proteins during TBSV infection may therefore be related to functions of P19 in addition to its silencing suppression activity.
Collapse
Affiliation(s)
- Joachim F Uhrig
- Max-Planck-Institut für Züchtungsforschung, 50829 Cologne, Germany
| | | | | | | |
Collapse
|
47
|
Malik P, Blackbourn DJ, Clements JB. The Evolutionarily Conserved Kaposi's Sarcoma-associated Herpesvirus ORF57 Protein Interacts with REF Protein and Acts as an RNA Export Factor. J Biol Chem 2004; 279:33001-11. [PMID: 15155762 DOI: 10.1074/jbc.m313008200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ORF57 (MTA) one of the earliest Kaposi's sarcoma-associated herpesvirus (KSHV) regulatory proteins to be expressed is essential for virus lytic replication. A counterpart is present in every herpesvirus sequenced, indicating the importance of this signature viral protein and those examined act post-transcriptionally, affecting RNA splicing and transport. In KSHV-infected cells, ORF57 protein was present in a complex with REF (Aly) and TAP (NXF1), factors involved in cellular mRNA export. The ORF57 N-terminal region interacts with REF, whereas both N- and C-terminal domains of REF interact with ORF57. The ORF57-REF interaction was direct, whereas TAP appeared to be recruited via REF. In somatic cells, ectopically expressed ORF57 protein was shown to function as a CRM1-independent nuclear mRNA export factor, promoting export of mRNAs that are poor substrates for splicing. The gamma-herpesvirus ORF57 protein, and its alpha-1 herpesvirus ICP27 counterpart both export RNA through pathways involving REF and TAP proteins, although divergence of these herpesvirus subfamilies occurred some 180-210 million years ago. The TAP-mediated cellular mRNA export pathway is CRM1-independent. However, human immunodeficiency virus type 1 Rev protein-mediated RNA export, which is CRM1-dependent, was considerably inhibited by ORF57, suggesting that Rev and ORF57 compete for a common export component. These data strengthen arguments that TAP and CRM1 pathways converge in accessing similar components of the nuclear pore complex. We propose that ORF57-mediated RNA export may use different export factors to accommodate the KSHV-infected host cell environments, for example, in B-cells or endothelial cells and during the different phases of lytic virus replication.
Collapse
Affiliation(s)
- Poonam Malik
- Division of Virology, Institute of Biomedical and Life Sciences, University of Glasgow, Church Street, Glasgow, G11 5JR, Scotland, United Kingdom
| | | | | |
Collapse
|
48
|
Custódio N, Carvalho C, Condado I, Antoniou M, Blencowe BJ, Carmo-Fonseca M. In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei. RNA (NEW YORK, N.Y.) 2004; 10:622-33. [PMID: 15037772 PMCID: PMC1370553 DOI: 10.1261/rna.5258504] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Studies over the past years indicate that there is extensive coupling between nuclear export of mRNA and pre-mRNA processing. Here, we visualized the distribution of exon junction complex (EJC) proteins and RNA export factors relative to sites of abundant pre-mRNA synthesis in the nucleus. We analyzed both HeLa cells infected with adenovirus and murine erythroleukemia (MEL) cells stably transfected with the human beta-globin gene. Using in situ hybridization and confocal microscopy, we observe accumulation of EJC proteins (REF/Aly, Y14, SRm160, UAP56, RNPS1, and Magoh) and core spliceosome components (U snRNPs) at sites of transcription. This suggests that EJC proteins bind stably to pre-mRNA cotranscriptionally. No concentration of the export factors NXF1/TAP, p15, and Dbp5 was detected on nascent transcripts, arguing that in mammalian cells these proteins bind the mRNA shortly before or after release from the sites of transcription. These results also suggest that binding of EJC proteins to the mRNA is not sufficient to recruit TAP-p15, consistent with recent findings showing that the EJC does not play a crucial role in mRNA export. Contrasting to the results obtained in MEL cells expressing normal human beta-globin transcripts, mutant pre-mRNAs defective in splicing and 3'end processing do not colocalize with SRm160, REF, UAP56, or Sm proteins. This shows that the accumulation of EJC proteins at transcription sites requires efficient processing of the nascent pre-mRNAs, arguing that transcription per se is not sufficient for the stable assembly of the EJC.
Collapse
Affiliation(s)
- Noélia Custódio
- Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, Lisbon 1649-028, Portugal
| | | | | | | | | | | |
Collapse
|
49
|
McCracken S, Longman D, Johnstone IL, Cáceres JF, Blencowe BJ. An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation. J Biol Chem 2003; 278:44153-60. [PMID: 12944400 DOI: 10.1074/jbc.m306856200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SRm160 (the SR-related nuclear matrix protein of 160 kDa) functions as a splicing coactivator and 3'-end cleavage-stimulatory factor. It is also a component of the splicing-dependent exon-junction complex (EJC), which has been implicated in coupling of pre-mRNA splicing with mRNA turnover and mRNA export. We have investigated whether the association of SRm160 with the EJC is important for efficient 3'-end cleavage. The EJC components RNPS1, REF, UAP56, and Y14 interact with SRm160. However, when these factors were tethered to transcripts, only SRm160 and RNPS1 stimulated 3'-end cleavage. Whereas SRm160 stimulated cleavage to a similar extent in the presence or absence of an active intron, stimulation of 3'-end cleavage by tethered RNPS1 is dependent on an active intron. Assembly of an EJC adjacent to the cleavage and polyadenylation signal in vitro did not significantly affect cleavage efficiency. These results suggest that SRm160 stimulates cleavage independently of its association with EJC components and that the cleavage-stimulatory activity of RNPS1 may be an indirect consequence of its ability to stimulate splicing. Using RNA interference (RNAi) in Caenorhabditis elegans, we determined whether interactions between SRm160 and the cleavage machinery are important in a whole organism context. Simultaneous RNAi of SRm160 and the cleavage factor CstF-50 (Cleavage stimulation factor 50-kDa subunit) resulted in late embryonic developmental arrest. In contrast, RNAi of CstF-50 in combination with RNPS1 or REFs did not result in an apparent phenotype. Our combined results provide evidence for an evolutionarily conserved interaction between SRm160 and the 3'-end cleavage machinery that functions independently of EJC formation.
Collapse
Affiliation(s)
- Susan McCracken
- Banting and Best Department of Medical Research, C. H. Best Institute, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | | | | | | | | |
Collapse
|
50
|
Ouwens D, de Ruiter ND, van der Zon GC, Carter AP, Schouten J, van der Burgt C, Kooistra K, Bos JL, Maassen J, van Dam H. Growth factors can activate ATF2 via a two-step mechanism: phosphorylation of Thr71 through the Ras-MEK-ERK pathway and of Thr69 through RalGDS-Src-p38. EMBO J 2002; 21:3782-93. [PMID: 12110590 PMCID: PMC126107 DOI: 10.1093/emboj/cdf361] [Citation(s) in RCA: 179] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Transcription factor ATF2 regulates gene expression in response to environmental changes. Upon exposure to cellular stresses, the mitogen-activated proteinkinase (MAPK) cascades including SAPK/JNK and p38 can enhance ATF2's transactivating function through phosphorylation of Thr69 and Thr71. How ever, the mechanism of ATF2 activation by growth factors that are poor activators of JNK and p38 is still elusive. Here, we show that in fibroblasts, insulin, epidermal growth factor (EGF) and serum activate ATF2 via a so far unknown two-step mechanism involving two distinct Ras effector pathways: the Raf-MEK-ERK pathway induces phosphorylation of ATF2 Thr71, whereas subsequent ATF2 Thr69 phosphorylation requires the Ral-RalGDS-Src-p38 pathway. Cooperation between ERK and p38 was found to be essential for ATF2 activation by these mitogens; the activity of p38 and JNK/SAPK in growth factor-stimulated fibroblasts is insufficient to phosphorylate ATF2 Thr71 or Thr69 + 71 significantly by themselves, while ERK cannot dual phosphorylate ATF2 Thr69 + 71 efficiently. These results reveal a so far unknown mechanism by which distinct MAPK pathways and Ras effector pathways cooperate to activate a transcription factor.
Collapse
Affiliation(s)
- D.Margriet Ouwens
- Department of Molecular Cell Biology, Section of Signal Transduction and Centre for Biomedical Genetics, Section Gene Regulation, Leiden University Medical Centre, Wassenaarseweg 72, 2333 AL Leiden and Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands Present address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Present address: Leadd BV, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands Corresponding author e-mail:
| | - Nancy D. de Ruiter
- Department of Molecular Cell Biology, Section of Signal Transduction and Centre for Biomedical Genetics, Section Gene Regulation, Leiden University Medical Centre, Wassenaarseweg 72, 2333 AL Leiden and Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands Present address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Present address: Leadd BV, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands Corresponding author e-mail:
| | - Gerard C.M. van der Zon
- Department of Molecular Cell Biology, Section of Signal Transduction and Centre for Biomedical Genetics, Section Gene Regulation, Leiden University Medical Centre, Wassenaarseweg 72, 2333 AL Leiden and Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands Present address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Present address: Leadd BV, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands Corresponding author e-mail:
| | - Andrew P. Carter
- Department of Molecular Cell Biology, Section of Signal Transduction and Centre for Biomedical Genetics, Section Gene Regulation, Leiden University Medical Centre, Wassenaarseweg 72, 2333 AL Leiden and Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands Present address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Present address: Leadd BV, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands Corresponding author e-mail:
| | - Jan Schouten
- Department of Molecular Cell Biology, Section of Signal Transduction and Centre for Biomedical Genetics, Section Gene Regulation, Leiden University Medical Centre, Wassenaarseweg 72, 2333 AL Leiden and Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands Present address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Present address: Leadd BV, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands Corresponding author e-mail:
| | - Corina van der Burgt
- Department of Molecular Cell Biology, Section of Signal Transduction and Centre for Biomedical Genetics, Section Gene Regulation, Leiden University Medical Centre, Wassenaarseweg 72, 2333 AL Leiden and Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands Present address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Present address: Leadd BV, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands Corresponding author e-mail:
| | - Klaas Kooistra
- Department of Molecular Cell Biology, Section of Signal Transduction and Centre for Biomedical Genetics, Section Gene Regulation, Leiden University Medical Centre, Wassenaarseweg 72, 2333 AL Leiden and Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands Present address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Present address: Leadd BV, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands Corresponding author e-mail:
| | - Johannes L. Bos
- Department of Molecular Cell Biology, Section of Signal Transduction and Centre for Biomedical Genetics, Section Gene Regulation, Leiden University Medical Centre, Wassenaarseweg 72, 2333 AL Leiden and Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands Present address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Present address: Leadd BV, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands Corresponding author e-mail:
| | - J.Antonie Maassen
- Department of Molecular Cell Biology, Section of Signal Transduction and Centre for Biomedical Genetics, Section Gene Regulation, Leiden University Medical Centre, Wassenaarseweg 72, 2333 AL Leiden and Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands Present address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Present address: Leadd BV, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands Corresponding author e-mail:
| | - Hans van Dam
- Department of Molecular Cell Biology, Section of Signal Transduction and Centre for Biomedical Genetics, Section Gene Regulation, Leiden University Medical Centre, Wassenaarseweg 72, 2333 AL Leiden and Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands Present address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Present address: Leadd BV, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands Corresponding author e-mail:
| |
Collapse
|