1
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Ghashghaei M, Liu Y, Ettles J, Bombaci G, Ramkumar N, Liu Z, Escano L, Miko SS, Kim Y, Waldron JA, Do K, MacPherson K, Yuen KA, Taibi T, Yue M, Arsalan A, Jin Z, Edin G, Karsan A, Morin GB, Kuchenbauer F, Perna F, Bushell M, Vu LP. Translation efficiency driven by CNOT3 subunit of the CCR4-NOT complex promotes leukemogenesis. Nat Commun 2024; 15:2340. [PMID: 38491013 PMCID: PMC10943099 DOI: 10.1038/s41467-024-46665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Protein synthesis is frequently deregulated during tumorigenesis. However, the precise contexts of selective translational control and the regulators of such mechanisms in cancer is poorly understood. Here, we uncovered CNOT3, a subunit of the CCR4-NOT complex, as an essential modulator of translation in myeloid leukemia. Elevated CNOT3 expression correlates with unfavorable outcomes in patients with acute myeloid leukemia (AML). CNOT3 depletion induces differentiation and apoptosis and delayed leukemogenesis. Transcriptomic and proteomic profiling uncovers c-MYC as a critical downstream target which is translationally regulated by CNOT3. Global analysis of mRNA features demonstrates that CNOT3 selectively influences expression of target genes in a codon usage dependent manner. Furthermore, CNOT3 associates with the protein network largely consisting of ribosomal proteins and translation elongation factors in leukemia cells. Overall, our work elicits the direct requirement for translation efficiency in tumorigenesis and propose targeting the post-transcriptional circuitry via CNOT3 as a therapeutic vulnerability in AML.
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Affiliation(s)
- Maryam Ghashghaei
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Yilin Liu
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, Canada
| | - James Ettles
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Giuseppe Bombaci
- Department of Medicine, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
| | - Niveditha Ramkumar
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Zongmin Liu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Leo Escano
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Sandra Spencer Miko
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Yerin Kim
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
- Bioinformatics program, University of British Columbia, Vancouver, Canada
| | - Joseph A Waldron
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kim Do
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyle MacPherson
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Katie A Yuen
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Thilelli Taibi
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Marty Yue
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Aaremish Arsalan
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Zhen Jin
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Glenn Edin
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Aly Karsan
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Gregg B Morin
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Florian Kuchenbauer
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Fabiana Perna
- Department of Medicine, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Moffit Cancer Center, Tampa, FL, USA
| | - Martin Bushell
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ly P Vu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada.
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2
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Reynaud K, McGeachy AM, Noble D, Meacham ZA, Ingolia NT. Surveying the global landscape of post-transcriptional regulators. Nat Struct Mol Biol 2023; 30:740-752. [PMID: 37231154 PMCID: PMC10279529 DOI: 10.1038/s41594-023-00999-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
Abstract
Numerous proteins regulate gene expression by modulating mRNA translation and decay. To uncover the full scope of these post-transcriptional regulators, we conducted an unbiased survey that quantifies regulatory activity across the budding yeast proteome and delineates the protein domains responsible for these effects. Our approach couples a tethered function assay with quantitative single-cell fluorescence measurements to analyze ~50,000 protein fragments and determine their effects on a tethered mRNA. We characterize hundreds of strong regulators, which are enriched for canonical and unconventional mRNA-binding proteins. Regulatory activity typically maps outside the RNA-binding domains themselves, highlighting a modular architecture that separates mRNA targeting from post-transcriptional regulation. Activity often aligns with intrinsically disordered regions that can interact with other proteins, even in core mRNA translation and degradation factors. Our results thus reveal networks of interacting proteins that control mRNA fate and illuminate the molecular basis for post-transcriptional gene regulation.
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Affiliation(s)
- Kendra Reynaud
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Anna M McGeachy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - David Noble
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Zuriah A Meacham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T Ingolia
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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3
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Wang P, Zhou J, Sun W, Li H, Rehman S, Xu C, Li D, Zhuge Q. Poplar CCR4-associated factor PtCAF1I is necessary for poplar development and defense response. Int J Biol Macromol 2023:125090. [PMID: 37247707 DOI: 10.1016/j.ijbiomac.2023.125090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023]
Abstract
Poplar is one of the most widely used tree species in afforestation projects. CCR4 associated factor 1 (CAF1) is a major member of CCR4-NOT and plays an important role in eukaryotic mRNA deadenylation. However, its role in poplar remains unclear. In this study, the full-length cDNA of the PtCAF1I gene was cloned from the poplar by screening the highly expressed PtCAF1I gene in the identified PtCAF1 gene family by poplar sterilization. PtCAF1I was localized in the nucleus. Through sequence alignment, it was found that the PtCAF1I sequence contains three motifs and is highly similar to the CAF1 protein sequence of other species. In the quantitative expression analysis of tissues, the expression of PtCAF1I in different tissues of Populus trichocarpa, 'Nanlin895', and Shanxinyang was not much different. In addition, the analysis of the expression of the PtCAF1I gene under different stress treatments showed that PtCAF1I responded to abscisic acid (ABA), salicylic acid (SA), methyl jasmonate (MeJA), NaCl, PEG6000, hydrogen peroxide (H2O2) and cold stress to different degrees. To study the potential biological functions of PtCAF1I, 6 transgenic lines were obtained through transformation using an Agrobacterium tumefaciens infection system. The transcriptome sequencing results showed that DEGs were mainly concentrated in pathways of phenylpropanoid biosynthesis, biosynthesis of secondary metabolites, carbon metabolism, and carotenoid biosynthesis. Compared with WT poplar, the contents of cellulose, hemicellulose, lignin, total sugar, and flavonoids, and the cell wall thickness of PtCAF1I overexpression poplars were significantly higher. Under Septotinia populiperda treatment, transgenic poplars clearly exhibited certain disease resistance. Meanwhile, upregulation of the expression of JA and SA pathway-related genes also contributed to improving the disease tolerance of transgenic poplar. In conclusion, our results suggest that PtCAF1I plays an important role in the growth and development of poplars and their resistance to pathogens.
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Affiliation(s)
- Pu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Jie Zhou
- Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Hongyan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Chen Xu
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Resource Utilization, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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4
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Hirano T, Wright D, Suzuki A, Saga Y. A cooperative mechanism of target RNA selection via germ-cell-specific RNA-binding proteins NANOS2 and DND1. Cell Rep 2022; 39:110894. [PMID: 35705038 DOI: 10.1016/j.celrep.2022.110894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 12/09/2021] [Accepted: 05/06/2022] [Indexed: 11/03/2022] Open
Abstract
The germ-cell-specific RNA-binding protein (RBP) NANOS2 plays a pivotal role in male gonocyte differentiation and spermatogonial stem cell maintenance. Although NANOS2 interacts with the CNOT deadenylation complex and Dead end 1 (DND1) to repress target RNAs, the molecular mechanisms underlying target mRNA selection remain unclear because of the limited cell resource in vivo. Here, we demonstrate that exogenous NANOS2-DND1 suppresses target mRNAs in somatic cells. Using this somatic cell system, we find that NANOS2 interacts with RNA-bound DND1 and recruits the CNOT complex to the mRNAs. However, a fusion construct composed of the CNOT1-binding site of NANOS2 (NIM) and DND1 fails to repress the target gene expression. Therefore, NANOS2 is required not only for recruitment of the CNOT complex but also for selecting the target mRNA with DND1. This study reveals that NANOS2 functions as a second-layer RBP for the target recognition and functional adaptation of DND1.
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Affiliation(s)
- Takamasa Hirano
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Mishima, Shizuoka 411-8582, Japan
| | - Danelle Wright
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Mishima, Shizuoka 411-8582, Japan; Department of Genetics, SOKENDAI, 1111 Mishima, Shizuoka 411-8582, Japan
| | - Atsushi Suzuki
- Division of Materials Science and Chemical Engineering, Graduate School of Engineering, Yokohama National University, Yokohama, Kanagawa 240-8501 Japan
| | - Yumiko Saga
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Mishima, Shizuoka 411-8582, Japan; Department of Genetics, SOKENDAI, 1111 Mishima, Shizuoka 411-8582, Japan; Division for Development of Genetic-Engineered Mouse Resource, Genetic Resource Center, National Institute of Genetics, 1111 Mishima, Shizuoka 411-8582, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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5
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Zhang Q, Pavanello L, Potapov A, Bartlam M, Winkler GS. Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements. Protein Sci 2022; 31:758-764. [PMID: 34923703 PMCID: PMC8862426 DOI: 10.1002/pro.4262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 11/11/2022]
Abstract
Regulated degradation of mature, cytoplasmic mRNA is a key step in eukaryotic gene regulation. This process is typically initiated by the recruitment of deadenylase enzymes by cis-acting elements in the 3' untranslated region resulting in the shortening and removal of the 3' poly(A) tail of the target mRNA. The Ccr4-Not complex, a major eukaryotic deadenylase, contains two exoribonuclease subunits with selectivity toward poly(A): Caf1 and Ccr4. The Caf1 deadenylase subunit binds the MIF4G domain of the large subunit CNOT1 (Not1) that is the scaffold of the complex. The Ccr4 nuclease is connected to the complex via its leucine-rich repeat (LRR) domain, which binds Caf1, whereas the catalytic activity of Ccr4 is provided by its EEP domain. While the relative positions of the MIF4G domain of CNOT1, the Caf1 subunit, and the LRR domain of Ccr4 are clearly defined in current models, the position of the EEP nuclease domain of Ccr4 is ambiguous. Here, we use X-ray crystallography, the AlphaFold resource of predicted protein structures, and pulse electron paramagnetic resonance spectroscopy to determine and validate the position of the EEP nuclease domain of Ccr4 resulting in an improved model of the human Ccr4-Not nuclease module.
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Affiliation(s)
- Qionglin Zhang
- Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
| | - Lorenzo Pavanello
- School of PharmacyUniversity of NottinghamNottinghamUK,Present address:
LifeArcStevenage Bioscience Catalyst Open Innovation CampusStevenageUK
| | - Alexey Potapov
- School of Physics and Astronomy, Sir Peter Mansfield Imaging CentreUniversity of NottinghamNottinghamUK
| | - Mark Bartlam
- Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjinChina
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6
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Hsieh FF, Korsunsky I, Shih AJ, Moss MA, Chatterjee PK, Deshpande J, Xue X, Madankumar S, Kumar G, Rochelson B, Metz CN. Maternal oxytocin administration modulates gene expression in the brains of perinatal mice. J Perinat Med 2022; 50:207-218. [PMID: 34717055 DOI: 10.1515/jpm-2020-0525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 10/01/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Oxytocin (OXT) is widely used to facilitate labor. However, little is known about the effects of perinatal OXT exposure on the developing brain. We investigated the effects of maternal OXT administration on gene expression in perinatal mouse brains. METHODS Pregnant C57BL/6 mice were treated with saline or OXT at term (n=6-7/group). Dams and pups were euthanized on gestational day (GD) 18.5 after delivery by C-section. Another set of dams was treated with saline or OXT (n=6-7/group) and allowed to deliver naturally; pups were euthanized on postnatal day 9 (PND9). Perinatal/neonatal brain gene expression was determined using Illumina BeadChip Arrays and real time quantitative PCR. Differential gene expression analyses were performed. In addition, the effect of OXT on neurite outgrowth was assessed using PC12 cells. RESULTS Distinct and sex-specific gene expression patterns were identified in offspring brains following maternal OXT administration at term. The microarray data showed that female GD18.5 brains exhibited more differential changes in gene expression compared to male GD18.5 brains. Specifically, Cnot4 and Frmd4a were significantly reduced by OXT exposure in male and female GD18.5 brains, whereas Mtap1b, Srsf11, and Syn2 were significantly reduced only in female GD18.5 brains. No significant microarray differences were observed in PND9 brains. By quantitative PCR, OXT exposure reduced Oxtr expression in female and male brains on GD18.5 and PND9, respectively. PC12 cell differentiation assays revealed that OXT induced neurite outgrowth. CONCLUSIONS Prenatal OXT exposure induces sex-specific differential regulation of several nervous system-related genes and pathways with important neural functions in perinatal brains.
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Affiliation(s)
- Frances F Hsieh
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.,Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology Stamford Hospital, Stamford, CT, USA
| | - Ilya Korsunsky
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA.,Division of Genetics, Department of Medicine at Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew J Shih
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Matthew A Moss
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Prodyot K Chatterjee
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Jaai Deshpande
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA.,Providence Community Health Center, Providence, RI, USA
| | - Xiangying Xue
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Swati Madankumar
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Gopal Kumar
- Elmezzi Graduate School of Molecular Medicine at Northwell Health, Manhasset, NY, USA
| | - Burton Rochelson
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Christine N Metz
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.,Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA.,Elmezzi Graduate School of Molecular Medicine at Northwell Health, Manhasset, NY, USA
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7
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Gillen SL, Giacomelli C, Hodge K, Zanivan S, Bushell M, Wilczynska A. Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization. Genome Biol 2021; 22:284. [PMID: 34615539 PMCID: PMC8496106 DOI: 10.1186/s13059-021-02494-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Regulation of protein output at the level of translation allows for a rapid adaptation to dynamic changes to the cell's requirements. This precise control of gene expression is achieved by complex and interlinked biochemical processes that modulate both the protein synthesis rate and stability of each individual mRNA. A major factor coordinating this regulation is the Ccr4-Not complex. Despite playing a role in most stages of the mRNA life cycle, no attempt has been made to take a global integrated view of how the Ccr4-Not complex affects gene expression. RESULTS This study has taken a comprehensive approach to investigate post-transcriptional regulation mediated by the Ccr4-Not complex assessing steady-state mRNA levels, ribosome position, mRNA stability, and protein production transcriptome-wide. Depletion of the scaffold protein CNOT1 results in a global upregulation of mRNA stability and the preferential stabilization of mRNAs enriched for G/C-ending codons. We also uncover that mRNAs targeted to the ER for their translation have reduced translational efficiency when CNOT1 is depleted, specifically downstream of the signal sequence cleavage site. In contrast, translationally upregulated mRNAs are normally localized in p-bodies, contain disorder-promoting amino acids, and encode nuclear localized proteins. Finally, we identify ribosome pause sites that are resolved or induced by the depletion of CNOT1. CONCLUSIONS We define the key mRNA features that determine how the human Ccr4-Not complex differentially regulates mRNA fate and protein synthesis through a mechanism linked to codon composition, amino acid usage, and mRNA localization.
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Affiliation(s)
- Sarah L Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- MRC Toxicology Unit, Lancaster Road, Leicester, LE1 9HN, UK
| | - Chiara Giacomelli
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Kelly Hodge
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Sara Zanivan
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - Ania Wilczynska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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8
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Hsieh HH, Chen YA, Chang YJ, Wang HH, Yu YH, Lin SW, Huang YJ, Lin S, Chang CJ. The functional characterization of phosphorylation of tristetraprolin at C-terminal NOT1-binding domain. JOURNAL OF INFLAMMATION-LONDON 2021; 18:22. [PMID: 34090459 PMCID: PMC8180021 DOI: 10.1186/s12950-021-00288-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/20/2021] [Indexed: 12/26/2022]
Abstract
Background Tristetraprolin (TTP) family proteins contain conserved tandem CCCH zinc-finger binding to AU-rich elements and C-terminal NOT1-binding domain. TTP is phosphorylated extensively in cells, and its mRNA destabilization activity is regulated by protein phosphorylation. Methods We generated an antibody against phospho-Serine316 located at the C-terminal NOT1-binding site and examined TTP phosphorylation in LPS-stimulated RAW264.7 cells. Knockout of TTP was created in RAW264.7 cells using CRISPR/Cas9 gene editing to explore TTP functions. Results We demonstrated that Ser316 was phosphorylated by p90 ribosomal S6 kinase 1 (RSK1) and p38-activated protein kinase (MK2) and dephosphorylated by Protein Phosphatase 2A (PP2A). A phosphorylation-mimic mutant of S316D resulted in dissociation with the CCR4-NOT deadenylase complex through weakening interaction with CNOT1. Furthermore, Ser316 and serines 52 and 178 were independently contributed to the CCR4-NOT complex recruitment in the immunoprecipitation assay using phosphor-mimic mutants. In RAW264.7 macrophages, TTP was induced, and Ser316 was phosphorylated through RSK1 and MK2 by LPS stimulation. Knockout of TTP resulted in TNFα mRNA increased due to mRNA stabilization. Overexpression of non-phosphorylated S316A TTP mutant can restore TTP activity and lead to TNFα mRNA decreased. GST pull-down and RNA pull-down analyses demonstrated that endogenous TTP with Ser316 phosphorylation decreased the interaction with CNOT1. Conclusions Our results suggest that the TTP-mediated mRNA stability is modulated by Ser316 phosphorylation via regulating the TTP interaction with the CCR4-NOT deadenylase complex. Supplementary Information The online version contains supplementary material available at 10.1186/s12950-021-00288-2.
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Affiliation(s)
- Hsin-Hui Hsieh
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan
| | - Yen-An Chen
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan
| | - Yao-Jen Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hsin-Hui Wang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Pediatrics, Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ya-Han Yu
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yin-Jung Huang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Steven Lin
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ching-Jin Chang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan. .,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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9
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Wang P, Li L, Wei H, Sun W, Zhou P, Zhu S, Li D, Zhuge Q. Genome-Wide and Comprehensive Analysis of the Multiple Stress-Related CAF1 (CCR4-Associated Factor 1) Family and Its Expression in Poplar. PLANTS 2021; 10:plants10050981. [PMID: 34068989 PMCID: PMC8155972 DOI: 10.3390/plants10050981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/06/2023]
Abstract
Poplar is one of the most widely used tree in afforestation projects. However, it is susceptible to abiotic and biotic stress. CCR4-associated factor 1 (CAF1) is a major member of CCR4-NOT, and it is mainly involved in transcriptional regulation and mRNA degradation in eukaryotes. However, there are no studies on the molecular phylogeny and expression of the CAF1 gene in poplar. In this study, a total of 19 PtCAF1 genes were identified in the Populus trichocarpa genome. Phylogenetic analysis of the PtCAF1 gene family was performed with two closely related species (Arabidopsis thaliana and Oryza sativa) to investigate the evolution of the PtCAF1 gene. The tissue expression of the PtCAF1 gene showed that 19 PtCAF1 genes were present in different tissues of poplar. Additionally, the analysis of the expression of the PtCAF1 gene showed that the CAF1 family was up-regulated to various degrees under biotic and abiotic stresses and participated in the poplar stress response. The results of our study provide a deeper understanding of the structure and function of the PtCAF1 gene and may contribute to our understanding of the molecular basis of stress tolerance in poplar.
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10
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The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
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11
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Swickley G, Bloch Y, Malka L, Meiri A, Noy-Lotan S, Yanai A, Tamary H, Motro B. Characterization of the interactions between Codanin-1 and C15Orf41, two proteins implicated in congenital dyserythropoietic anemia type I disease. BMC Mol Cell Biol 2020; 21:18. [PMID: 32293259 PMCID: PMC7092493 DOI: 10.1186/s12860-020-00258-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/04/2020] [Indexed: 12/30/2022] Open
Abstract
Background Congenital dyserythropoietic anemia type I (CDA I), is an autosomal recessive disease with macrocytic anemia in which erythroid precursors in the bone marrow exhibit pathognomonic abnormalities including spongy heterochromatin and chromatin bridges. We have shown previously that the gene mutated in CDA I encodes Codanin-1, a ubiquitously expressed and evolutionarily conserved large protein. Recently, an additional etiologic factor for CDA I was reported, C15Orf41, a predicted nuclease. Mutations in both CDAN1 and C15Orf41 genes results in very similar erythroid phenotype. However, the possible relationships between these two etiologic factors is not clear. Results We demonstrate here that Codanin-1 and C15Orf41 bind to each other, and that Codanin-1 stabilizes C15Orf41. C15Orf41 protein is mainly nuclear and Codanin-1 overexpression shifts it to the cytoplasm. Phylogenetic analyses demonstrated that even though Codanin-1 is an essential protein in mammals, it was lost from several diverse and unrelated animal taxa. Interestingly, C15Orf41 was eliminated in the exact same animal taxa. This is an extreme case of the Phylogenetic Profiling phenomenon, which strongly suggests common pathways for these two proteins. Lastly, as the 3D structure is more conserved through evolution than the protein sequence, we have used the Phyre2 alignment program to find structurally homologous proteins. We found that Codanin-1 is highly similar to CNOT1, a conserved protein which serves as a scaffold for proteins involved in mRNA stability and transcriptional control. Conclusions The physical interaction and the stabilization of C15Orf41 by Codanin-1, combined with the phylogenetic co-existence and co-loss of these two proteins during evolution, suggest that the major function of the presumptive scaffold protein, Codanin-1, is to regulate C15Orf41 activities. The similarity between Codanin-1 and CNOT1 suggest that Codanin-1 is involved in RNA metabolism and activity, and opens up a new avenue for the study of the molecular pathways affected in CDAI.
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Affiliation(s)
- Grace Swickley
- The Mina and Everard Goodman faculty of life sciences Bar-Ilan University, 52900, Ramat-Gan, Israel
| | - Yehoshua Bloch
- The Mina and Everard Goodman faculty of life sciences Bar-Ilan University, 52900, Ramat-Gan, Israel
| | - Lidor Malka
- The Mina and Everard Goodman faculty of life sciences Bar-Ilan University, 52900, Ramat-Gan, Israel
| | - Adi Meiri
- The Mina and Everard Goodman faculty of life sciences Bar-Ilan University, 52900, Ramat-Gan, Israel
| | - Sharon Noy-Lotan
- Hematology/Oncology Department, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Amiel Yanai
- The Mina and Everard Goodman faculty of life sciences Bar-Ilan University, 52900, Ramat-Gan, Israel
| | - Hannah Tamary
- Hematology/Oncology Department, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Felsenstain Medical Research Center, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Benny Motro
- The Mina and Everard Goodman faculty of life sciences Bar-Ilan University, 52900, Ramat-Gan, Israel.
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12
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A Quantitative Genetic Interaction Map of HIV Infection. Mol Cell 2020; 78:197-209.e7. [PMID: 32084337 DOI: 10.1016/j.molcel.2020.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/10/2020] [Accepted: 02/02/2020] [Indexed: 12/16/2022]
Abstract
We have developed a platform for quantitative genetic interaction mapping using viral infectivity as a functional readout and constructed a viral host-dependency epistasis map (vE-MAP) of 356 human genes linked to HIV function, comprising >63,000 pairwise genetic perturbations. The vE-MAP provides an expansive view of the genetic dependencies underlying HIV infection and can be used to identify drug targets and study viral mutations. We found that the RNA deadenylase complex, CNOT, is a central player in the vE-MAP and show that knockout of CNOT1, 10, and 11 suppressed HIV infection in primary T cells by upregulating innate immunity pathways. This phenotype was rescued by deletion of IRF7, a transcription factor regulating interferon-stimulated genes, revealing a previously unrecognized host signaling pathway involved in HIV infection. The vE-MAP represents a generic platform that can be used to study the global effects of how different pathogens hijack and rewire the host during infection.
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Che X, Zhao R, Xu H, Liu X, Zhao S, Ma H. Differently Expressed Genes (DEGs) Relevant to Type 2 Diabetes Mellitus Identification and Pathway Analysis via Integrated Bioinformatics Analysis. Med Sci Monit 2019; 25:9237-9244. [PMID: 31797865 PMCID: PMC6909911 DOI: 10.12659/msm.918407] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The aim of this study was to evaluate the differently expressed genes (DEGs) relevant to type 2 diabetes mellitus (T2DM) and pathway by performing integrated bioinformatics analysis. MATERIAL AND METHODS The gene expression datasets GSE7014 and GSE29221 were downloaded in GEO database, and DEGs from type 2 diabetes mellitus and normal skeletal muscle tissues were identified. Biological function analysis of the DEGs was enriched by GO and KEEG pathway. A PPI network for the identified DEGs was built using the STRING database. RESULTS Thirty top DEGs were identified from 2 datasets: GSE7014 and GSE29221. Of the 30 top DEGs, 20 were up-regulated and 10 were down-regulated. The 20 up-regulated genes were enriched in regulation of mRNA, protein biding, and phospholipase D signaling pathway. The 10 down-regulated genes were enriched in telomere maintenance via semi-conservative replication, AGE-RAGE signaling pathway in diabetic complications, and insulin resistance pathway. In the PPI network of 20 up-regulated DEGs, there were 40 nodes and 84 edges, with an average node degree of 4.2. For the 10 down-regulated DEGs, we found a total of 30 nodes and 105 edges, with an average node degree of 7.0 and local clustering coefficient of 0.812. Among the 30 DEGs, 10 hub genes (CNOT6L, CNOT6, CNOT1, CNOT7, RQCD1, RFC2, PRIM1, RFC4, RFC5, and RFC1) were also identified through Cytoscape. CONCLUSIONS DEGs of T2DM may play an essential role in disease development and may be potential pathogeneses of T2DM.
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Affiliation(s)
- Xuanqiang Che
- Department of Endocrinology, Fifth People's Hospital of Jinan, Jinan, Shandong, China (mainland)
| | - Ran Zhao
- Department of Endocrinology, Fifth People's Hospital of Jinan, Jinan, Shandong, China (mainland)
| | - Hua Xu
- Department of Endocrinology, Fifth People's Hospital of Jinan, Jinan, Shandong, China (mainland)
| | - Xue Liu
- Department of Endocrinology, Fifth People's Hospital of Jinan, Jinan, Shandong, China (mainland)
| | - Shumiao Zhao
- Department of Endocrinology, Fifth People's Hospital of Jinan, Jinan, Shandong, China (mainland)
| | - Hongwei Ma
- Department of Endocrinology, Fifth People's Hospital of Jinan, Jinan, Shandong, China (mainland)
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The central region of CNOT1 and CNOT9 stimulates deadenylation by the Ccr4-Not nuclease module. Biochem J 2018; 475:3437-3450. [PMID: 30309886 DOI: 10.1042/bcj20180456] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022]
Abstract
Regulated degradation of cytoplasmic mRNA is important for the accurate execution of gene expression programmes in eukaryotic cells. A key step in this process is the shortening and removal of the mRNA poly(A) tail, which can be achieved by the recruitment of the multi-subunit Ccr4-Not nuclease complex via sequence-specific RNA-binding proteins or the microRNA machinery. The Ccr4-Not complex contains several modules that are attached to its large subunit CNOT1. Modules include the nuclease module, which associates with the MIF4G domain of CNOT1 and contains the catalytic subunits Caf1 and Ccr4, as well as the module containing the non-catalytic CNOT9 subunit, which binds to the DUF3819 domain of CNOT1. To understand the contributions of the individual modules to the activity of the complex, we have started to reconstitute sub-complexes of the human Ccr4-Not complex containing one or several functional modules. Here, we report the reconstitution of a pentameric complex including a BTG2-Caf1-Ccr4 nuclease module, CNOT9 and the central region of CNOT1 encompassing the MIF4G and DUF3819 domains. By comparing the biochemical activities of the pentameric complex and the nuclease module, we conclude that the CNOT1-CNOT9 components stimulate deadenylation by the nuclease module. In addition, we show that a pentameric complex containing the melanoma-associated CNOT9 P131L variant is able to support deadenylation similar to a complex containing the wild-type CNOT9 protein.
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Chicco D, Palluzzi F, Masseroli M. Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:954-965. [PMID: 28436884 DOI: 10.1109/tcbb.2017.2695459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biomolecular controlled annotations have become pivotal in computational biology, because they allow scientists to analyze large amounts of biological data to better understand test results, and to infer new knowledge. Yet, biomolecular annotation databases are incomplete by definition, like our knowledge of biology, and might contain errors and inconsistent information. In this context, machine-learning algorithms able to predict and prioritize new annotations are both effective and efficient, especially if compared with time-consuming trials of biological validation. To limit the possibility that these techniques predict obvious and trivial high-level features, and to help prioritize their results, we introduce a new element that can improve accuracy and relevance of the results of an annotation prediction and prioritization pipeline. We propose a novelty indicator able to state the level of "originality" of the annotations predicted for a specific gene to Gene Ontology (GO) terms. This indicator, joint with our previously introduced prediction steps, helps by prioritizing the most novel interesting annotations predicted. We performed an accurate biological functional analysis of the prioritized annotations predicted with high accuracy by our indicator and previously proposed methods. The relevance of our biological findings proves effectiveness and trustworthiness of our indicator and of its prioritization of predicted annotations.
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16
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Goossens J, De Geyter N, Walton A, Eeckhout D, Mertens J, Pollier J, Fiallos-Jurado J, De Keyser A, De Clercq R, Van Leene J, Gevaert K, De Jaeger G, Goormachtig S, Goossens A. Isolation of protein complexes from the model legume Medicago truncatula by tandem affinity purification in hairy root cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:476-489. [PMID: 27377668 DOI: 10.1111/tpj.13258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/21/2016] [Accepted: 06/30/2016] [Indexed: 05/26/2023]
Abstract
Tandem affinity purification coupled to mass spectrometry (TAP-MS) is one of the most powerful techniques to isolate protein complexes and elucidate protein interaction networks. Here, we describe the development of a TAP-MS strategy for the model legume Medicago truncatula, which is widely studied for its ability to produce valuable natural products and to engage in endosymbiotic interactions. As biological material, transgenic hairy roots, generated through Agrobacterium rhizogenes-mediated transformation of M. truncatula seedlings, were used. As proof of concept, proteins involved in the cell cycle, transcript processing and jasmonate signalling were chosen as bait proteins, resulting in a list of putative interactors, many of which confirm the interologue concept of protein interactions, and which can contribute to biological information about the functioning of these bait proteins in planta. Subsequently, binary protein-protein interactions among baits and preys, and among preys were confirmed by a systematic yeast two-hybrid screen. Together, by establishing a M. truncatula TAP-MS platform, we extended the molecular toolbox of this model species.
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Affiliation(s)
- Jonas Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Nathan De Geyter
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alan Walton
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jan Mertens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jennifer Fiallos-Jurado
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Annick De Keyser
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
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CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State. Stem Cell Reports 2016; 7:897-910. [PMID: 27746116 PMCID: PMC5106518 DOI: 10.1016/j.stemcr.2016.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 01/07/2023] Open
Abstract
Poly(A) tail length and mRNA deadenylation play important roles in gene regulation. However, how they regulate embryonic development and pluripotent cell fate is not fully understood. Here we present evidence that CNOT3-dependent mRNA deadenylation governs the pluripotent state. We show that CNOT3, a component of the Ccr4-Not deadenylase complex, is required for mouse epiblast maintenance. It is highly expressed in blastocysts and its deletion leads to peri-implantation lethality. The epiblast cells in Cnot3 deletion embryos are quickly lost during diapause and fail to outgrow in culture. Mechanistically, CNOT3 C terminus is required for its interaction with the complex and its function in embryonic stem cells (ESCs). Furthermore, Cnot3 deletion results in increases in the poly(A) tail lengths, half-lives, and steady-state levels of differentiation gene mRNAs. The half-lives of CNOT3 target mRNAs are shorter in ESCs and become longer during normal differentiation. Together, we propose that CNOT3 maintains the pluripotent state by promoting differentiation gene mRNA deadenylation and degradation, and we identify poly(A) tail-length regulation as a post-transcriptional mechanism that controls pluripotency. CNOT3 is required for mouse epiblast maintenance during early development CNOT3 C-terminal domain is necessary for the maintenance of the pluripotent state CNOT3 promotes differentiation gene mRNA deadenylation and degradation mRNA poly(A) tail regulation plays a critical role in pluripotency
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18
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Abstract
In a recent issue of Nature Communications Ukleja and co‐workers reported a cryo‐EM 3D reconstruction of the Ccr4‐Not complex from Schizosaccharomyces pombe with an immunolocalization of the different subunits. The newly gained architectural knowledge provides cues to apprehend the functional diversity of this major eukaryotic regulator. Indeed, in the cytoplasm alone, Ccr4‐Not regulates translational repression, decapping and deadenylation, and the Not module additionally plays a positive role in translation. The spatial distribution of the subunits within the structure is compatible with a model proposing that the Ccr4‐Not complex interacts with the 5′ and 3′ ends of target mRNAs, allowing different functional modules of the complex to act at different stages of the translation process, possibly within a circular constellation of the mRNA. This work opens new avenues, and reveals important gaps in our understanding regarding structure and mode of function of the Ccr4‐Not complex that need to be addressed in the future.
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Affiliation(s)
- Zoltan Villanyi
- Faculty of Medicine, Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics Geneva, Geneva, Switzerland
| | - Martine A Collart
- Faculty of Medicine, Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics Geneva, Geneva, Switzerland.
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19
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Ukleja M, Valpuesta JM, Dziembowski A, Cuellar J. Beyond the known functions of the CCR4-NOT complex in gene expression regulatory mechanisms: New structural insights to unravel CCR4-NOT mRNA processing machinery. Bioessays 2016; 38:1048-58. [PMID: 27502453 DOI: 10.1002/bies.201600092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Large protein assemblies are usually the effectors of major cellular processes. The intricate cell homeostasis network is divided into numerous interconnected pathways, each controlled by a set of protein machines. One of these master regulators is the CCR4-NOT complex, which ultimately controls protein expression levels. This multisubunit complex assembles around a scaffold platform, which enables a wide variety of well-studied functions from mRNA synthesis to transcript decay, as well as other tasks still being identified. Solving the structure of the entire CCR4-NOT complex will help to define the distribution of its functions. The recently published three-dimensional reconstruction of the complex, in combination with the known crystal structures of some of the components, has begun to address this. Methodological improvements in structural biology, especially in cryoelectron microscopy, encourage further structural and protein-protein interaction studies, which will advance our comprehension of the gene expression machinery.
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Affiliation(s)
- Marta Ukleja
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland. .,Faculty of Biology, Department of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland. .,Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain. .,Institute of Structural and Molecular Biology, University College London and Birkbeck, London, UK.
| | - José María Valpuesta
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, Department of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Jorge Cuellar
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
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20
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Tristetraprolin as a Therapeutic Target in Inflammatory Disease. Trends Pharmacol Sci 2016; 37:811-821. [PMID: 27503556 DOI: 10.1016/j.tips.2016.07.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 11/22/2022]
Abstract
Members of the tristetraprolin (TTP) family of RNA-binding proteins are found in all major eukaryotic groups. TTP family members, from plants through humans, can bind adenosine-uridine rich elements in target mRNAs with high affinity. In mammalian cells, these proteins then promote deadenylation and decay of target transcripts. Four such proteins are found in mice, of which the best studied is TTP. When the gene encoding TTP is disrupted in mice, the animals develop a severe syndrome of arthritis, autoimmunity, cachexia, dermatitis, and myeloid hyperplasia. Conversely, recent overexpression studies have demonstrated protection against several experimental models of immune inflammatory disease. This endogenous anti-inflammatory protein could serve as the basis for novel approaches to therapy of similar conditions in humans.
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21
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Stigliani S, Scaruffi P, Lagazio C, Persico L, Carlini B, Varesio L, Morandi F, Morini M, Gigliotti AR, Esposito MR, Viscardi E, Cecinati V, Conte M, Corrias MV. Deregulation of focal adhesion pathway mediated by miR-659-3p is implicated in bone marrow infiltration of stage M neuroblastoma patients. Oncotarget 2016; 6:13295-308. [PMID: 25980492 PMCID: PMC4537015 DOI: 10.18632/oncotarget.3745] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/08/2015] [Indexed: 11/25/2022] Open
Abstract
To get insights on the metastatic process of human neuroblastoma (NB), the miRNA expression profile of bone marrow (BM)-infiltrating cells has been determined and compared to that of primary tumors.Twenty-two BM-infiltrating cells, 22 primary tumors, and 4 paired samples from patients with metastatic NB aged > 12 months were analyzed for the expression of 670 miRNAs by stem-loop RT-qPCR. The miRNAs whose expression was significantly different were subjected to selection criteria, and 20 selected miRNAs were tested in 10 additional BM-infiltrating cells and primary tumors. Among the miRNAs confirmed to be differentially expressed, miR-659-3p was further analyzed. Transfection of miR-659-3p mimic and inhibitor demonstrated the specific suppression and over-expression, respectively, of the miR-659-3p target gene CNOT1, a regulator of transcription of genes containing AU-rich element (ARE) sequence. Among the ARE-containing genes, miR-659-3p mimic and inhibitor specifically modified the expression of AKT3, BCL2, CYR61 and THSB2, belonging to the focal adhesion pathway. Most importantly, in BM-infiltrating cells CNOT1 expression was significantly higher, and that of AKT3, BCL2, THSB2 and CYR61 was significantly lower than in primary tumors. Thus, our study suggests a role of the focal adhesion pathway, regulated by miR-659-3p through CNOT1, in the human NB metastatic process.
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Affiliation(s)
- Sara Stigliani
- U.O.S. Physiopathology of Human Reproduction, IRCCS A.O.U. San Martino-IST, Genova, Italy
| | - Paola Scaruffi
- U.O.S. Physiopathology of Human Reproduction, IRCCS A.O.U. San Martino-IST, Genova, Italy
| | | | - Luca Persico
- Department of Economy, University of Genoa, Genova, Italy
| | - Barbara Carlini
- Laboratory of Oncology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Luigi Varesio
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Fabio Morandi
- Laboratory of Oncology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Anna Rita Gigliotti
- Epidemiology, Biostatistics and Committees Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Maria Rosaria Esposito
- Neuroblastoma Laboratory, Pediatric Research Institute, Fondazione Città della Speranza, Padova, Italy
| | - Elisabetta Viscardi
- Pediatric Hematology and Oncology Division, Padova University Hospital, Padova, Italy
| | - Valerio Cecinati
- UOS Divisione Oncoematologia Pediatrica, Ospedale Civile di Pescara, Pescara, Italy
| | - Massimo Conte
- Oncology Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
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Stupfler B, Birck C, Séraphin B, Mauxion F. BTG2 bridges PABPC1 RNA-binding domains and CAF1 deadenylase to control cell proliferation. Nat Commun 2016; 7:10811. [PMID: 26912148 PMCID: PMC4773420 DOI: 10.1038/ncomms10811] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/24/2016] [Indexed: 12/12/2022] Open
Abstract
While BTG2 plays an important role in cellular differentiation and cancer, its precise molecular function remains unclear. BTG2 interacts with CAF1 deadenylase through its APRO domain, a defining feature of BTG/Tob factors. Our previous experiments revealed that expression of BTG2 promoted mRNA poly(A) tail shortening through an undefined mechanism. Here we report that the APRO domain of BTG2 interacts directly with the first RRM domain of the poly(A)-binding protein PABPC1. Moreover, PABPC1 RRM and BTG2 APRO domains are sufficient to stimulate CAF1 deadenylase activity in vitro in the absence of other CCR4–NOT complex subunits. Our results unravel thus the mechanism by which BTG2 stimulates mRNA deadenylation, demonstrating its direct role in poly(A) tail length control. Importantly, we also show that the interaction of BTG2 with the first RRM domain of PABPC1 is required for BTG2 to control cell proliferation. BTG2 promotes mRNA poly(A) tail shortening and regulates cellular differentiation. Here, Stupfler et al. show that the BTG2 APRO domain interacts with PABPC1 RRM1, allowing the former to recruit and stimulate the poly(A) tail shortening activity of CAF1 deadenylase and to control cell proliferation.
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Affiliation(s)
- Benjamin Stupfler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Catherine Birck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Fabienne Mauxion
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
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23
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Collart MA. The Ccr4-Not complex is a key regulator of eukaryotic gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:438-54. [PMID: 26821858 PMCID: PMC5066686 DOI: 10.1002/wrna.1332] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/07/2015] [Accepted: 12/10/2015] [Indexed: 12/22/2022]
Abstract
The Ccr4‐Not complex is a multisubunit complex present in all eukaryotes that contributes to regulate gene expression at all steps, from production of messenger RNAs (mRNAs) in the nucleus to their degradation in the cytoplasm. In the nucleus it influences the post‐translational modifications of the chromatin template that has to be remodeled for transcription, it is present at sites of transcription and associates with transcription factors as well as with the elongating polymerase, it interacts with the factors that prepare the new transcript for export to the cytoplasm and finally is important for nuclear quality control and influences mRNA export. In the cytoplasm it is present in polysomes where mRNAs are translated and in RNA granules where mRNAs will be redirected upon inhibition of translation. It influences mRNA translatability, and is needed during translation, on one hand for co‐translational protein interactions and on the other hand to preserve translation that stalls. It is one of the relevant players during co‐translational quality control. It also interacts with factors that will repress translation or induce mRNA decapping when recruited to the translating template. Finally, Ccr4‐Not carries deadenylating enzymes and is a key player in mRNA decay, generic mRNA decay that follows normal translation termination, co‐translational mRNA decay of transcripts on which the ribosomes stall durably or which carry a non‐sense mutation and finally mRNA decay that is induced by external signaling for a change in genetic programming. Ccr4‐Not is a master regulator of eukaryotic gene expression. WIREs RNA 2016, 7:438–454. doi: 10.1002/wrna.1332 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Martine A Collart
- Department Microbiology and Molecular Medicine, CMU, Geneva, Switzerland.,Institute of Genetics and Genomics, Geneva, Switzerland
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24
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The architecture of the Schizosaccharomyces pombe CCR4-NOT complex. Nat Commun 2016; 7:10433. [PMID: 26804377 PMCID: PMC4737751 DOI: 10.1038/ncomms10433] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 12/11/2015] [Indexed: 11/08/2022] Open
Abstract
CCR4-NOT is a large protein complex present both in cytoplasm and the nucleus of eukaryotic cells. Although it is involved in a variety of distinct processes related to expression of genetic information such as poly(A) tail shortening, transcription regulation, nuclear export and protein degradation, there is only fragmentary information available on some of its nine subunits. Here we show a comprehensive structural characterization of the native CCR4-NOT complex from Schizosaccharomyces pombe. Our cryo-EM 3D reconstruction of the complex, combined with techniques such as immunomicroscopy, RNA-nanogold labelling, docking of the available high-resolution structures and models of different subunits and domains, allow us to propose its full molecular architecture. We locate all functionally defined domains endowed with deadenylating and ubiquitinating activities, the nucleus-specific RNA-interacting subunit Mmi1, as well as surfaces responsible for protein–protein interactions. This information provides insight into cooperation of the different CCR4-NOT complex functions. CCR4-NOT is a protein complex involved in a variety of important genetic processes. Here, the authors report the mid-resolution structure of this complex, and model the positions and contacts between the subunits, providing structural support for the previously reported functions of the complex.
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25
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Waghray S, Williams C, Coon JJ, Wickens M. Xenopus CAF1 requires NOT1-mediated interaction with 4E-T to repress translation in vivo. RNA (NEW YORK, N.Y.) 2015; 21:1335-45. [PMID: 26015597 PMCID: PMC4478352 DOI: 10.1261/rna.051565.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/22/2015] [Indexed: 05/25/2023]
Abstract
RNA-regulatory factors bound to 3' UTRs control translation and stability. Repression often is associated with poly(A) removal. The deadenylase CAF1 is a core component of the CCR4-NOT complex. Our prior studies established that CAF1 represses translation independent of deadenylation. We sought the mechanism of its deadenylation-independent repression in Xenopus oocytes. Our data reveal a chain of interacting proteins that links CAF1 to CCR4-NOT and to Xp54 and 4E-T. Association of CAF1 with NOT1, the major subunit of CCR4-NOT, is required for repression by CAF1 tethered to a reporter mRNA. Affinity purification-mass spectrometry and coimmunoprecipitation revealed that at least five members of the CCR4-NOT complex were recruited by CAF1. The recruitment of these proteins required NOT1, as did the ability of tethered CAF1 to repress translation. In turn, NOT1 was needed to recruit Xp54 and 4E-T. We examined the role of 4E-T in repression using mutations that disrupted either eIF4E-dependent or -independent mechanisms. Expression of a 4E-T truncation that still bound eIF4E alleviated repression by tethered CAF1, NOT1, and Xp54. In contrast, a mutant 4E-T that failed to bind eIF4E did not. Repression of global translation was affected only by the eIF4E-dependent mechanism. Reporters bearing IRES elements revealed that repression via tethered CAF1 and Xp54 is cap- and eIF4E-independent, but requires one or more of eIF4A, eIF4B, and eIF4G. We propose that RNA-binding proteins, and perhaps miRNAs, repress translation through an analogous chain of interactions that begin with the 3' UTR-bound repressor and end with the noncanonical activity of 4E-T.
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Affiliation(s)
- Shruti Waghray
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Clay Williams
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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26
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The enzyme activities of Caf1 and Ccr4 are both required for deadenylation by the human Ccr4-Not nuclease module. Biochem J 2015; 469:169-76. [PMID: 25944446 PMCID: PMC4613498 DOI: 10.1042/bj20150304] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/06/2015] [Indexed: 01/02/2023]
Abstract
In eukaryotic cells, the shortening and removal of the poly(A) tail (deadenylation) of cytoplasmic mRNA is a key event in regulated mRNA degradation. A major enzyme involved in deadenylation is the Ccr4-Not deadenylase complex, which can be recruited to its target mRNA by RNA-binding proteins or the miRNA repression complex. In addition to six non-catalytic components, the complex contains two enzymatic subunits with ribonuclease activity: Ccr4 and Caf1 (Pop2). In vertebrates, each deadenylase subunit is encoded by two paralogues: Caf1, which can interact with the anti-proliferative protein BTG2, is encoded by CNOT7 and CNOT8, whereas Ccr4 is encoded by the highly similar genes CNOT6 and CNOT6L. Currently, it is unclear whether the catalytic subunits work co-operatively or whether the nuclease components have unique roles in deadenylation. We therefore developed a method to express and purify a minimal human BTG2-Caf1-Ccr4 nuclease sub-complex from bacterial cells. By using chemical inhibition and well-characterized inactivating amino acid substitutions, we demonstrate that the enzyme activities of Caf1 and Ccr4 are both required for deadenylation in vitro. These results indicate that Caf1 and Ccr4 cooperate in mRNA deadenylation and suggest that the enzyme activities of Caf1 and Ccr4 are regulated via allosteric interactions within the nuclease module.
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27
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Suzuki Y, Arae T, Green PJ, Yamaguchi J, Chiba Y. AtCCR4a and AtCCR4b are Involved in Determining the Poly(A) Length of Granule-bound starch synthase 1 Transcript and Modulating Sucrose and Starch Metabolism in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2015; 56:863-74. [PMID: 25630334 DOI: 10.1093/pcp/pcv012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/21/2015] [Indexed: 05/11/2023]
Abstract
Removing the poly(A) tail is the first and rate-limiting step of mRNA degradation and apparently an effective step not only for modulating mRNA stability but also for translation of many eukaryotic transcripts. Carbon catabolite repressor 4 (CCR4) has been identified as a major cytoplasmic deadenylase in Saccharomyces cerevisiae. The Arabidopsis thaliana homologs of the yeast CCR4, AtCCR4a and AtCCR4b, were identified by sequence-based analysis; however, their role and physiological significance in plants remain to be elucidated. In this study, we revealed that AtCCR4a and AtCCR4b are localized to cytoplasmic mRNA processing bodies, which are specific granules consisting of many enzymes involved in mRNA turnover. Double mutants of AtCCR4a and AtCCR4b exhibited tolerance to sucrose application but not to glucose. The levels of sucrose in the seedlings of the atccr4a/4b double mutants were reduced, whereas no difference was observed in glucose levels. Further, amylose levels were slightly but significantly increased in the atccr4a/4b double mutants. Consistent with this observation, we found that the transcript encoding granule-bound starch synthase 1 (GBSS1), which is responsible for amylose synthesis, is accumulated to a higher level in the atccr4a/4b double mutant plants than in the control plants. Moreover, we revealed that GBSS1 has a longer poly(A) tail in the double mutant than in the control plant, suggesting that AtCCR4a and AtCCR4b can influence the poly(A) length of transcripts related to starch metabolism. Our results collectively suggested that AtCCR4a and AtCCR4b are involved in sucrose and starch metabolism in A. thaliana.
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Affiliation(s)
- Yuya Suzuki
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Toshihiro Arae
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Pamela J Green
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Junji Yamaguchi
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Yukako Chiba
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan JST PRESTO, Kawaguchi, 332-0012 Japan
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28
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Chen L, Chu C, Kong X, Huang T, Cai YD. Discovery of new candidate genes related to brain development using protein interaction information. PLoS One 2015; 10:e0118003. [PMID: 25635857 PMCID: PMC4311913 DOI: 10.1371/journal.pone.0118003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/03/2015] [Indexed: 12/18/2022] Open
Abstract
Human brain development is a dramatic process composed of a series of complex and fine-tuned spatiotemporal gene expressions. A good comprehension of this process can assist us in developing the potential of our brain. However, we have only limited knowledge about the genes and gene functions that are involved in this biological process. Therefore, a substantial demand remains to discover new brain development-related genes and identify their biological functions. In this study, we aimed to discover new brain-development related genes by building a computational method. We referred to a series of computational methods used to discover new disease-related genes and developed a similar method. In this method, the shortest path algorithm was executed on a weighted graph that was constructed using protein-protein interactions. New candidate genes fell on at least one of the shortest paths connecting two known genes that are related to brain development. A randomization test was then adopted to filter positive discoveries. Of the final identified genes, several have been reported to be associated with brain development, indicating the effectiveness of the method, whereas several of the others may have potential roles in brain development.
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Affiliation(s)
- Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People’s Republic of China
| | - Chen Chu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People’s Republic of China
| | - Xiangyin Kong
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People’s Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People’s Republic of China
- * E-mail: (TH); (YDC)
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai 200444, People’s Republic of China
- * E-mail: (TH); (YDC)
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