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Zahreddine HA, Culjkovic-Kraljacic B, Emond A, Pettersson F, Midura R, Lauer M, Del Rincon S, Cali V, Assouline S, Miller WH, Hascall V, Borden KL. The eukaryotic translation initiation factor eIF4E harnesses hyaluronan production to drive its malignant activity. eLife 2017; 6:29830. [PMID: 29111978 PMCID: PMC5705209 DOI: 10.7554/elife.29830] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/03/2017] [Indexed: 01/03/2023] Open
Abstract
The microenvironment provides a functional substratum supporting tumour growth. Hyaluronan (HA) is a major component of this structure. While the role of HA in malignancy is well-defined, the mechanisms driving its biosynthesis in cancer are poorly understood. We show that the eukaryotic translation initiation factor eIF4E, an oncoprotein, drives HA biosynthesis. eIF4E stimulates production of enzymes that synthesize the building blocks of HA, UDP-Glucuronic acid and UDP-N-Acetyl-Glucosamine, as well as hyaluronic acid synthase which forms the disaccharide chain. Strikingly, eIF4E inhibition alone repressed HA levels as effectively as directly targeting HA with hyaluronidase. Unusually, HA was retained on the surface of high-eIF4E cells, rather than being extruded into the extracellular space. Surface-associated HA was required for eIF4E’s oncogenic activities suggesting that eIF4E potentiates an oncogenic HA program. These studies provide unique insights into the mechanisms driving HA production and demonstrate that an oncoprotein can co-opt HA biosynthesis to drive malignancy.
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Affiliation(s)
- Hiba Ahmad Zahreddine
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Québec, Canada
| | - Biljana Culjkovic-Kraljacic
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Québec, Canada
| | - Audrey Emond
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Québec, Canada
| | - Filippa Pettersson
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Québec, Canada
| | - Ronald Midura
- Orthopaedic Research Center, The Cleveland Clinic Foundation, Cleveland, United States.,Department of Biomedical Engineering, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, United States
| | - Mark Lauer
- Orthopaedic Research Center, The Cleveland Clinic Foundation, Cleveland, United States.,Department of Biomedical Engineering, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, United States
| | - Sonia Del Rincon
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Québec, Canada
| | - Valbona Cali
- Orthopaedic Research Center, The Cleveland Clinic Foundation, Cleveland, United States.,Department of Biomedical Engineering, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, United States
| | - Sarit Assouline
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Québec, Canada
| | - Wilson H Miller
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Québec, Canada
| | - Vincent Hascall
- Orthopaedic Research Center, The Cleveland Clinic Foundation, Cleveland, United States.,Department of Biomedical Engineering, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, United States
| | - Katherine Lb Borden
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Québec, Canada
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52
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Bell JB, Eckerdt F, Dhruv HD, Finlay D, Peng S, Kim S, Kroczynska B, Beauchamp EM, Alley K, Clymer J, Goldman S, Cheng SY, James CD, Nakano I, Horbinski C, Mazar AP, Vuori K, Kumthekar P, Raizer J, Berens ME, Platanias LC. Differential Response of Glioma Stem Cells to Arsenic Trioxide Therapy Is Regulated by MNK1 and mRNA Translation. Mol Cancer Res 2017; 16:32-46. [PMID: 29042487 DOI: 10.1158/1541-7786.mcr-17-0397] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/13/2017] [Accepted: 10/11/2017] [Indexed: 12/16/2022]
Abstract
Mesenchymal (MES) and proneural (PN) are two distinct glioma stem cell (GSC) populations that drive therapeutic resistance in glioblastoma (GBM). We screened a panel of 650 small molecules against patient-derived GBM cells to discover compounds targeting specific GBM subtypes. Arsenic trioxide (ATO), an FDA-approved drug that crosses the blood-brain barrier, was identified as a potent PN-specific compound in the initial screen and follow-up validation studies. Furthermore, MES and PN GSCs exhibited differential sensitivity to ATO. As ATO has been shown to activate the MAPK-interacting kinase 1 (MNK1)-eukaryotic translation initiation factor 4E (eIF4E) pathway and subsequent mRNA translation in a negative regulatory feedback manner, the mechanistic role of ATO resistance in MES GBM was explored. In GBM cells, ATO-activated translation initiation cellular events via the MNK1-eIF4E signaling axis. Furthermore, resistance to ATO in intracranial PDX tumors correlated with high eIF4E phosphorylation. Polysomal fractionation and microarray analysis of GBM cells were performed to identify ATO's effect on mRNA translation and enrichment of anti-apoptotic mRNAs in the ATO-induced translatome was found. Additionally, it was determined that MNK inhibition sensitized MES GSCs to ATO in neurosphere and apoptosis assays. Finally, examination of the effect of ATO on patients from a phase I/II clinical trial of ATO revealed that PN GBM patients responded better to ATO than other subtypes as demonstrated by longer overall and progression-free survival.Implications: These findings raise the possibility of a unique therapeutic approach for GBM, involving MNK1 targeting to sensitize MES GSCs to drugs like arsenic trioxide. Mol Cancer Res; 16(1); 32-46. ©2017 AACR.
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Affiliation(s)
- Jonathan B Bell
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Frank Eckerdt
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Harshil D Dhruv
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Darren Finlay
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Sen Peng
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Seungchan Kim
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, Arizona.,Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, Texas
| | - Barbara Kroczynska
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Elspeth M Beauchamp
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Department of Medicine, Jesse Brown VA Medical Center, Chicago, Illinois
| | - Kristen Alley
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jessica Clymer
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Division of Hematology/Oncology/Stem Cell Transplantation, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Stewart Goldman
- Division of Hematology/Oncology/Stem Cell Transplantation, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Shi-Yuan Cheng
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - C David James
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ichiro Nakano
- Department of Neurosurgery and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Andrew P Mazar
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Developmental Therapeutics Core, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois
| | - Kristiina Vuori
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Priya Kumthekar
- Division of Neuro-Oncology, Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jeffrey Raizer
- Division of Neuro-Oncology, Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois. .,Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Department of Medicine, Jesse Brown VA Medical Center, Chicago, Illinois
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53
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Napoli S, Piccinelli V, Mapelli SN, Pisignano G, Catapano CV. Natural antisense transcripts drive a regulatory cascade controlling c-MYC transcription. RNA Biol 2017; 14:1742-1755. [PMID: 28805496 PMCID: PMC5731802 DOI: 10.1080/15476286.2017.1356564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are long noncoding RNAs transcribed from the opposite strand and overlapping coding and noncoding genes on the sense strand. cis-NATs are widely present in the human genome and can be involved in multiple mechanisms of gene regulation. Here, we describe the presence of cis-NATs in the 3′ distal region of the c-MYC locus and investigate their impact on transcriptional regulation of this key oncogene in human cancers. We found that cis-NATs are produced as consequence of the activation of cryptic transcription initiation sites in the 3′ distal region downstream of the c-MYC 3′UTR. The process is tightly regulated and leads to the formation of two main transcripts, NAT6531 and NAT6558, which differ in their ability to fold into stem-loop secondary structures. NAT6531 acts as a substrate for DICER and as a source of small RNAs capable of modulating c-MYC transcription. This complex system, based on the interplay between cis-NATs and NAT-derived small RNAs, may represent an important layer of epigenetic regulation of the expression of c-MYC and other genes in human cells.
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Affiliation(s)
- Sara Napoli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Valentina Piccinelli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Sarah N Mapelli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Giuseppina Pisignano
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Carlo V Catapano
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland.,b Department of Oncology , Faculty of Biology and Medicine, University of Lausanne , Lausanne , Switzerland
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54
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Major splice variants and multiple polyadenylation site utilization in mRNAs encoding human translation initiation factors eIF4E1 and eIF4E3 regulate the translational regulators? Mol Genet Genomics 2017; 293:167-186. [PMID: 28942592 DOI: 10.1007/s00438-017-1375-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/19/2017] [Indexed: 01/01/2023]
Abstract
Alternative polyadenylation is an important and pervasive mechanism that generates heterogeneous 3'-termini of mRNA and is considered an important regulator of gene expression. We performed bioinformatics analyses of ESTs and the 3'-UTRs of the main transcript splice variants of the translational initiation factor eIF4E1 and its family members, eIF4E2 and eIF4E3. This systematic analysis led to the prediction of new polyadenylation signals. All identified polyadenylation sites were subsequently verified by 3'RACE of transcripts isolated from human lymphoblastic cell lines. This led to the observation that multiple simultaneous polyadenylation site utilization occurs in single cell population. Importantly, we described the use of new polyadenylation site in the eIF4E1 mRNA, which lacked any known polyadenylation signal. The proportion of eIF4E1 transcripts derived from the first two polyadenylation sites in eIF4E1 mRNA achieved 15% in a wide range of cell lines. This result demonstrates the ubiquitous presence of ARE-lacking transcripts, which escape HuR/Auf1-mediated control, the main mechanism of eIF4E1 gene expression regulation. We found many EST clones documenting the significant production of transcript variants 2-4 of eIF4E2 gene that encode proteins with C-termini that were distinct from the mainly studied prototypical isoform A. Similarly, eIF4E3 mRNAs are produced as two main variants with the same very long 3'-UTR with potential for heavy post-transcriptional regulation. We identified sparsely documented transcript variant 1 of eIF4E3 gene in human placenta. eIF4E3 truncated transcript variants were found mainly in brain. We propose to elucidate the minor splice variants of eIF4E2 and eIF4E3 in great detail because they might produce proteins with modified features that fulfill different cellular roles from their major counterparts.
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55
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Boeynaems S, Bogaert E, Kovacs D, Konijnenberg A, Timmerman E, Volkov A, Guharoy M, De Decker M, Jaspers T, Ryan VH, Janke AM, Baatsen P, Vercruysse T, Kolaitis RM, Daelemans D, Taylor JP, Kedersha N, Anderson P, Impens F, Sobott F, Schymkowitz J, Rousseau F, Fawzi NL, Robberecht W, Van Damme P, Tompa P, Van Den Bosch L. Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics. Mol Cell 2017; 65:1044-1055.e5. [PMID: 28306503 PMCID: PMC5364369 DOI: 10.1016/j.molcel.2017.02.013] [Citation(s) in RCA: 352] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 12/14/2016] [Accepted: 02/14/2017] [Indexed: 01/01/2023]
Abstract
Liquid-liquid phase separation (LLPS) of RNA-binding proteins plays an important role in the formation of multiple membrane-less organelles involved in RNA metabolism, including stress granules. Defects in stress granule homeostasis constitute a cornerstone of ALS/FTLD pathogenesis. Polar residues (tyrosine and glutamine) have been previously demonstrated to be critical for phase separation of ALS-linked stress granule proteins. We now identify an active role for arginine-rich domains in these phase separations. Moreover, arginine-rich dipeptide repeats (DPRs) derived from C9orf72 hexanucleotide repeat expansions similarly undergo LLPS and induce phase separation of a large set of proteins involved in RNA and stress granule metabolism. Expression of arginine-rich DPRs in cells induced spontaneous stress granule assembly that required both eIF2α phosphorylation and G3BP. Together with recent reports showing that DPRs affect nucleocytoplasmic transport, our results point to an important role for arginine-rich DPRs in the pathogenesis of C9orf72 ALS/FTLD. Arginine-rich peptides undergo LLPS dependent on counterions or polyaromates Toxic arginine-rich DPRs perturb stress granule dynamics and protein content PR-induced stress granule formation is dependent on eIF2α phosphorylation and G3BP PR promotes aggregation of ALS-related proteins containing prion-like domains
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Affiliation(s)
- Steven Boeynaems
- Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Department of Neurosciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium; Laboratory of Neurobiology, VIB, Center for Brain and Disease Research, 3000 Leuven, Belgium
| | - Elke Bogaert
- Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Department of Neurosciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium; Laboratory of Neurobiology, VIB, Center for Brain and Disease Research, 3000 Leuven, Belgium
| | - Denes Kovacs
- Center for Structural Biology (CSB), VIB, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Albert Konijnenberg
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
| | - Evy Timmerman
- VIB-UGent Center for Medical Biotechnology, 9000 Gent, Belgium; VIB Proteomics Core, 9000 Gent, Belgium; Department of Biochemistry, Ghent University, 9000 Gent, Belgium
| | - Alex Volkov
- Center for Structural Biology (CSB), VIB, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Mainak Guharoy
- Center for Structural Biology (CSB), VIB, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Mathias De Decker
- Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Department of Neurosciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium; Laboratory of Neurobiology, VIB, Center for Brain and Disease Research, 3000 Leuven, Belgium
| | - Tom Jaspers
- Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Department of Neurosciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium; Laboratory of Neurobiology, VIB, Center for Brain and Disease Research, 3000 Leuven, Belgium
| | - Veronica H Ryan
- Neuroscience Graduate Program, Brown University, Providence, RI 02912, USA
| | - Abigail M Janke
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | | | - Thomas Vercruysse
- Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Regina-Maria Kolaitis
- Howard Hughes Medical Institute, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dirk Daelemans
- Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - J Paul Taylor
- Howard Hughes Medical Institute, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nancy Kedersha
- Division of Rheumatology, Immunology, and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Paul Anderson
- Division of Rheumatology, Immunology, and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, 9000 Gent, Belgium; VIB Proteomics Core, 9000 Gent, Belgium; Department of Biochemistry, Ghent University, 9000 Gent, Belgium
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Joost Schymkowitz
- Switch Laboratory, Center for Brain and Disease Research, VIB, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, Center for Brain and Disease Research, VIB, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Wim Robberecht
- Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Department of Neurosciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium; Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Philip Van Damme
- Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Department of Neurosciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium; Laboratory of Neurobiology, VIB, Center for Brain and Disease Research, 3000 Leuven, Belgium; Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Peter Tompa
- Center for Structural Biology (CSB), VIB, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, 1117 Budapest, Hungary.
| | - Ludo Van Den Bosch
- Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Department of Neurosciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium; Laboratory of Neurobiology, VIB, Center for Brain and Disease Research, 3000 Leuven, Belgium.
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56
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Heerma van Voss MR, Vesuna F, Bol GM, Meeldijk J, Raman A, Offerhaus GJ, Buerger H, Patel AH, van der Wall E, van Diest PJ, Raman V. Nuclear DDX3 expression predicts poor outcome in colorectal and breast cancer. Onco Targets Ther 2017; 10:3501-3513. [PMID: 28761359 PMCID: PMC5522823 DOI: 10.2147/ott.s140639] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Purpose DEAD box protein 3 (DDX3) is an RNA helicase with oncogenic properties that shuttles between the cytoplasm and nucleus. The majority of DDX3 is found in the cytoplasm, but a subset of tumors has distinct nuclear DDX3 localization of yet unknown biological significance. This study aimed to evaluate the significance of and mechanisms behind nuclear DDX3 expression in colorectal and breast cancer. Methods Expression of nuclear DDX3 and the nuclear exporter chromosome region maintenance 1 (CRM1) was evaluated by immunohistochemistry in 304 colorectal and 292 breast cancer patient samples. Correlations between the subcellular localization of DDX3 and CRM1 and the difference in overall survival between patients with and without nuclear DDX3 were studied. In addition, DDX3 mutants were created for in vitro evaluation of the mechanism behind nuclear retention of DDX3. Results DDX3 was present in the nucleus of 35% of colorectal and 48% of breast cancer patient samples and was particularly strong in the nucleolus. Nuclear DDX3 correlated with worse overall survival in both colorectal (hazard ratio [HR] 2.34, P<0.001) and breast cancer (HR 2.39, P=0.004) patients. Colorectal cancers with nuclear DDX3 expression more often had cytoplasmic expression of the nuclear exporter CRM1 (relative risk 1.67, P=0.04). In vitro analysis of DDX3 deletion mutants demonstrated that CRM1-mediated export was most dependent on the N-terminal nuclear export signal. Conclusion Overall, we conclude that nuclear DDX3 is partially CRM1-mediated and predicts worse survival in colorectal and breast cancer patients, putting it forward as a target for therapeutic intervention with DDX3 inhibitors under development in these cancer types.
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Affiliation(s)
- Marise R Heerma van Voss
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Farhad Vesuna
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guus M Bol
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jan Meeldijk
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.,Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ana Raman
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - G Johan Offerhaus
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Arvind H Patel
- Centre for Virus Research, MRC-University of Glasgow, Glasgow, UK
| | - Elsken van der Wall
- Cancer Center, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Venu Raman
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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57
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Volpon L, Culjkovic-Kraljacic B, Sohn HS, Blanchet-Cohen A, Osborne MJ, Borden KLB. A biochemical framework for eIF4E-dependent mRNA export and nuclear recycling of the export machinery. RNA (NEW YORK, N.Y.) 2017; 23:927-937. [PMID: 28325843 PMCID: PMC5435865 DOI: 10.1261/rna.060137.116] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/09/2017] [Indexed: 05/26/2023]
Abstract
The eukaryotic translation initiation factor eIF4E acts in the nuclear export and translation of a subset of mRNAs. Both of these functions contribute to its oncogenic potential. While the biochemical mechanisms that underlie translation are relatively well understood, the molecular basis for eIF4E's role in mRNA export remains largely unexplored. To date, over 3000 transcripts, many encoding oncoproteins, were identified as potential nuclear eIF4E export targets. These target RNAs typically contain a ∼50-nucleotide eIF4E sensitivity element (4ESE) in the 3' UTR and a 7-methylguanosine cap on the 5' end. While eIF4E associates with the cap, an unknown factor recognizes the 4ESE element. We previously identified cofactors that functionally interacted with eIF4E in mammalian cell nuclei including the leucine-rich pentatricopeptide repeat protein LRPPRC and the export receptor CRM1/XPO1. LRPPRC simultaneously interacts with both eIF4E bound to the 5' mRNA cap and the 4ESE element in the 3' UTR. In this way, LRPPRC serves as a specificity factor to recruit 4ESE-containing RNAs within the nucleus. Further, we show that CRM1 directly binds LRPPRC likely acting as the export receptor for the LRPPRC-eIF4E-4ESE RNA complex. We also found that Importin 8, the nuclear importer for cap-free eIF4E, imports RNA-free LRPPRC, potentially providing both coordinated nuclear recycling of the export machinery and an important surveillance mechanism to prevent futile export cycles. Our studies provide the first biochemical framework for the eIF4E-dependent mRNA export pathway.
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Affiliation(s)
- Laurent Volpon
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillon Marcelle-Coutu, Chemin de Polytechnique, Montreal, Québec, H3T 1J4, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillon Marcelle-Coutu, Chemin de Polytechnique, Montreal, Québec, H3T 1J4, Canada
| | - Hye Seon Sohn
- Cancer Science Institute of Singapore and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Alexis Blanchet-Cohen
- Department of Human Genetics, Segal Cancer Centre and Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, H3T 1E2, Canada
| | - Michael J Osborne
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillon Marcelle-Coutu, Chemin de Polytechnique, Montreal, Québec, H3T 1J4, Canada
| | - Katherine L B Borden
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillon Marcelle-Coutu, Chemin de Polytechnique, Montreal, Québec, H3T 1J4, Canada
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58
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Pisignano G, Napoli S, Magistri M, Mapelli SN, Pastori C, Di Marco S, Civenni G, Albino D, Enriquez C, Allegrini S, Mitra A, D'Ambrosio G, Mello-Grand M, Chiorino G, Garcia-Escudero R, Varani G, Carbone GM, Catapano CV. A promoter-proximal transcript targeted by genetic polymorphism controls E-cadherin silencing in human cancers. Nat Commun 2017; 8:15622. [PMID: 28555645 PMCID: PMC5459991 DOI: 10.1038/ncomms15622] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 04/12/2017] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs are emerging players in the epigenetic machinery with key roles in development and diseases. Here we uncover a complex network comprising a promoter-associated noncoding RNA (paRNA), microRNA and epigenetic regulators that controls transcription of the tumour suppressor E-cadherin in epithelial cancers. E-cadherin silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter. A single nucleotide polymorphism (rs16260) linked to increased cancer risk alters the secondary structure of the paRNA, with the risk allele facilitating the assembly of the microRNA-guided Argonaute 1 complex and gene silencing. Collectively, these data demonstrate the role of a paRNA in E-cadherin regulation and the impact of a noncoding genetic variant on its function. Deregulation of paRNA-based epigenetic networks may contribute to cancer and other diseases making them promising targets for drug discovery.
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Affiliation(s)
- Giuseppina Pisignano
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Sara Napoli
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Marco Magistri
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Sarah N Mapelli
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Chiara Pastori
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Stefano Di Marco
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Gianluca Civenni
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Domenico Albino
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Claudia Enriquez
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Sara Allegrini
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Abhishek Mitra
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | | | | | - Giovanna Chiorino
- Laboratory of Cancer Genomics, Fondo Edo Tempia, Biella 13900, Italy
| | - Ramon Garcia-Escudero
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland.,Molecular Oncology Unit, CIEMAT and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid 28040, Spain
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - Giuseppina M Carbone
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Carlo V Catapano
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland.,Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne 1066, Switzerland
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59
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Yang X, Yang Y, Sun BF, Chen YS, Xu JW, Lai WY, Li A, Wang X, Bhattarai DP, Xiao W, Sun HY, Zhu Q, Ma HL, Adhikari S, Sun M, Hao YJ, Zhang B, Huang CM, Huang N, Jiang GB, Zhao YL, Wang HL, Sun YP, Yang YG. 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m 5C reader. Cell Res 2017; 27:606-625. [PMID: 28418038 PMCID: PMC5594206 DOI: 10.1038/cr.2017.55] [Citation(s) in RCA: 589] [Impact Index Per Article: 84.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 12/15/2022] Open
Abstract
5-methylcytosine (m5C) is a post-transcriptional RNA modification identified in both stable and highly abundant tRNAs and rRNAs, and in mRNAs. However, its regulatory role in mRNA metabolism is still largely unknown. Here, we reveal that m5C modification is enriched in CG-rich regions and in regions immediately downstream of translation initiation sites and has conserved, tissue-specific and dynamic features across mammalian transcriptomes. Moreover, m5C formation in mRNAs is mainly catalyzed by the RNA methyltransferase NSUN2, and m5C is specifically recognized by the mRNA export adaptor ALYREF as shown by in vitro and in vivo studies. NSUN2 modulates ALYREF's nuclear-cytoplasmic shuttling, RNA-binding affinity and associated mRNA export. Dysregulation of ALYREF-mediated mRNA export upon NSUN2 depletion could be restored by reconstitution of wild-type but not methyltransferase-defective NSUN2. Our study provides comprehensive m5C profiles of mammalian transcriptomes and suggests an essential role for m5C modification in mRNA export and post-transcriptional regulation.
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Affiliation(s)
- Xin Yang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China.,Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bao-Fa Sun
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu-Sheng Chen
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Wei Xu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China.,Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Yi Lai
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ang Li
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Wang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Devi Prasad Bhattarai
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Xiao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui-Ying Sun
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qin Zhu
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Li Ma
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Samir Adhikari
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Sun
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ya-Juan Hao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chun-Min Huang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Niu Huang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Gui-Bin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Liang Zhao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hai-Lin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ying-Pu Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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60
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Björk P, Wieslander L. Integration of mRNP formation and export. Cell Mol Life Sci 2017; 74:2875-2897. [PMID: 28314893 PMCID: PMC5501912 DOI: 10.1007/s00018-017-2503-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 12/13/2022]
Abstract
Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA–protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs. After release from the gene, the mRNPs move by diffusion within the interchromatin compartment, making up pools of mRNPs. Here, splicing and polyadenylation can be completed and the mRNPs recruit the major export receptor NXF1. Export competent mRNPs interact with the nuclear pore complex, leading to export, concomitant with compositional and conformational changes of the mRNPs. We summarize the integrated nuclear processes involved in the formation and export of mRNPs.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
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61
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Sesma A, Castresana C, Castellano MM. Regulation of Translation by TOR, eIF4E and eIF2α in Plants: Current Knowledge, Challenges and Future Perspectives. FRONTIERS IN PLANT SCIENCE 2017; 8:644. [PMID: 28491073 PMCID: PMC5405063 DOI: 10.3389/fpls.2017.00644] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/10/2017] [Indexed: 05/06/2023]
Abstract
An important step in eukaryotic gene expression is the synthesis of proteins from mRNA, a process classically divided into three stages, initiation, elongation, and termination. Translation is a precisely regulated and conserved process in eukaryotes. The presence of plant-specific translation initiation factors and the lack of well-known translational regulatory pathways in this kingdom nonetheless indicate how a globally conserved process can diversify among organisms. The control of protein translation is a central aspect of plant development and adaptation to environmental stress, but the mechanisms are still poorly understood. Here we discuss current knowledge of the principal mechanisms that regulate translation initiation in plants, with special attention to the singularities of this eukaryotic kingdom. In addition, we highlight the major recent breakthroughs in the field and the main challenges to address in the coming years.
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Affiliation(s)
- Ane Sesma
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
- Departamento Biotecnología y Biología Vegetal, Universidad Politécnica de MadridMadrid, Spain
| | - Carmen Castresana
- Centro Nacional de Biotecnología – Consejo Superior de Investigaciones Científicas (CSIC)Madrid, Spain
| | - M. Mar Castellano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
- *Correspondence: M. Mar Castellano,
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62
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Heerma van Voss MR, Schrijver WAME, Ter Hoeve ND, Hoefnagel LD, Manson QF, van der Wall E, Raman V, van Diest PJ. The prognostic effect of DDX3 upregulation in distant breast cancer metastases. Clin Exp Metastasis 2016; 34:85-92. [PMID: 27999982 PMCID: PMC5285427 DOI: 10.1007/s10585-016-9832-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/01/2016] [Indexed: 02/01/2023]
Abstract
Metastatic breast cancer remains one of the leading causes of death in women and identification of novel treatment targets is therefore warranted. Functional studies showed that the RNA helicase DDX3 promotes metastasis, but DDX3 expression was never studied in patient samples of metastatic cancer. In order to validate previous functional studies and to evaluate DDX3 as a potential therapeutic target, we investigated DDX3 expression in paired samples of primary and metastatic breast cancer. Samples from 79 breast cancer patients with distant metastases at various anatomical sites were immunohistochemically stained for DDX3. Both cytoplasmic and nuclear DDX3 expression were compared between primary and metastatic tumors. In addition, the correlation between DDX3 expression and overall survival was assessed. Upregulation of cytoplasmic (28%; OR 3.7; p = 0.002) was common in breast cancer metastases, especially in triple negative (TN) and high grade cases. High cytoplasmic DDX3 levels were most frequent in brain lesions (65%) and significantly correlated with high mitotic activity and triple negative subtype. In addition, worse overall survival was observed for patients with high DDX3 expression in the metastasis (HR 1.79, p = 0.039). Overall, we conclude that DDX3 expression is upregulated in distant breast cancer metastases, especially in the brain and in TN cases. In addition, high metastatic DDX3 expression correlates with worse survival, implying that DDX3 is a potential therapeutic target in metastatic breast cancer, in particular in the clinically important group of TN patients.
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Affiliation(s)
- Marise R Heerma van Voss
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Radiology and Radiological Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Natalie D Ter Hoeve
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Laurien D Hoefnagel
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Quirine F Manson
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elsken van der Wall
- Cancer Center, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Venu Raman
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Radiology and Radiological Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.,Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands. .,Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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63
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Borden KLB. The eukaryotic translation initiation factor eIF4E wears a "cap" for many occasions. ACTA ACUST UNITED AC 2016; 4:e1220899. [PMID: 28090419 PMCID: PMC5173310 DOI: 10.1080/21690731.2016.1220899] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/12/2016] [Accepted: 08/02/2016] [Indexed: 01/11/2023]
Abstract
The eukaryotic translation initiation factor eIF4E plays important roles in controlling the composition of the proteome. Indeed, dysregulation of eIF4E is associated with poor prognosis cancers. The traditional view has been that eIF4E acts solely in translation. However, over the last ∼25 years, eIF4E was found in the nucleus where it acts in mRNA export and in the last ∼10 years, eIF4E was found in cytoplasmic processing bodies (P-bodies) where it functions in mRNA sequestration and stability. The common biochemical thread for these activities is the ability of eIF4E to bind the 7-methylguanosine cap on the 5′ end of mRNAs. Recently, the possibility that eIF4E directly binds some mRNA elements independently of the cap has also been raised. Importantly, the effects of eIF4E are not genome-wide with a subset of transcripts targeted depending on the presence of specific mRNA elements and context-dependent regulatory factors. Indeed, eIF4E governs RNA regulons through co-regulating the expression of groups of transcripts acting in the same biochemical pathways. In addition, studies over the past ∼15 years indicate that there are multiple strategies that regulatory factors employ to modulate eIF4E activities in context-dependent manners. This perspective focuses on these new findings and incorporates them into a broader model for eIF4E function.
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Affiliation(s)
- Katherine L B Borden
- Department of Pathology and Cell Biology, Institute of Research in Immunology and Cancer (IRIC), Université de Montréal , Montreal, Québec, Canada
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64
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Importin 8 mediates m7G cap-sensitive nuclear import of the eukaryotic translation initiation factor eIF4E. Proc Natl Acad Sci U S A 2016; 113:5263-8. [PMID: 27114554 DOI: 10.1073/pnas.1524291113] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Regulation of nuclear-cytoplasmic trafficking of oncoproteins is critical for growth homeostasis. Dysregulated trafficking contributes to malignancy, whereas understanding the process can reveal unique therapeutic opportunities. Here, we focus on eukaryotic translation initiation factor 4E (eIF4E), a prooncogenic protein highly elevated in many cancers, including acute myeloid leukemia (AML). Typically, eIF4E is localized to both the nucleus and cytoplasm, where it acts in export and translation of specific methyl 7-guanosine (m(7)G)-capped mRNAs, respectively. Nuclear accumulation of eIF4E in patients who have AML is correlated with increased eIF4E-dependent export of transcripts encoding oncoproteins. The subcellular localization of eIF4E closely correlates with patients' responses. During clinical responses to the m(7)G-cap competitor ribavirin, eIF4E is mainly cytoplasmic. At relapse, eIF4E reaccumulates in the nucleus, leading to elevated eIF4E-dependent mRNA export. We have identified importin 8 as a factor that directly imports eIF4E into the nucleus. We found that importin 8 is highly elevated in untreated patients with AML, leading to eIF4E nuclear accumulation. Importin 8 only imports cap-free eIF4E. Cap-dependent changes to the structure of eIF4E underpin this selectivity. Indeed, m(7)G cap analogs or ribavirin prevents nuclear entry of eIF4E, which mirrors the trafficking phenotypes observed in patients with AML. Our studies also suggest that nuclear entry is important for the prooncogenic activity of eIF4E, at least in this context. These findings position nuclear trafficking of eIF4E as a critical step in its regulation and position the importin 8-eIF4E complex as a novel therapeutic target.
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65
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Sakaguchi N, Maeda K. Germinal Center B-Cell-Associated Nuclear Protein (GANP) Involved in RNA Metabolism for B Cell Maturation. Adv Immunol 2016; 131:135-86. [PMID: 27235683 DOI: 10.1016/bs.ai.2016.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Germinal center B-cell-associated nuclear protein (GANP) is upregulated in germinal center B cells against T-cell-dependent antigens in mice and humans. In mice, GANP depletion in B cells impairs antibody affinity maturation. Conversely, its transgenic overexpression augments the generation of high-affinity antigen-specific B cells. GANP associates with AID in the cytoplasm, shepherds AID into the nucleus, and augments its access to the rearranged immunoglobulin (Ig) variable (V) region of the genome in B cells, thereby precipitating the somatic hypermutation of V region genes. GANP is also upregulated in human CD4(+) T cells and is associated with APOBEC3G (A3G). GANP interacts with A3G and escorts it to the virion cores to potentiate its antiretroviral activity by inactivating HIV-1 genomic cDNA. Thus, GANP is characterized as a cofactor associated with AID/APOBEC cytidine deaminase family molecules in generating diversity of the IgV region of the genome and genetic alterations of exogenously introduced viral targets. GANP, encoded by human chromosome 21, as well as its mouse equivalent on chromosome 10, contains a region homologous to Saccharomyces Sac3 that was characterized as a component of the transcription/export 2 (TREX-2) complex and was predicted to be involved in RNA export and metabolism in mammalian cells. The metabolism of RNA during its maturation, from the transcription site at the chromosome within the nucleus to the cytoplasmic translation apparatus, needs to be elaborated with regard to acquired and innate immunity. In this review, we summarize the current knowledge on GANP as a component of TREX-2 in mammalian cells.
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Affiliation(s)
- N Sakaguchi
- WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan; Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
| | - K Maeda
- WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan; Laboratory of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
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66
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Nakano K, Watanabe T. HTLV-1 Rex Tunes the Cellular Environment Favorable for Viral Replication. Viruses 2016; 8:58. [PMID: 26927155 PMCID: PMC4810248 DOI: 10.3390/v8030058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/09/2016] [Accepted: 02/09/2016] [Indexed: 12/18/2022] Open
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) Rex is a viral RNA binding protein. The most important and well-known function of Rex is stabilizing and exporting viral mRNAs from the nucleus, particularly for unspliced/partially-spliced mRNAs encoding the structural proteins essential for viral replication. Without Rex, these unspliced viral mRNAs would otherwise be completely spliced. Therefore, Rex is vital for the translation of structural proteins and the stabilization of viral genomic RNA and, thus, for viral replication. Rex schedules the period of extensive viral replication and suppression to enter latency. Although the importance of Rex in the viral life-cycle is well understood, the underlying molecular mechanism of how Rex achieves its function has not been clarified. For example, how does Rex protect unspliced/partially-spliced viral mRNAs from the host cellular splicing machinery? How does Rex protect viral mRNAs, antigenic to eukaryotic cells, from cellular mRNA surveillance mechanisms? Here we will discuss these mechanisms, which explain the function of Rex as an organizer of HTLV-1 expression based on previously and recently discovered aspects of Rex. We also focus on the potential influence of Rex on the homeostasis of the infected cell and how it can exert its function.
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Affiliation(s)
- Kazumi Nakano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1, Shirokanedai, Minatoku, Tokyo 108-8639, Japan.
| | - Toshiki Watanabe
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1, Shirokanedai, Minatoku, Tokyo 108-8639, Japan.
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67
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Zhou H, Zhang J, Gu Y, Gan X, Gan Y, Zheng W, Kim BW, Xu X, Lu X, Dong Q, Zheng S, Huang W, Xu R. Identification of a novel RNA giant nuclear body in cancer cells. Oncotarget 2016; 7:4724-34. [PMID: 26678034 PMCID: PMC4826238 DOI: 10.18632/oncotarget.6619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/25/2015] [Indexed: 12/18/2022] Open
Abstract
Constitutive synthesis of oncogenic mRNAs is essential for maintaining the uncontrolled growth of cancer cells. However, little is known about how these mRNAs are exported from the nucleus to the cytoplasm. Here, we report the identification of a RNA giant nuclear body (RNA-GNB) that is abundant in cancer cells but rare in normal cells. The RNA-GNB contains a RNA core surrounded by a protein shell. We identify 782 proteins from cancer-associated RNA-GNBs, 40% of which are involved in the nuclear mRNA trafficking. RNA-GNB is required for cell proliferation, and its abundance is positively associated with tumor burden and outcome of therapies. Our findings suggest that the RNA-GNB is a novel nuclear RNA trafficking organelle that may contribute to the nuclear mRNA exporting and proliferation of cancer cells.
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Affiliation(s)
- Hong Zhou
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China.,Hangzhou First People's Hospital, Hangzhou 310006, China
| | - Jiawei Zhang
- Cancer Institute of Zhejiang University, Hangzhou 310009, China.,Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Ying Gu
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China.,Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Xiaoxian Gan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA.,Zhejiang Academy of Medical Sciences, Hangzhou 310012, China
| | - Yichao Gan
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China
| | - Weiwei Zheng
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China
| | - Byung-Wook Kim
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Xiaohua Xu
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Xiaoya Lu
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China
| | - Qi Dong
- Cancer Institute of Zhejiang University, Hangzhou 310009, China
| | - Shu Zheng
- Cancer Institute of Zhejiang University, Hangzhou 310009, China
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Rongzhen Xu
- Department of Hematology, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.,Cancer Institute of Zhejiang University, Hangzhou 310009, China
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68
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Abstract
The translation initiation factor eIF4E mediates a rate-limiting process that drives selective translation of many oncongenic proteins such as cyclin D1, survivin and VEGF, thereby contributing to tumour growth, metastasis and therapy resistance. As an essential regulatory hub in cancer signalling network, many oncogenic signalling pathways appear to converge on eIF4E. Therefore, targeting eIF4E-mediated cap-dependent translation is considered a promising anticancer strategy. This paper reviews the strategies that can be used to target eIF4E, highlighting agents that target eIF4E activity at each distinct level.
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69
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Ryu YH, Macdonald PM. RNA sequences required for the noncoding function of oskar RNA also mediate regulation of Oskar protein expression by Bicoid Stability Factor. Dev Biol 2015; 407:211-23. [PMID: 26433064 DOI: 10.1016/j.ydbio.2015.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/13/2015] [Accepted: 09/24/2015] [Indexed: 10/23/2022]
Abstract
The Drosophila oskar (osk) mRNA is unusual in having both coding and noncoding functions. As an mRNA, osk encodes a protein which is deployed specifically at the posterior of the oocyte. This spatially-restricted deployment relies on a program of mRNA localization and both repression and activation of translation, all dependent on regulatory elements located primarily in the 3' untranslated region (UTR) of the mRNA. The 3' UTR also mediates the noncoding function of osk, which is essential for progression through oogenesis. Mutations which most strongly disrupt the noncoding function are positioned in a short region (the C region) near the 3' end of the mRNA, in close proximity to elements required for activation of translation. We show that Bicoid Stability Factor (BSF) binds specifically to the C region of the mRNA. Both knockdown of bsf and mutation of BSF binding sites in osk mRNA have the same consequences: Osk expression is largely eliminated late in oogenesis, with both mRNA localization and translation disrupted. Although the C region of the osk 3' UTR is required for the noncoding function, BSF binding does not appear to be essential for that function.
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Affiliation(s)
- Young Hee Ryu
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Paul M Macdonald
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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70
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Tabe Y, Kojima K, Yamamoto S, Sekihara K, Matsushita H, Davis RE, Wang Z, Ma W, Ishizawa J, Kazuno S, Kauffman M, Shacham S, Fujimura T, Ueno T, Miida T, Andreeff M. Ribosomal Biogenesis and Translational Flux Inhibition by the Selective Inhibitor of Nuclear Export (SINE) XPO1 Antagonist KPT-185. PLoS One 2015; 10:e0137210. [PMID: 26340096 PMCID: PMC4560410 DOI: 10.1371/journal.pone.0137210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 08/13/2015] [Indexed: 01/01/2023] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive B-cell lymphoma characterized by the aberrant expression of several growth-regulating, oncogenic effectors. Exportin 1 (XPO1) mediates the nucleocytoplasmic transport of numerous molecules including oncogenic growth-regulating factors, RNAs, and ribosomal subunits. In MCL cells, the small molecule KPT-185 blocks XPO1 function and exerts anti-proliferative effects. In this study, we investigated the molecular mechanisms of this putative anti-tumor effect on MCL cells using cell growth/viability assays, immunoblotting, gene expression analysis, and absolute quantification proteomics. KPT-185 exhibited a p53-independent anti-lymphoma effect on MCL cells, by suppression of oncogenic mediators (e.g., XPO1, cyclin D1, c-Myc, PIM1, and Bcl-2 family members), repression of ribosomal biogenesis, and downregulation of translation/chaperone proteins (e.g., PIM2, EEF1A1, EEF2, and HSP70) that are part of the translational/transcriptional network regulated by heat shock factor 1. These results elucidate a novel mechanism in which ribosomal biogenesis appears to be a key component through which XPO1 contributes to tumor cell survival. Thus, we propose that the blockade of XPO1 could be a promising, novel strategy for the treatment of MCL and other malignancies overexpressing XPO1.
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Affiliation(s)
- Yoko Tabe
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
- Department of Clinical Laboratory Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kensuke Kojima
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
| | - Shinichi Yamamoto
- Department of Clinical Laboratory Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Leading Center for the Development and Research of Cancer Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kazumasa Sekihara
- Department of Clinical Laboratory Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Leading Center for the Development and Research of Cancer Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hiromichi Matsushita
- Department of Laboratory Medicine, Tokai University of Medicine, Kanagawa, Japan
| | - Richard Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
| | - Zhiqiang Wang
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
| | - Wencai Ma
- Department of Lymphoma and Myeloma, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
| | - Jo Ishizawa
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
| | - Saiko Kazuno
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Michael Kauffman
- Karyopharm Therapeutics Inc., Natick, MA, United States of America
| | - Sharon Shacham
- Karyopharm Therapeutics Inc., Natick, MA, United States of America
| | - Tsutomu Fujimura
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Takashi Ueno
- Laboratory of Proteomics and Biomolecular Science, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Takashi Miida
- Department of Clinical Laboratory Medicine, Biomedical Research Center Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States of America
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71
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Delaleau M, Borden KLB. Multiple Export Mechanisms for mRNAs. Cells 2015; 4:452-73. [PMID: 26343730 PMCID: PMC4588045 DOI: 10.3390/cells4030452] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 12/20/2022] Open
Abstract
Nuclear mRNA export plays an important role in gene expression. We describe the mechanisms of mRNA export including the importance of mRNP assembly, docking with the nuclear basket of the nuclear pore complex (NPC), transit through the central channel of the NPC and cytoplasmic release. We describe multiple mechanisms of mRNA export including NXF1 and CRM1 mediated pathways. Selective groups of mRNAs can be preferentially transported in order to respond to cellular stimuli. RNAs can be selected based on the presence of specific cis-acting RNA elements and binding of specific adaptor proteins. The role that dysregulation of this process plays in human disease is also discussed.
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Affiliation(s)
- Mildred Delaleau
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3C 3J7, Canada.
| | - Katherine L B Borden
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3C 3J7, Canada.
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72
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Osborne MJ, Borden KLB. The eukaryotic translation initiation factor eIF4E in the nucleus: taking the road less traveled. Immunol Rev 2015; 263:210-23. [PMID: 25510279 DOI: 10.1111/imr.12240] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The eukaryotic translation initiation factor eIF4E is a potent oncogene. Although eIF4E has traditional roles in translation initiation in the cytoplasm, it is also found in the nucleus, suggesting that it has activities beyond its role in protein synthesis. The road less traveled has been taken to study these nuclear activities and to understand their contribution to the oncogenic potential of eIF4E. The molecular features and biological pathways underpinning eIF4E's nuclear mRNA export are described. New classes of eIF4E regulators have been identified and their relevance to cancer shown. The studies presented here reveal the molecular, biophysical, and structural bases for eIF4E regulation. Finally, recent clinical work targeting eIF4E in acute myeloid leukemia patients with ribavirin is discussed. In summary, these findings provide a novel paradigm for eIF4E function and the molecular basis for targeting it in leukemia patients.
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Affiliation(s)
- Michael J Osborne
- Institute for Research in Immunology and Cancer & Dept. of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
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73
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Wickramasinghe VO, Laskey RA. Control of mammalian gene expression by selective mRNA export. Nat Rev Mol Cell Biol 2015; 16:431-42. [PMID: 26081607 DOI: 10.1038/nrm4010] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nuclear export of mRNAs is a crucial step in the regulation of gene expression, linking transcription in the nucleus to translation in the cytoplasm. Although important components of the mRNA export machinery are well characterized, such as transcription-export complexes TREX and TREX-2, recent work has shown that, in some instances, mammalian mRNA export can be selective and can regulate crucial biological processes such as DNA repair, gene expression, maintenance of pluripotency, haematopoiesis, proliferation and cell survival. Such findings show that mRNA export is an unexpected, yet potentially important, mechanism for the control of gene expression and of the mammalian transcriptome.
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Affiliation(s)
- Vihandha O Wickramasinghe
- Medical Research Centre (MRC) Cancer Unit, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Ronald A Laskey
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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74
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Lee ES, Akef A, Mahadevan K, Palazzo AF. The consensus 5' splice site motif inhibits mRNA nuclear export. PLoS One 2015; 10:e0122743. [PMID: 25826302 PMCID: PMC4380460 DOI: 10.1371/journal.pone.0122743] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 02/12/2015] [Indexed: 11/19/2022] Open
Abstract
In eukaryotes, mRNAs are synthesized in the nucleus and then exported to the cytoplasm where they are translated into proteins. We have mapped an element, which when present in the 3’terminal exon or in an unspliced mRNA, inhibits mRNA nuclear export. This element has the same sequence as the consensus 5’splice site motif that is used to define the start of introns. Previously it was shown that when this motif is retained in the mRNA, it causes defects in 3’cleavage and polyadenylation and promotes mRNA decay. Our new data indicates that this motif also inhibits nuclear export and promotes the targeting of transcripts to nuclear speckles, foci within the nucleus which have been linked to splicing. The motif, however, does not disrupt splicing or the recruitment of UAP56 or TAP/Nxf1 to the RNA, which are normally required for nuclear export. Genome wide analysis of human mRNAs, lncRNA and eRNAs indicates that this motif is depleted from naturally intronless mRNAs and eRNAs, but less so in lncRNAs. This motif is also depleted from the beginning and ends of the 3’terminal exons of spliced mRNAs, but less so for lncRNAs. Our data suggests that the presence of the 5’splice site motif in mature RNAs promotes their nuclear retention and may help to distinguish mRNAs from misprocessed transcripts and transcriptional noise.
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Affiliation(s)
- Eliza S. Lee
- Department of Biochemistry, University of Toronto, 1 King’s College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Abdalla Akef
- Department of Biochemistry, University of Toronto, 1 King’s College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Kohila Mahadevan
- Department of Biochemistry, University of Toronto, 1 King’s College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
| | - Alexander F. Palazzo
- Department of Biochemistry, University of Toronto, 1 King’s College Circle, MSB Room 5336, Toronto, ON, M5S 1A8, Canada
- * E-mail:
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75
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RNA Export through the NPC in Eukaryotes. Genes (Basel) 2015; 6:124-49. [PMID: 25802992 PMCID: PMC4377836 DOI: 10.3390/genes6010124] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/27/2015] [Accepted: 03/10/2015] [Indexed: 02/08/2023] Open
Abstract
In eukaryotic cells, RNAs are transcribed in the nucleus and exported to the cytoplasm through the nuclear pore complex. The RNA molecules that are exported from the nucleus into the cytoplasm include messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), micro RNAs (miRNAs), and viral mRNAs. Each RNA is transported by a specific nuclear export receptor. It is believed that most of the mRNAs are exported by Nxf1 (Mex67 in yeast), whereas rRNAs, snRNAs, and a certain subset of mRNAs are exported in a Crm1/Xpo1-dependent manner. tRNAs and miRNAs are exported by Xpot and Xpo5. However, multiple export receptors are involved in the export of some RNAs, such as 60S ribosomal subunit. In addition to these export receptors, some adapter proteins are required to export RNAs. The RNA export system of eukaryotic cells is also used by several types of RNA virus that depend on the machineries of the host cell in the nucleus for replication of their genome, therefore this review describes the RNA export system of two representative viruses. We also discuss the NPC anchoring-dependent mRNA export factors that directly recruit specific genes to the NPC.
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76
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Abstract
In eukaryotic organisms, the orthologs of the DEAD-box RNA helicase Ded1p from yeast and DDX3 from human form a well-defined subfamily that is characterized by high sequence conservation in their helicase core and their N- and C- termini. Individual members of this Ded1/DDX3 subfamily perform multiple functions in RNA metabolism in both nucleus and cytoplasm. Ded1/DDX3 subfamily members have also been implicated in cellular signaling pathways and are targeted by diverse viruses. In this review, we discuss the considerable body of work on the biochemistry and biology of these proteins, including the recently discovered link of human DDX3 to tumorigenesis.
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Affiliation(s)
- Deepak Sharma
- Center for RNA Molecular Biology & Department of Biochemistry, School of Medicine, Case Western Reserve University , Cleveland, OH , USA
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77
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Senissar M, Le Saux A, Belgareh-Touzé N, Adam C, Banroques J, Tanner NK. The DEAD-box helicase Ded1 from yeast is an mRNP cap-associated protein that shuttles between the cytoplasm and nucleus. Nucleic Acids Res 2014; 42:10005-22. [PMID: 25013175 PMCID: PMC4150762 DOI: 10.1093/nar/gku584] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 06/02/2014] [Accepted: 06/17/2014] [Indexed: 01/13/2023] Open
Abstract
The DEAD-box helicase Ded1 is an essential yeast protein that is closely related to mammalian DDX3 and to other DEAD-box proteins involved in developmental and cell cycle regulation. Ded1 is considered to be a translation-initiation factor that helps the 40S ribosome scan the mRNA from the 5' 7-methylguanosine cap to the AUG start codon. We used IgG pull-down experiments, mass spectrometry analyses, genetic experiments, sucrose gradients, in situ localizations and enzymatic assays to show that Ded1 is a cap-associated protein that actively shuttles between the cytoplasm and the nucleus. NanoLC-MS/MS analyses of purified complexes show that Ded1 is present in both nuclear and cytoplasmic mRNPs. Ded1 physically interacts with purified components of the nuclear CBC and the cytoplasmic eIF4F complexes, and its enzymatic activity is stimulated by these factors. In addition, we show that Ded1 is genetically linked to these factors. Ded1 comigrates with these proteins on sucrose gradients, but treatment with rapamycin does not appreciably alter the distribution of Ded1; thus, most of the Ded1 is in stable mRNP complexes. We conclude that Ded1 is an mRNP cofactor of the cap complex that may function to remodel the different mRNPs and thereby regulate the expression of the mRNAs.
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Affiliation(s)
- Meriem Senissar
- Expression Génétique Microbienne, CNRS FRE3630 (UPR9073), in association with Université Paris Diderot, Sorbonne Paris Cité, Paris 75005, France Université Paris-Sud, Ecole Doctorale 426 GGC, Orsay, France
| | - Agnès Le Saux
- Expression Génétique Microbienne, CNRS FRE3630 (UPR9073), in association with Université Paris Diderot, Sorbonne Paris Cité, Paris 75005, France
| | - Naïma Belgareh-Touzé
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, CNRS UMR8226 (FRE3354), UPMC, Paris 75005, France
| | - Céline Adam
- Expression Génétique Microbienne, CNRS FRE3630 (UPR9073), in association with Université Paris Diderot, Sorbonne Paris Cité, Paris 75005, France
| | - Josette Banroques
- Expression Génétique Microbienne, CNRS FRE3630 (UPR9073), in association with Université Paris Diderot, Sorbonne Paris Cité, Paris 75005, France
| | - N Kyle Tanner
- Expression Génétique Microbienne, CNRS FRE3630 (UPR9073), in association with Université Paris Diderot, Sorbonne Paris Cité, Paris 75005, France
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78
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Mitochondrion-associated protein LRPPRC suppresses the initiation of basal levels of autophagy via enhancing Bcl-2 stability. Biochem J 2013; 454:447-57. [PMID: 23822101 PMCID: PMC3778712 DOI: 10.1042/bj20130306] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mitochondrion-associated protein LRPPRC (leucine-rich pentatricopeptide repeat-containing) interacts with one of the microtubule-associated protein family members MAP1S (microtubule-associated protein 1 small form), originally named C19ORF5 (chromosome 19 open reading frame 5), to form a complex. MAP1S interacts with LC3 (light chain 3), the mammalian homologue of yeast autophagy marker ATG8 and one of the most important autophagy markers in mammalian cells, and helps the attachment of autophagosomes with microtubules for trafficking and recruitment of substrate mitochondria into autophagosomes for degradation. MAP1S activates autophagosomal biogenesis and degradation to remove misfolded/aggregated proteins and dysfunctional organelles such as mitochondria and suppress oxidative stress-induced genomic instability and tumorigenesis. Previously, various studies have attributed LRPPRC nucleic acid-associated functions. Instead, in the present study, we show that LRPPRC associates with mitochondria, interacts with Beclin 1 and Bcl-2 and forms a ternary complex to maintain the stability of Bcl-2. Suppression of LRPPRC leads to reduction in mitochondrial potential and reduction in Bcl-2. Lower levels of Bcl-2 lead to release of more Beclin 1 to form the Beclin 1–PI3KCIII (class III phosphoinositide 3-kinase) complex to activate autophagy and accelerate the turnover of dysfunctional mitochondria through the PI3K (phosphoinositide 3-kinase)/Akt/mTOR (mammalian target of rapamycin) pathway. The activation of autophagy induced by LRPPRC suppression occurs upstream of the ATG5–ATG12 conjugate-mediated conversion of LC3-I into LC3-II and has been confirmed in multiple mammalian cell lines with multiple autophagy markers including the size of GFP–LC3 punctate foci, the intensity of LC3-II and p62 protein and the size of the vacuolar structure. The activated autophagy enhances the removal of mitochondria through lysosomes. LRPPRC therefore acts to suppress the initiation of basal levels of autophagy to clean up dysfunctional mitochondria and other cellular debris during the normal cell cycle. Mitochondrial protein LRPPRC interacts with LC3-interactive microtubule-associated MAP1S and regulates autophagy. It interacts with Beclin 1 and Bcl-2 to form a ternary complex to maintain Bcl-2 stability. LRPPRC suppression enriches the Beclin 1-PI3KCIII complex to activate autophagy and mitophagy.
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79
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Gosselin P, Martineau Y, Morales J, Czjzek M, Glippa V, Gauffeny I, Morin E, Le Corguillé G, Pyronnet S, Cormier P, Cosson B. Tracking a refined eIF4E-binding motif reveals Angel1 as a new partner of eIF4E. Nucleic Acids Res 2013; 41:7783-92. [PMID: 23814182 PMCID: PMC3763552 DOI: 10.1093/nar/gkt569] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The initiation factor 4E (eIF4E) is implicated in most of the crucial steps of the mRNA life cycle and is recognized as a pivotal protein in gene regulation. Many of these roles are mediated by its interaction with specific proteins generally known as eIF4E-interacting partners (4E-IPs), such as eIF4G and 4E-BP. To screen for new 4E-IPs, we developed a novel approach based on structural, in silico and biochemical analyses. We identified the protein Angel1, a member of the CCR4 deadenylase family. Immunoprecipitation experiments provided evidence that Angel1 is able to interact in vitro and in vivo with eIF4E. Point mutation variants of Angel1 demonstrated that the interaction of Angel1 with eIF4E is mediated through a consensus eIF4E-binding motif. Immunofluorescence and cell fractionation experiments showed that Angel1 is confined to the endoplasmic reticulum and Golgi apparatus, where it partially co-localizes with eIF4E and eIF4G, but not with 4E-BP. Furthermore, manipulating Angel1 levels in living cells had no effect on global translation rates, suggesting that the protein has a more specific function. Taken together, our results illustrate that we developed a powerful method for identifying new eIF4E partners and open new perspectives for understanding eIF4E-specific regulation.
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Affiliation(s)
- Pauline Gosselin
- UPMC Univ Paris 06, UMR 7150, Mer et Santé, Station Biologique, F-29680 Roscoff, France, CNRS, UMR 7150, Mer et Santé, Station Biologique, F-29680 Roscoff, France. Université Européenne de Bretagne, Bretagne, Roscoff, France, INSERM, UMR 1037, Centre de Recherche en Cancérologie de Toulouse, Toulouse 31432, France, UPMC Univ Paris 06, UMR 7139, Végétaux Marins et Biomolécules, Station Biologique, F-29680 Roscoff, France, CNRS, UMR 7139, Végétaux Marins et Biomolécules, Station Biologique, F-29680 Roscoff, France, UPMC Univ Paris 06, FR2424, ABiMS, Station Biologique, F-29680 Roscoff, France and CNRS, FR2424, ABiMS, Station Biologique, F-29680 Roscoff, France
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80
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Lightowlers RN, Chrzanowska-Lightowlers ZMA. Human pentatricopeptide proteins: only a few and what do they do? RNA Biol 2013; 10:1433-8. [PMID: 23635806 PMCID: PMC3858426 DOI: 10.4161/rna.24770] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins constitute a large family of RNA-binding proteins that contain a canonical 35 residue repeat motif. Originally identified in Arabidopsis thaliana, family members are found in protists, fungi, and metazoan but are by far most abundant in plant organelles. Seven examples have been identified in human mitochondria and roles have been tentatively ascribed to each. In this review, we briefly outline each of these PPR proteins and discuss the role each is believed to play in facilitating mitochondrial gene expression.
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Affiliation(s)
- Robert N Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research; Institute for Cell and Molecular Biosciences; Newcastle University; The Medical School; Framlington Place; Newcastle upon Tyne, UK
| | - Zofia M A Chrzanowska-Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research; Institute for Ageing and Health; Newcastle University; The Medical School; Framlington Place; Newcastle upon Tyne, UK
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81
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Soto-Rifo R, Ohlmann T. The role of the DEAD-box RNA helicase DDX3 in mRNA metabolism. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:369-85. [PMID: 23606618 DOI: 10.1002/wrna.1165] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
DDX3 belongs to the DEAD-box proteins, a large family of ATP-dependent RNA helicases that participate in all aspects of RNA metabolism. Human DDX3 is a component of several messenger ribonucleoproteins that are found in the spliceosome, the export and the translation initiation machineries but also in different cytoplasmic mRNA granules. DDX3 has been involved in several cellular processes such as cell cycle progression, apoptosis, cancer, innate immune response, and also as a host factor for viral replication. Interestingly, not all these functions require the catalytic activities of DDX3 and thus, the precise roles of this apparently multifaceted protein remain largely obscure. The aim of this review is to provide a rapid and critical overview of the structure and functions of DDX3 with a particular emphasis on its role during mRNA metabolism.
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Affiliation(s)
- Ricardo Soto-Rifo
- Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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82
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Natalizio BJ, Wente SR. Postage for the messenger: designating routes for nuclear mRNA export. Trends Cell Biol 2013; 23:365-73. [PMID: 23583578 DOI: 10.1016/j.tcb.2013.03.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 01/22/2023]
Abstract
Transcription of mRNA occurs in the nucleus, making the translocation of mRNA across the nuclear envelope (NE) boundary a critical determinant of proper gene expression and cell survival. A major mRNA export route occurs via the NXF1-dependent pathway through the nuclear pore complexes (NPCs) embedded in the NE. However, recent findings have discovered new evidence supporting the existence of multiple mechanisms for crossing the NE, including both NPC-mediated and NE budding-mediated pathways. An analysis of the trans-acting factors and cis components that define these pathways reveals shared elements as well as mechanistic differences. We review here the current understanding of the mechanisms that characterize each pathway and highlight the determinants that influence mRNA transport fate.
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Affiliation(s)
- Barbara J Natalizio
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37323, USA
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83
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Culjkovic-Kraljacic B, Borden KLB. Aiding and abetting cancer: mRNA export and the nuclear pore. Trends Cell Biol 2013; 23:328-35. [PMID: 23582887 DOI: 10.1016/j.tcb.2013.03.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 12/21/2022]
Abstract
mRNA export is a critical step in gene expression. Export of transcripts can be modulated in response to cellular signaling or stress. Consistently, mRNA export is dysregulated in primary human specimens derived from many different forms of cancer. Aberrant expression of export factors can alter the export of specific transcripts encoding proteins involved in proliferation, survival, and oncogenesis. These specific factors, which are not used for bulk mRNA export, are obvious therapeutic targets. Indeed, given the emerging role of mRNA export in cancer, it is not surprising that efforts to target different aspects of this pathway have reached the clinical trial stage. Thus, like transcription and translation, mRNA export may also play a critical role in cancer genesis and maintenance.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montréal, Québec H3T 1J4, Canada
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84
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Carroll M, Borden KLB. The oncogene eIF4E: using biochemical insights to target cancer. J Interferon Cytokine Res 2013; 33:227-38. [PMID: 23472659 DOI: 10.1089/jir.2012.0142] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The eukaryotic translation initiation factor eIF4E is overexpressed in many human malignancies where it is typically a harbinger of poor prognosis. eIF4E is positioned as a nexus in post-transcriptional gene expression. To carry out these functions, eIF4E needs to bind the m(7)G cap moiety on mRNAs. It plays critical roles in mRNA translation, mRNA export, and most likely in mRNA stability as well. Through these activities, eIF4E coordinately modulates the expression of many transcripts involved in proliferation and survival. eIF4E function is controlled by interactions with protein cofactors in concert with many signaling pathways, including Ras, Mnk, Erk, MAPK, PI3K, mTOR, and Akt. This review describes the eIF4E activity and provides several examples of cellular control mechanisms. Further, we describe some therapeutic strategies in preclinical and clinical development.
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Affiliation(s)
- Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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85
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Duchêne AM, Giegé P. Dual localized mitochondrial and nuclear proteins as gene expression regulators in plants? FRONTIERS IN PLANT SCIENCE 2012; 3:221. [PMID: 23056004 PMCID: PMC3457046 DOI: 10.3389/fpls.2012.00221] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 09/10/2012] [Indexed: 05/29/2023]
Abstract
Mitochondria heavily depend on the coordinated expression of both mitochondrial and nuclear genomes because some of their most significant activities are held by multi-subunit complexes composed of both mitochondrial and nuclear encoded proteins. Thus, precise communication and signaling pathways are believed to exist between the two compartments. Proteins dual localized to both mitochondria and the nucleus make excellent candidates for a potential involvement in the envisaged communication. Here, we review the identified instances of dual localized nucleo-mitochondrial proteins with an emphasis on plant proteins and discuss their functions, which are seemingly mostly related to gene expression regulation. We discuss whether dual localization could be achieved by dual targeting and/or by re-localization and try to apprehend the signals required for the respective processes. Finally, we propose that in some instances, dual localized mitochondrial and nuclear proteins might act as retrograde signaling molecules for mitochondrial biogenesis.
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Affiliation(s)
| | - Philippe Giegé
- *Correspondence: Philippe Giegé, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, University of Strasbourg, 12 Rue du General Zimmer, 67084 Strasbourg, France. e-mail:
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86
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Culjkovic-Kraljacic B, Baguet A, Volpon L, Amri A, Borden KLB. The oncogene eIF4E reprograms the nuclear pore complex to promote mRNA export and oncogenic transformation. Cell Rep 2012; 2:207-15. [PMID: 22902403 DOI: 10.1016/j.celrep.2012.07.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 06/04/2012] [Accepted: 07/17/2012] [Indexed: 01/12/2023] Open
Abstract
The eukaryotic translation initiation factor eIF4E is a potent oncogene that promotes the nuclear export and translation of specific transcripts. Here, we have discovered that eIF4E alters the cytoplasmic face of the nuclear pore complex (NPC), which leads to enhanced mRNA export of eIF4E target mRNAs. Specifically, eIF4E substantially reduces the major component of the cytoplasmic fibrils of the NPC, RanBP2, relocalizes an associated nucleoporin, Nup214, and elevates RanBP1 and the RNA export factors, Gle1 and DDX19. Genetic or pharmacological inhibition of eIF4E impedes these effects. RanBP2 overexpression specifically inhibits the eIF4E mRNA export pathway and impairs oncogenic transformation by eIF4E. The RanBP2 cytoplasmic fibrils most likely slow the release and/or recycling of critical export factors to the nucleus. eIF4E overcomes this inhibitory mechanism by indirectly reducing levels of RanBP2. More generally, these results suggest that reprogramming the NPC is a means by which oncogenes can harness the proliferative capacity of the cell.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Québec, Canada
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87
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Rajyaguru P, Parker R. RGG motif proteins: modulators of mRNA functional states. Cell Cycle 2012; 11:2594-9. [PMID: 22767211 PMCID: PMC3873214 DOI: 10.4161/cc.20716] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A recent report demonstrates that a subset of RGG-motif proteins can bind translation initiation factor eIF4G and repress mRNA translation. This adds to the growing number of roles RGG-motif proteins play in modulating transcription, splicing, mRNA export and now translation. Herein, we review the nature and breadth of functions of RGG-motif proteins. In addition, the interaction of some RGG-motif proteins and other translation repressors with eIF4G highlights the role of eIF4G as a general modulator of mRNA function and not solely as a translation initiation factor.
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Affiliation(s)
- Purusharth Rajyaguru
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, The University of Arizona, Tucson, Tucson, AZ, USA
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88
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Schweitzer CJ, Matthews JM, Madson CJ, Donnellan MR, Cerny RL, Belshan M. Knockdown of the cellular protein LRPPRC attenuates HIV-1 infection. PLoS One 2012; 7:e40537. [PMID: 22808186 PMCID: PMC3395635 DOI: 10.1371/journal.pone.0040537] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 06/12/2012] [Indexed: 01/28/2023] Open
Abstract
HIV-1 exploits numerous host cellular pathways for productive infection. To identify novel factors involved in HIV-1 replication, HIV-1 integrase and matrix protein complexes were captured at 4 hours post infection for proteomic analysis using an affinity purification system. Leucine-rich PPR-motif containing (LRPPRC) protein, a cellular protein involved in mitochondrial function, cell metabolism, and cell-cycle progression was identified as one of the candidate HIV-1 factors. Co-immunoprecipitation RT-PCR experiments confirmed that LRPPRC associated with HIV-1 nucleic acids during the early steps of virus infection. To establish if LRPPRC was critical for HIV-1 infection, three independent LRPPRC knockdown cell lines were constructed (2.7, 3.6, and 4.1). Subcellular fractionation of these cell lines revealed differential knockdown of LRPPRC in subcellular compartments. LRPPRC was knocked down in the insoluble/cytoskeletal fractions of all three cell lines, but the 3.6 and 4.1 cells also showed a reduction in nuclear LRPPRC. Additionally, several cellular factors were downregulated and/or disrupted by loss of LRPPRC. HIV-1 infection was reduced in all three cell lines, but virus production and RNA encapsidation were unaffected, suggesting that LRPPRC was critical for the afferent stage of virus replication. Two of the three cell lines (3.6, 4.1) were refractory for murine leukemia virus infection, a virus dependent on cellular proliferation for productive infection. Consistent with this, these two cell lines exhibited reduced cellular growth with no loss of cellular viability or change in cell cycle phenotype. The early steps of virus infection were also differentially affected among the cell lines. A reduced level of preintegration complex formation was observed in all three cell lines, but viral DNA nuclear import was reduced only in the 3.6 and 4.1 cells. Combined, these data identify LRPPRC as a HIV-1 factor that is involved in HIV-1 replication through more than one mechanism.
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Affiliation(s)
- Cameron J. Schweitzer
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - John M. Matthews
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Christian J. Madson
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Meghan R. Donnellan
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Ronald L. Cerny
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- The Nebraska Center for Virology, Lincoln, Nebraska, United States of America
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
- The Nebraska Center for Virology, Lincoln, Nebraska, United States of America
- * E-mail:
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89
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Rajyaguru P, She M, Parker R. Scd6 targets eIF4G to repress translation: RGG motif proteins as a class of eIF4G-binding proteins. Mol Cell 2012; 45:244-54. [PMID: 22284680 DOI: 10.1016/j.molcel.2011.11.026] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 07/25/2011] [Accepted: 11/04/2011] [Indexed: 12/30/2022]
Abstract
The formation of mRNPs controls the interaction of the translation and degradation machinery with individual mRNAs. The yeast Scd6 protein and its orthologs regulate translation and mRNA degradation in yeast, C. elegans, D. melanogaster, and humans by an unknown mechanism. We demonstrate that Scd6 represses translation by binding the eIF4G subunit of eIF4F in a manner dependent on its RGG domain, thereby forming an mRNP repressed for translation initiation. Strikingly, several other RGG domain-containing proteins in yeast copurify with eIF4E/G and we demonstrate that two such proteins, Npl3 and Sbp1, also directly bind eIF4G and repress translation in a manner dependent on their RGG motifs. These observations identify the mechanism of Scd6 function through its RGG motif and indicate that eIF4G plays an important role as a scaffolding protein for the recruitment of translation repressors.
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Affiliation(s)
- Purusharth Rajyaguru
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
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90
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Abstract
Studies in the past several years highlight important features of the messenger RNA (mRNA) export process. For instance, groups of mRNAs acting in the same biochemical processes can be retained or exported in a coordinated manner thereby impacting on specific biochemistries and ultimately on cell physiology. mRNAs can be transported by either bulk export pathways involving NXF1/TAP or more specialized pathways involving chromosome region maintenance 1 (CRM1). Studies on primary tumor specimens indicate that many common and specialized mRNA export factors are dysregulated in cancer including CRM1, eukaryotic translation initiation factor 4E (eIF4E), HuR, nucleoporin 88, REF/Aly, and THO. This positions these pathways as potential therapeutic targets. Recently, specific targeting of the eIF4E-dependent mRNA export pathway in a phase II proof-of-principle trial with ribavirin led to impaired eIF4E-dependent mRNA export correlating with clinical responses including remissions in leukemia patients. Here, we provide an overview of these mRNA export pathways and highlight their relationship to cancer.
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Affiliation(s)
- Nadeem Siddiqui
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada
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91
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Liu L, Sanosaka M, Lei S, Bestwick ML, Frey JH, Surovtseva YV, Shadel GS, Cooper MP. LRP130 protein remodels mitochondria and stimulates fatty acid oxidation. J Biol Chem 2011; 286:41253-41264. [PMID: 21971050 PMCID: PMC3308838 DOI: 10.1074/jbc.m111.276121] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/21/2011] [Indexed: 11/06/2022] Open
Abstract
Impaired oxidative phosphorylation (OXPHOS) is implicated in several metabolic disorders. Even though mitochondrial DNA encodes several subunits critical for OXPHOS, the metabolic consequence of activating mitochondrial transcription remains unclear. We show here that LRP130, a protein involved in Leigh syndrome, increases hepatic β-fatty acid oxidation. Using convergent genetic and biochemical approaches, we demonstrate LRP130 complexes with the mitochondrial RNA polymerase to activate mitochondrial transcription. Activation of mitochondrial transcription is associated with increased OXPHOS activity, increased supercomplexes, and denser cristae, independent of mitochondrial biogenesis. Consistent with increased oxidative phosphorylation, ATP levels are increased in both cells and mouse liver, whereas coupled respiration is increased in cells. We propose activation of mitochondrial transcription remodels mitochondria and enhances oxidative metabolism.
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Affiliation(s)
- Lijun Liu
- Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Masato Sanosaka
- Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Shi Lei
- Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Megan L Bestwick
- Departments of Pathology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Joseph H Frey
- Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Yulia V Surovtseva
- Departments of Pathology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Gerald S Shadel
- Departments of Pathology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Marcus P Cooper
- Division of Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605.
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92
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Ruzzenente B, Metodiev MD, Wredenberg A, Bratic A, Park CB, Cámara Y, Milenkovic D, Zickermann V, Wibom R, Hultenby K, Erdjument-Bromage H, Tempst P, Brandt U, Stewart JB, Gustafsson CM, Larsson NG. LRPPRC is necessary for polyadenylation and coordination of translation of mitochondrial mRNAs. EMBO J 2011; 31:443-56. [PMID: 22045337 DOI: 10.1038/emboj.2011.392] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 09/30/2011] [Indexed: 11/09/2022] Open
Abstract
Regulation of mtDNA expression is critical for maintaining cellular energy homeostasis and may, in principle, occur at many different levels. The leucine-rich pentatricopeptide repeat containing (LRPPRC) protein regulates mitochondrial mRNA stability and an amino-acid substitution of this protein causes the French-Canadian type of Leigh syndrome (LSFC), a neurodegenerative disorder characterized by complex IV deficiency. We have generated conditional Lrpprc knockout mice and show here that the gene is essential for embryonic development. Tissue-specific disruption of Lrpprc in heart causes mitochondrial cardiomyopathy with drastic reduction in steady-state levels of most mitochondrial mRNAs. LRPPRC forms an RNA-dependent protein complex that is necessary for maintaining a pool of non-translated mRNAs in mammalian mitochondria. Loss of LRPPRC does not only decrease mRNA stability, but also leads to loss of mRNA polyadenylation and the appearance of aberrant mitochondrial translation. The translation pattern without the presence of LRPPRC is misregulated with excessive translation of some transcripts and no translation of others. Our findings point to the existence of an elaborate machinery that regulates mammalian mtDNA expression at the post-transcriptional level.
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Affiliation(s)
- Benedetta Ruzzenente
- Department of Mitochondrial Genetics, Max Planck Institute for Biology of Ageing, Cologne, Germany
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93
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Rackham O, Filipovska A. The role of mammalian PPR domain proteins in the regulation of mitochondrial gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:1008-16. [PMID: 22051507 DOI: 10.1016/j.bbagrm.2011.10.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 10/14/2011] [Accepted: 10/17/2011] [Indexed: 12/26/2022]
Abstract
Pentatricopeptide repeat (PPR) domain proteins are a large family of RNA-binding proteins that are involved in the maturation and translation of organelle transcripts in eukaryotes. They were first identified in plant organelles and their important role in mammalian mitochondrial gene regulation is now emerging. Mammalian PPR proteins, like their plant counterparts, have diverse roles in mitochondrial transcription, RNA metabolism and translation and consequently are important for mitochondrial function and cell health. Here we discuss the current knowledge about the seven mammalian PPR proteins identified to date and their roles in the regulation of mitochondrial gene expression. Furthermore we discuss the mitochondrial RNA targets of the mammalian PPR proteins and methods to investigate the RNA targets of these mitochondrial RNA-binding proteins. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Oliver Rackham
- Western Australian Institute for Medical Research and Centre for Medical Research, The University of Western Australia, Perth, WA 6000, Australia
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94
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Bratic A, Wredenberg A, Grönke S, Stewart JB, Mourier A, Ruzzenente B, Kukat C, Wibom R, Habermann B, Partridge L, Larsson NG. The bicoid stability factor controls polyadenylation and expression of specific mitochondrial mRNAs in Drosophila melanogaster. PLoS Genet 2011; 7:e1002324. [PMID: 22022283 PMCID: PMC3192837 DOI: 10.1371/journal.pgen.1002324] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 08/04/2011] [Indexed: 11/18/2022] Open
Abstract
The bicoid stability factor (BSF) of Drosophila melanogaster has been reported to be present in the cytoplasm, where it stabilizes the maternally contributed bicoid mRNA and binds mRNAs expressed from early zygotic genes. BSF may also have other roles, as it is ubiquitously expressed and essential for survival of adult flies. We have performed immunofluorescence and cell fractionation analyses and show here that BSF is mainly a mitochondrial protein. We studied two independent RNAi knockdown fly lines and report that reduced BSF protein levels lead to a severe respiratory deficiency and delayed development at the late larvae stage. Ubiquitous knockdown of BSF results in a severe reduction of the polyadenylation tail lengths of specific mitochondrial mRNAs, accompanied by an enrichment of unprocessed polycistronic RNA intermediates. Furthermore, we observed a significant reduction in mRNA steady state levels, despite increased de novo transcription. Surprisingly, mitochondrial de novo translation is increased and abnormal mitochondrial translation products are present in knockdown flies, suggesting that BSF also has a role in coordinating the mitochondrial translation in addition to its role in mRNA maturation and stability. We thus report a novel function of BSF in flies and demonstrate that it has an important intra-mitochondrial role, which is essential for maintaining mtDNA gene expression and oxidative phosphorylation. The majority of the cellular energy currency ATP is formed in a tubular network, termed mitochondria, present within virtually all eukaryotic cells. The mitochondria are unique among cellular organelles in that they contain their own genome, which encodes critical proteins necessary for cellular energy production. However, the vast majority of mitochondrial proteins are encoded in the nucleus and imported into mitochondria. Gene expression thus needs to be coordinated between the two genomes to ensure efficient mitochondrial function and sufficient adaptation to different physiological demands. The regulation of the mitochondrial genome is poorly understood, with many of the basic regulators not yet being characterized. We used RNAi in the fruit fly to study the in vivo function of the bicoid stability factor (BSF), previously thought to be a cytoplasmic and nuclear protein important for fly development. We show here that BSF is mainly localized to mitochondria, where it is essential for mtDNA gene expression, regulating the polyadenylation and maturation of specific mRNAs. Furthermore, BSF coordinates the translation and assembly of mitochondrial peptides in the inner mitochondrial membrane.
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Affiliation(s)
- Ana Bratic
- Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Anna Wredenberg
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | | | - Arnaud Mourier
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Christian Kukat
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Rolf Wibom
- Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden
| | | | - Linda Partridge
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nils-Göran Larsson
- Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- * E-mail:
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95
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Kühl I, Dujeancourt L, Gaisne M, Herbert CJ, Bonnefoy N. A genome wide study in fission yeast reveals nine PPR proteins that regulate mitochondrial gene expression. Nucleic Acids Res 2011; 39:8029-41. [PMID: 21727087 PMCID: PMC3185421 DOI: 10.1093/nar/gkr511] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are particularly numerous in plant mitochondria and chloroplasts, where they are involved in different steps of RNA metabolism, probably due to the repeated 35 amino acid PPR motifs that are thought to mediate interactions with RNA. In non-photosynthetic eukaryotes only a handful of PPR proteins exist, for example the human LRPPRC, which is involved in a mitochondrial disease. We have conducted a systematic study of the PPR proteins in the fission yeast Schizosaccharomyces pombe and identified, in addition to the mitochondrial RNA polymerase, eight proteins all of which localized to the mitochondria, and showed some association with the membrane. The absence of all but one of these PPR proteins leads to a respiratory deficiency and modified patterns of steady state mt-mRNAs or newly synthesized mitochondrial proteins. Some cause a general defect, whereas others affect specific mitochondrial RNAs, either coding or non-coding: cox1, cox2, cox3, 15S rRNA, atp9 or atp6, sometimes leading to secondary defects. Interestingly, the two possible homologs of LRPPRC, ppr4 and ppr5, play opposite roles in the expression of the cox1 mt-mRNA, ppr4 being the first mRNA-specific translational activator identified in S. pombe, whereas ppr5 appears to be a general negative regulator of mitochondrial translation.
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Affiliation(s)
- Inge Kühl
- Centre de Génétique Moléculaire du CNRS, UPR3404, FRC3115, Avenue de Terrasse, 91198 Gif-sur-Yvette Cedex, France
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96
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Rakovic A, Grünewald A, Voges L, Hofmann S, Orolicki S, Lohmann K, Klein C. PINK1-Interacting Proteins: Proteomic Analysis of Overexpressed PINK1. PARKINSONS DISEASE 2011; 2011:153979. [PMID: 21437181 PMCID: PMC3062077 DOI: 10.4061/2011/153979] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 12/22/2010] [Indexed: 11/20/2022]
Abstract
Recent publications suggest that the Parkinson's disease- (PD-) related PINK1/Parkin pathway promotes elimination of dysfunctional mitochondria by autophagy. We used tandem affinity purification (TAP), SDS-PAGE, and mass spectrometry as a first step towards identification of possible substrates for PINK1. The cellular abundance of selected identified interactors was investigated by Western blotting. Furthermore, one candidate gene was sequenced in 46 patients with atypical PD. In addition to two known binding partners (HSP90, CDC37), 12 proteins were identified using the TAP assay; four of which are mitochondrially localized (GRP75, HSP60, LRPPRC, and TUFM). Western blot analysis showed no differences in cellular abundance of these proteins comparing PINK1 mutant and control fibroblasts. When sequencing LRPPRC, four exonic synonymous changes and 20 polymorphisms in noncoding regions were detected. Our study provides a list of putative PINK1 binding partners, confirming previously described interactions, but also introducing novel mitochondrial proteins as potential components of the PINK1/Parkin mitophagy pathway.
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Affiliation(s)
- Aleksandar Rakovic
- Section of Clinical and Molecular Neurogenetics, Department of Neurology, University of Lübeck, Maria-Goeppert-Straße 1, 23562 Lübeck, Germany
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97
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Martin F, Barends S, Jaeger S, Schaeffer L, Prongidi-Fix L, Eriani G. Cap-assisted internal initiation of translation of histone H4. Mol Cell 2011; 41:197-209. [PMID: 21255730 DOI: 10.1016/j.molcel.2010.12.019] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 09/08/2010] [Accepted: 11/10/2010] [Indexed: 11/30/2022]
Abstract
In eukaryotes, a crucial step of translation initiation is the binding of the multifactor complex eIF4F to the 5' end of the mRNA, a prerequisite to recruitment of the activated small ribosomal 43S particle. Histone H4 mRNAs have short 5'UTRs, which do not conform to the conventional scanning-initiation model. Here we show that the ORF of histone mRNA contains two structural elements critical for translation initiation. One of the two structures binds eIF4E without the need of the cap. Ribosomal 43S particles become tethered to this site and directly loaded in the vicinity of the AUG. The other structure, 19 nucleotides downstream of the initiation codon, forms a three-way helix junction, which sequesters the m(7)G cap. This element facilitates direct positioning of the ribosome on the cognate start codon. This unusual translation initiation mode might be considered as a hybrid mechanism between the canonical and the IRES-driven translation initiation process.
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Affiliation(s)
- Franck Martin
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg CEDEX, France
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98
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Freire ER, Dhalia R, Moura DMN, da Costa Lima TD, Lima RP, Reis CRS, Hughes K, Figueiredo RCBQ, Standart N, Carrington M, de Melo Neto OP. The four trypanosomatid eIF4E homologues fall into two separate groups, with distinct features in primary sequence and biological properties. Mol Biochem Parasitol 2010; 176:25-36. [PMID: 21111007 DOI: 10.1016/j.molbiopara.2010.11.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 10/15/2010] [Accepted: 11/16/2010] [Indexed: 10/18/2022]
Abstract
Translation initiation in eukaryotes requires eIF4E, the cap binding protein, which mediates its function through an interaction with the scaffolding protein eIF4G, as part of the eIF4F complex. In trypanosomatids, four eIF4E homologues have been described but the specific function of each is not well characterized. Here, we report a study of these proteins in Trypanosoma brucei (TbEIF4E1 through 4). At the sequence level, they can be assigned to two groups: TbEIF4E1 and 2, similar in size to metazoan eIF4E1; and TbEIF4E3 and 4, with long N-terminal extensions. All are constitutively expressed, but whilst TbEIF4E1 and 2 localize to both the nucleus and cytoplasm, TbEIF4E3 and 4 are strictly cytoplasmic and are also more abundant. After knockdown through RNAi, TbEIF4E3 was the only homologue confirmed to be essential for viability of the insect procyclic form. In contrast, TbEIF4E1, 3 and 4 were all essential for the mammalian bloodstream form. Simultaneous RNAi knockdown of TbEIF4E1 and 2 caused cessation of growth and death in procyclics, but with a delayed impact on translation, whilst knockdown of TbEIF4E3 alone or a combined TbEIF4E1 and 4 knockdown led to substantial translation inhibition which preceded cellular death by several days, at least. Only TbEIF4E3 and 4 were found to interact with T. brucei eIF4G homologues; TbEIF4E3 bound both TbEIF4G3 and 4 whilst TbEIF4E4 bound only to TbEIF4G3. These results are consistent with TbEIF4E3 and 4 having distinct but relevant roles in initiation of protein synthesis.
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Affiliation(s)
- Eden R Freire
- Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Av. Moraes Rego s/n, Campus UFPE, Recife, PE 50670-420, Brazil
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99
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Topisirovic I, Svitkin YV, Sonenberg N, Shatkin AJ. Cap and cap-binding proteins in the control of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:277-98. [PMID: 21957010 DOI: 10.1002/wrna.52] [Citation(s) in RCA: 280] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The 5' mRNA cap structure is essential for efficient gene expression from yeast to human. It plays a critical role in all aspects of the life cycle of an mRNA molecule. Capping occurs co-transcriptionally on the nascent pre-mRNA as it emerges from the RNA exit channel of RNA polymerase II. The cap structure protects mRNAs from degradation by exonucleases and promotes transcription, polyadenylation, splicing, and nuclear export of mRNA and U-rich, capped snRNAs. In addition, the cap structure is required for the optimal translation of the vast majority of cellular mRNAs, and it also plays a prominent role in the expression of eukaryotic, viral, and parasite mRNAs. Cap-binding proteins specifically bind to the cap structure and mediate its functions in the cell. Two major cellular cap-binding proteins have been described to date: eukaryotic translation initiation factor 4E (eIF4E) in the cytoplasm and nuclear cap binding complex (nCBC), a nuclear complex consisting of a cap-binding subunit cap-binding protein 20 (CBP 20) and an auxiliary protein cap-binding protein 80 (CBP 80). nCBC plays an important role in various aspects of nuclear mRNA metabolism such as pre-mRNA splicing and nuclear export, whereas eIF4E acts primarily as a facilitator of mRNA translation. In this review, we highlight recent findings on the role of the cap structure and cap-binding proteins in the regulation of gene expression. We also describe emerging regulatory pathways that control mRNA capping and cap-binding proteins in the cell.
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Affiliation(s)
- Ivan Topisirovic
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montréal, QC, Canada
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100
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Sondheimer N, Fang JK, Polyak E, Falk MJ, Avadhani NG. Leucine-rich pentatricopeptide-repeat containing protein regulates mitochondrial transcription. Biochemistry 2010; 49:7467-73. [PMID: 20677761 DOI: 10.1021/bi1008479] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mitochondrial function depends upon the coordinated expression of the mitochondrial and nuclear genomes. Although the basal factors that carry out the process of mitochondrial transcription are known, the regulation of this process is incompletely understood. To further our understanding of mitochondrial gene regulation, we identified proteins that bound to the previously described point of termination for the major mRNA-coding transcript H2. One was the leucine-rich pentatricopeptide-repeat containing protein (LRPPRC), which has been linked to the French-Canadian variant of Leigh syndrome. Cells with reduced expression of LRPPRC had a reduction in oxygen consumption. The expression of mitochondrial mRNA and tRNA was dependent upon LRPPRC levels, but reductions in LRPPRC did not affect the expression of mitochondrial rRNA. Reduction of LRPPRC levels interfered with mitochondrial transcription in vitro but did not affect the stability of mitochondrial mRNAs or alter the expression of nuclear genes responsible for mitochondrial transcription in vivo. These findings demonstrate the control of mitochondrial mRNA synthesis by a protein that has an established role in regulating nuclear transcription and a link to mitochondrial disease.
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Affiliation(s)
- Neal Sondheimer
- Department of Pediatrics, The University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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