1
|
Yamagishi R, Inagaki H, Suzuki J, Hosoda N, Sugiyama H, Tomita K, Hotta T, Hoshino SI. Concerted action of ataxin-2 and PABPC1-bound mRNA poly(A) tail in the formation of stress granules. Nucleic Acids Res 2024; 52:9193-9209. [PMID: 38869059 PMCID: PMC11347130 DOI: 10.1093/nar/gkae497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
Stress induces global stabilization of the mRNA poly(A) tail (PAT) and the assembly of untranslated poly(A)-tailed mRNA into mRNPs that accumulate in stress granules (SGs). While the mechanism behind stress-induced global PAT stabilization has recently emerged, the biological significance of PAT stabilization under stress remains elusive. Here, we demonstrate that stress-induced PAT stabilization is a prerequisite for SG formation. Perturbations in PAT length impact SG formation; PAT shortening, achieved by overexpressing mRNA deadenylases, inhibits SG formation, whereas PAT lengthening, achieved by overexpressing their dominant negative mutants or downregulating deadenylases, promotes it. PABPC1, which specifically binds to the PAT, is crucial for SG formation. Complementation analyses reveal that the PABC/MLLE domain of PABPC1, responsible for binding PAM2 motif-containing proteins, plays a key role. Among them, ataxin-2 is a known SG component. A dominant-negative approach reveals that the PAM2 motif of ataxin-2 is essential for SG formation. Notably, ataxin-2 increases stress sensitivity, lowering the threshold for SG formation, probably by promoting the aggregation of PABPC1-bound mRNA. The C-terminal region is responsible for the self-aggregation of ataxin-2. These findings underscore the critical roles of mRNA PAT, PABPC1 and ataxin-2 in SG formation and provide mechanistic insights into this process.
Collapse
Affiliation(s)
- Ryota Yamagishi
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Hiroto Inagaki
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Jun Suzuki
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Nao Hosoda
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Haruka Sugiyama
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Kazunori Tomita
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Takashi Hotta
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Shin-ichi Hoshino
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| |
Collapse
|
2
|
Wang Y, Niu K, Shi Y, Zhou F, Li X, Li Y, Chen T, Zhang Y. A review: targeting UBR5 domains to mediate emerging roles and mechanisms - chance or necessity? Int J Surg 2024; 110:4947-4964. [PMID: 38701508 PMCID: PMC11326040 DOI: 10.1097/js9.0000000000001541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024]
Abstract
Ubiquitinases are known to catalyze ubiquitin chains on target proteins to regulate various physiological functions like cell proliferation, autophagy, apoptosis, and cell cycle progression. As a member of E3 ligase, ubiquitin protein ligase E3 component n-recognin 5 (UBR5) belongs to the HECT E3 ligase and has been reported to be correlated with various pathophysiological processes. In this review, the authors give a comprehensive insight into the structure and function of UBR5. The authors discuss the specific domains of UBR5 and explore their biological functions separately. Furthermore, the authors describe the involvement of UBR5 in different pathophysiological conditions, including immune response, virus infection, DNA damage response, and protein quality control. Moreover, the authors provide a thorough summary of the important roles and regulatory mechanisms of UBR5 in cancers and other diseases. On the whole, investigating the domains and functions of UBR5, elucidating the underlying mechanisms of UBR5 with various substrates in detail may provide new theoretical basis for the treatment of diseases, including cancers, which could improve future studies to construct novel UBR5-targeted therapy strategies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Yewei Zhang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People’s Republic of China
| |
Collapse
|
3
|
Nakashima M, Suga N, Ikeda Y, Yoshikawa S, Matsuda S. Circular RNAs, Noncoding RNAs, and N6-methyladenosine Involved in the Development of MAFLD. Noncoding RNA 2024; 10:11. [PMID: 38392966 PMCID: PMC10893449 DOI: 10.3390/ncrna10010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs), including circular RNAs (circRNAs) and N6-methyladenosine (m6A), have been shown to play a critical role in the development of various diseases including obesity and metabolic disorder-associated fatty liver disease (MAFLD). Obesity is a chronic disease caused by excessive fat accumulation in the body, which has recently become more prevalent and is the foremost risk factor for MAFLD. Causes of obesity may involve the interaction of genetic, behavioral, and social factors. m6A RNA methylation might add a novel inspiration for understanding the development of obesity and MAFLD with post-transcriptional regulation of gene expression. In particular, circRNAs, microRNAs (miRNAs), and m6A might be implicated in the progression of MAFLD. Interestingly, m6A modification can modulate the translation, degradation, and other functions of ncRNAs. miRNAs/circRNAs can also modulate m6A modifications by affecting writers, erasers, and readers. In turn, ncRNAs could modulate the expression of m6A regulators in different ways. However, there is limited evidence on how these ncRNAs and m6A interact to affect the promotion of liver diseases. It seems that m6A can occur in DNA, RNA, and proteins that may be associated with several biological properties. This study provides a mechanistic understanding of the association of m6A modification and ncRNAs with liver diseases, especially for MAFLD. Comprehension of the association between m6A modification and ncRNAs may contribute to the development of treatment tactics for MAFLD.
Collapse
Affiliation(s)
| | | | | | | | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women’s University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| |
Collapse
|
4
|
Hehl LA, Horn-Ghetko D, Prabu JR, Vollrath R, Vu DT, Pérez Berrocal DA, Mulder MPC, van der Heden van Noort GJ, Schulman BA. Structural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5. Nat Chem Biol 2024; 20:190-200. [PMID: 37620400 PMCID: PMC10830417 DOI: 10.1038/s41589-023-01414-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/30/2023] [Indexed: 08/26/2023]
Abstract
Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron microscopy (cryo-EM) to visualize stable mimics of the intermediates along K48-linked Ub chain formation by the human E3, UBR5. The structural data reveal a ≈ 620 kDa UBR5 dimer as the functional unit, comprising a scaffold with flexibly tethered Ub-associated (UBA) domains, and elaborately arranged HECT domains. Chains are forged by a UBA domain capturing an acceptor Ub, with its K48 lured into the active site by numerous interactions between the acceptor Ub, manifold UBR5 elements and the donor Ub. The cryo-EM reconstructions allow defining conserved HECT domain conformations catalyzing Ub transfer from E2 to E3 and from E3. Our data show how a full-length E3, ubiquitins to be adjoined, E2 and intermediary products guide a feed-forward HECT domain conformational cycle establishing a highly efficient, broadly targeting, K48-linked Ub chain forging machine.
Collapse
Affiliation(s)
- Laura A Hehl
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ronnald Vollrath
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - D Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David A Pérez Berrocal
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Brenda A Schulman
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany.
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
| |
Collapse
|
5
|
Ikeda Y, Morikawa S, Nakashima M, Yoshikawa S, Taniguchi K, Sawamura H, Suga N, Tsuji A, Matsuda S. CircRNAs and RNA-Binding Proteins Involved in the Pathogenesis of Cancers or Central Nervous System Disorders. Noncoding RNA 2023; 9:23. [PMID: 37104005 PMCID: PMC10142617 DOI: 10.3390/ncrna9020023] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Circular RNAs (circRNAs), a newly recognized group of noncoding RNA transcripts, have established widespread attention due to their regulatory role in cell signaling. They are covalently closed noncoding RNAs that form a loop, and are typically generated during the splicing of precursor RNAs. CircRNAs are key post-transcriptional and post-translational regulators of gene expression programs that might influence cellular response and/or function. In particular, circRNAs have been considered to function as sponges of specific miRNA, regulating cellular processes at the post-transcription stage. Accumulating evidence has shown that the aberrant expression of circRNAs could play a key role in the pathogenesis of several diseases. Notably, circRNAs, microRNAs, and several RNA-binding proteins, including the antiproliferative (APRO) family proteins, could be indispensable gene modulators, which might be strongly linked to the occurrence of diseases. In addition, circRNAs have attracted general interest for their stability, abundance in the brain, and their capability to cross the blood-brain barrier. Here, we present the current findings and theragnostic potentials of circRNAs in several diseases. With this, we aim to provide new insights to support the development of novel diagnostic and/or therapeutic strategies for these diseases.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women’s University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| |
Collapse
|
6
|
Wu B, Song M, Dong Q, Xiang G, Li J, Ma X, Wei F. UBR5 promotes tumor immune evasion through enhancing IFN-γ-induced PDL1 transcription in triple negative breast cancer. Am J Cancer Res 2022; 12:5086-5102. [PMID: 35836797 PMCID: PMC9274738 DOI: 10.7150/thno.74989] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023] Open
Abstract
Background: The up-regulation of PD-L1 is recognized as an adaption of cancer cells to evade immune surveillance and attack. However, the intrinsic mechanisms of the induction of PD-L1 by interferon-γ (IFN-γ) in tumor microenvironment remain incompletely characterized. Ubiquitin ligase E3 component N-recognition protein 5 (UBR5) has a critical role in tumorigenesis of triple negative breast cancer (TNBC) by triggering specific immune responses to the tumor. Dual targeting of UBR5 and PD-L1 exhibited superior therapeutic benefits in a preclinical TNBC model in short term. Methods: The regulation of UBR5 to PD-L1 upon IFN-γ stimulation was evaluated through in UBR5 deficiency, reconstitution or overexpression cell line models by quantitative PCR, immunohistochemistry and RNA-seq. The effects of PD-L1 regulation by UBR5 and double blockade of both genes were evaluated in mouse TNBC model. Luciferase reporter assay, chromatin immunoprecipitation-qPCR and bioinformatics analysis were performed to explore the transcription factors involved in the regulation of UBR5 to PD-L1. Results: E3 ubiquitin ligase UBR5 plays a key role in IFN-γ-induced PDL1 transcription in TNBC in an E3 ubiquitination activity-independent manner. RNA-seq-based transcriptomic analyses reveal that UBR5 globally affects the genes in the IFN-γ-induced signaling pathway. Through its poly adenylate binding (PABC) domain, UBR5 enhances the transactivation of PDL1 by upregulating protein kinase RNA-activated (PKR), and PKR's downstream factors including signal transducers and activators of transcription 1 (STAT1) and interferon regulatory factor 1 (IRF1). Restoration of PD-L1 expression in UBR5-deficient tumor cells recoups their malignancy in vivo, whereas CRISPR/Cas9-mediated simultaneous abrogation of UBR5 and PD-L1 expression yields synergistic therapeutic benefits than either blockade alone, with a strong impact on the tumor microenvironment. Conclusions: This study identifies a novel regulator of PDL1 transcription, elucidates the underlying molecular mechanisms and provides a strong rationale for combination cancer immunotherapies targeting UBR5 and PD-L1.
Collapse
Affiliation(s)
- Bingbing Wu
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mei Song
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Qun Dong
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Xiang
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojing Ma
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York.,✉ Corresponding author: Fang Wei, 800 Dongchuan Road, Minghang, Shanghai 200240, China. Phone: 86-21-34205287; Fax: 86-21-34205287; E-mail: ; Xiaojing Ma,
| | - Fang Wei
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,✉ Corresponding author: Fang Wei, 800 Dongchuan Road, Minghang, Shanghai 200240, China. Phone: 86-21-34205287; Fax: 86-21-34205287; E-mail: ; Xiaojing Ma,
| |
Collapse
|
7
|
Devan SK, Schott-Verdugo S, Müntjes K, Bismar L, Reiners J, Hachani E, Schmitt L, Höppner A, Smits SHJ, Gohlke H, Feldbrügge M. A MademoiseLLE domain binding platform links the key RNA transporter to endosomes. PLoS Genet 2022; 18:e1010269. [PMID: 35727840 PMCID: PMC9249222 DOI: 10.1371/journal.pgen.1010269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/01/2022] [Accepted: 05/20/2022] [Indexed: 11/19/2022] Open
Abstract
Spatiotemporal expression can be achieved by transport and translation of mRNAs at defined subcellular sites. An emerging mechanism mediating mRNA trafficking is microtubule-dependent co-transport on shuttling endosomes. Although progress has been made in identifying various components of the endosomal mRNA transport machinery, a mechanistic understanding of how these RNA-binding proteins are connected to endosomes is still lacking. Here, we demonstrate that a flexible MademoiseLLE (MLLE) domain platform within RNA-binding protein Rrm4 of Ustilago maydis is crucial for endosomal attachment. Our structure/function analysis uncovered three MLLE domains at the C-terminus of Rrm4 with a functionally defined hierarchy. MLLE3 recognises two PAM2-like sequences of the adaptor protein Upa1 and is essential for endosomal shuttling of Rrm4. MLLE1 and MLLE2 are most likely accessory domains exhibiting a variable binding mode for interaction with currently unknown partners. Thus, endosomal attachment of the mRNA transporter is orchestrated by a sophisticated MLLE domain binding platform.
Collapse
Affiliation(s)
- Senthil-Kumar Devan
- Institute of Microbiology, Heinrich Heine University Düsseldorf, Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Stephan Schott-Verdugo
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Bioinformatics), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kira Müntjes
- Institute of Microbiology, Heinrich Heine University Düsseldorf, Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Lilli Bismar
- Institute of Microbiology, Heinrich Heine University Düsseldorf, Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Jens Reiners
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eymen Hachani
- Institute of Biochemistry I, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry I, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Astrid Höppner
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander HJ Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Biochemistry I, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Bioinformatics), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute of Microbiology, Heinrich Heine University Düsseldorf, Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| |
Collapse
|
8
|
Benz C, Ali M, Krystkowiak I, Simonetti L, Sayadi A, Mihalic F, Kliche J, Andersson E, Jemth P, Davey NE, Ivarsson Y. Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. Mol Syst Biol 2022; 18:e10584. [PMID: 35044719 PMCID: PMC8769072 DOI: 10.15252/msb.202110584] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 12/18/2022] Open
Abstract
Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional, and cell type-specific interactions are likely to be disproportionately underrepresented. Here, we describe an optimized proteomic peptide-phage display library that tiles all disordered regions of the human proteome and allows the screening of ~ 1,000,000 overlapping peptides in a single binding assay. We define guidelines for processing, filtering, and ranking the results and provide PepTools, a toolkit to annotate the identified hits. We uncovered >2,000 interaction pairs for 35 known short linear motif (SLiM)-binding domains and confirmed the quality of the produced data by complementary biophysical or cell-based assays. Finally, we show how the amino acid resolution-binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. The optimized human disorderome library paired with PepTools represents a powerful pipeline for unbiased proteome-wide discovery of SLiM-based interactions.
Collapse
Affiliation(s)
- Caroline Benz
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Muhammad Ali
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | | | | | - Ahmed Sayadi
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Filip Mihalic
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Johanna Kliche
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| | - Eva Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Per Jemth
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Norman E Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Ylva Ivarsson
- Department of Chemistry ‐ BMCUppsala UniversityUppsalaSweden
| |
Collapse
|
9
|
Galimova IA, Dorogova NV, Fedorova SA. Functions of E3 Ubiquitin Ligase Hyd in Drosophila Tissues. Mol Biol 2021. [DOI: 10.1134/s0026893321020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
10
|
Ikeda Y, Taniguchi K, Nagase N, Tsuji A, Kitagishi Y, Matsuda S. Reactive oxygen species may influence on the crossroads of stemness, senescence, and carcinogenesis in a cell via the roles of APRO family proteins. EXPLORATION OF MEDICINE 2021. [DOI: 10.37349/emed.2021.00062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Excessive reactive oxygen species (ROS) may cause oxidative stress which is involved in aging and in the pathogenesis of various human diseases. Whereas unregulated levels of the ROS may be harmful, regulated basal level of ROS are even necessary to support cellular functions as a second messenger for homeostasis under physiological conditions. Therefore, redox medicine could develop as a new therapeutic concept for human health-benefits. Here, we introduce the involvement of ROS on the crossroads of stemness, senescence, and carcinogenesis in a stem cell and cancer cell biology. Amazingly, the anti-proliferative (APRO) family anti-proliferative proteins characterized by immediate early growth responsive genes may also be involved in the crossroads machinery. The biological functions of APRO proteins (APROs) seem to be quite intricate, however, which might be a key modulator of microRNAs (miRNAs). Given the crucial roles of ROS and APROs for pathophysiological functions, upcoming novel therapeutics should include vigilant modulation of the redox state. Next generation of medicine including regenerative medicine and/or cancer therapy will likely comprise strategies for altering the redox environment with the APROs via the modulation of miRNAs as well as with the regulation of ROS of cells in a sustainable manner.
Collapse
Affiliation(s)
- Yuka Ikeda
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Kurumi Taniguchi
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Nozomi Nagase
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Ai Tsuji
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Yasuko Kitagishi
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| |
Collapse
|
11
|
Mattijssen S, Kozlov G, Fonseca BD, Gehring K, Maraia RJ. LARP1 and LARP4: up close with PABP for mRNA 3' poly(A) protection and stabilization. RNA Biol 2021; 18:259-274. [PMID: 33522422 PMCID: PMC7928012 DOI: 10.1080/15476286.2020.1868753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
La-related proteins (LARPs) share a La motif (LaM) followed by an RNA recognition motif (RRM). Together these are termed the La-module that, in the prototypical nuclear La protein and LARP7, mediates binding to the UUU-3'OH termination motif of nascent RNA polymerase III transcripts. We briefly review La and LARP7 activities for RNA 3' end binding and protection from exonucleases before moving to the more recently uncovered poly(A)-related activities of LARP1 and LARP4. Two features shared by LARP1 and LARP4 are direct binding to poly(A) and to the cytoplasmic poly(A)-binding protein (PABP, also known as PABPC1). LARP1, LARP4 and other proteins involved in mRNA translation, deadenylation, and decay, contain PAM2 motifs with variable affinities for the MLLE domain of PABP. We discuss a model in which these PABP-interacting activities contribute to poly(A) pruning of active mRNPs. Evidence that the SARS-CoV-2 RNA virus targets PABP, LARP1, LARP 4 and LARP 4B to control mRNP activity is also briefly reviewed. Recent data suggests that LARP4 opposes deadenylation by stabilizing PABP on mRNA poly(A) tails. Other data suggest that LARP1 can protect mRNA from deadenylation. This is dependent on a PAM2 motif with unique characteristics present in its La-module. Thus, while nuclear La and LARP7 stabilize small RNAs with 3' oligo(U) from decay, LARP1 and LARP4 bind and protect mRNA 3' poly(A) tails from deadenylases through close contact with PABP.Abbreviations: 5'TOP: 5' terminal oligopyrimidine, LaM: La motif, LARP: La-related protein, LARP1: La-related protein 1, MLLE: mademoiselle, NTR: N-terminal region, PABP: cytoplasmic poly(A)-binding protein (PABPC1), Pol III: RNA polymerase III, PAM2: PABP-interacting motif 2, PB: processing body, RRM: RNA recognition motif, SG: stress granule.
Collapse
Affiliation(s)
- Sandy Mattijssen
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
12
|
Mattijssen S, Kozlov G, Gaidamakov S, Ranjan A, Fonseca BD, Gehring K, Maraia RJ. The isolated La-module of LARP1 mediates 3' poly(A) protection and mRNA stabilization, dependent on its intrinsic PAM2 binding to PABPC1. RNA Biol 2021; 18:275-289. [PMID: 33292040 PMCID: PMC7928023 DOI: 10.1080/15476286.2020.1860376] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/18/2022] Open
Abstract
The protein domain arrangement known as the La-module, comprised of a La motif (LaM) followed by a linker and RNA recognition motif (RRM), is found in seven La-related proteins: LARP1, LARP1B, LARP3 (La protein), LARP4, LARP4B, LARP6, and LARP7 in humans. Several LARPs have been characterized for their distinct activity in a specific aspect of RNA metabolism. The La-modules vary among the LARPs in linker length and RRM subtype. The La-modules of La protein and LARP7 bind and protect nuclear RNAs with UUU-3' tails from degradation by 3' exonucleases. LARP4 is an mRNA poly(A) stabilization factor that binds poly(A) and the cytoplasmic poly(A)-binding protein PABPC1 (also known as PABP). LARP1 exhibits poly(A) length protection and mRNA stabilization similar to LARP4. Here, we show that these LARP1 activities are mediated by its La-module and dependent on a PAM2 motif that binds PABP. The isolated La-module of LARP1 is sufficient for PABP-dependent poly(A) length protection and mRNA stabilization in HEK293 cells. A point mutation in the PAM2 motif in the La-module impairs mRNA stabilization and PABP binding in vivo but does not impair oligo(A) RNA binding by the purified recombinant La-module in vitro. We characterize the unusual PAM2 sequence of LARP1 and show it may differentially affect stable and unstable mRNAs. The unique LARP1 La-module can function as an autonomous factor to confer poly(A) protection and stabilization to heterologous mRNAs.
Collapse
Affiliation(s)
- Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Sergei Gaidamakov
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Amitabh Ranjan
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
- Commissioned Corps, U.S. Public Health Service, Rockville, MD, USA
| |
Collapse
|
13
|
Crystal Structure of a Variant PAM2 Motif of LARP4B Bound to the MLLE Domain of PABPC1. Biomolecules 2020; 10:biom10060872. [PMID: 32517187 PMCID: PMC7356810 DOI: 10.3390/biom10060872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/31/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic cells determine the protein output of their genetic program by regulating mRNA transcription, localization, translation and turnover rates. This regulation is accomplished by an ensemble of RNA-binding proteins (RBPs) that bind to any given mRNA, thus forming mRNPs. Poly(A) binding proteins (PABPs) are prominent members of virtually all mRNPs that possess poly(A) tails. They serve as multifunctional scaffolds, allowing the recruitment of diverse factors containing a poly(A)-interacting motif (PAM) into mRNPs. We present the crystal structure of the variant PAM motif (termed PAM2w) in the N-terminal part of the positive translation factor LARP4B, which binds to the MLLE domain of the poly(A) binding protein C1 cytoplasmic 1 (PABPC1). The structural analysis, along with mutational studies in vitro and in vivo, uncovered a new mode of interaction between PAM2 motifs and MLLE domains.
Collapse
|
14
|
Egorova PA, Bezprozvanny IB. Molecular Mechanisms and Therapeutics for Spinocerebellar Ataxia Type 2. Neurotherapeutics 2019; 16:1050-1073. [PMID: 31435879 PMCID: PMC6985344 DOI: 10.1007/s13311-019-00777-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The effective therapeutic treatment and the disease-modifying therapy for spinocerebellar ataxia type 2 (SCA2) (a progressive hereditary disease caused by an expansion of polyglutamine in the ataxin-2 protein) is not available yet. At present, only symptomatic treatment and methods of palliative care are prescribed to the patients. Many attempts were made to study the physiological, molecular, and biochemical changes in SCA2 patients and in a variety of the model systems to find new therapeutic targets for SCA2 treatment. A better understanding of the uncovered molecular mechanisms of the disease allowed the scientific community to develop strategies of potential therapy and helped to create some promising therapeutic approaches for SCA2 treatment. Recent progress in this field will be discussed in this review article.
Collapse
Affiliation(s)
- Polina A Egorova
- Laboratory of Molecular Neurodegeneration, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Ilya B Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, 195251, Russia.
- Department of Physiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, ND12.200, Dallas, Texas, 75390, USA.
| |
Collapse
|
15
|
Lorenz S. Structural mechanisms of HECT-type ubiquitin ligases. Biol Chem 2018; 399:127-145. [PMID: 29016349 DOI: 10.1515/hsz-2017-0184] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/25/2017] [Indexed: 12/31/2022]
Abstract
Ubiquitin ligases (E3 enzymes) transfer ubiquitin from ubiquitin-conjugating (E2) enzymes to target proteins. By determining the selection of target proteins, modification sites on those target proteins, and the types of ubiquitin modifications that are formed, E3 enzymes are key specificity factors in ubiquitin signaling. Here, I summarize our knowledge of the structural mechanisms in the HECT E3 subfamily, many members of which play important roles in human disease. I discuss interactions of the conserved HECT domain with E2 enzymes, ubiquitin and target proteins, as well as macromolecular interactions with regulatory functions. While we understand individual steps in the catalytic cycle of HECT E3 enzymes on a structural level, this review also highlights key aspects that have yet to be elucidated. For instance, it remains unclear how diverse target proteins are presented to the catalytic center and how certain HECT E3 enzymes achieve specificity in ubiquitin linkage formation. The structural and functional properties of the N-terminal regions of HECT E3 enzymes that likely act as signaling hubs are also largely unknown. Structural insights into these aspects may open up routes for a therapeutic intervention with specific HECT E3 functions in distinct pathophysiological settings.
Collapse
Affiliation(s)
- Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| |
Collapse
|
16
|
Lastres-Becker I, Nonis D, Eich F, Klinkenberg M, Gorospe M, Kötter P, Klein FAC, Kedersha N, Auburger G. Mammalian ataxin-2 modulates translation control at the pre-initiation complex via PI3K/mTOR and is induced by starvation. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1862:1558-69. [PMID: 27240544 PMCID: PMC4967000 DOI: 10.1016/j.bbadis.2016.05.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/11/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
Ataxin-2 is a cytoplasmic protein, product of the ATXN2 gene, whose deficiency leads to obesity, while its gain-of-function leads to neural atrophy. Ataxin-2 affects RNA homeostasis, but its effects are unclear. Here, immunofluorescence analysis suggested that ataxin-2 associates with 48S pre-initiation components at stress granules in neurons and mouse embryonic fibroblasts, but is not essential for stress granule formation. Coimmunoprecipitation analysis showed associations of ataxin-2 with initiation factors, which were concentrated at monosome fractions of polysome gradients like ataxin-2, unlike its known interactor PABP. Mouse embryonic fibroblasts lacking ataxin-2 showed increased phosphorylation of translation modulators 4E-BP1 and ribosomal protein S6 through the PI3K-mTOR pathways. Indeed, human neuroblastoma cells after trophic deprivation showed a strong induction of ATXN2 transcript via mTOR inhibition. Our results support the notion that ataxin-2 is a nutritional stress-inducible modulator of mRNA translation at the pre-initiation complex.
Collapse
Affiliation(s)
- Isabel Lastres-Becker
- Section of Molecular Neurogenetics, Dept. of Neurology, Building 89, 3rd floor, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany.
| | - David Nonis
- Section of Molecular Neurogenetics, Dept. of Neurology, Building 89, 3rd floor, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Florian Eich
- Section of Molecular Neurogenetics, Dept. of Neurology, Building 89, 3rd floor, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Michael Klinkenberg
- Section of Molecular Neurogenetics, Dept. of Neurology, Building 89, 3rd floor, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Peter Kötter
- Center of Excellence Macromolecular Complexes, Institute of Molecular Biosciences, Goethe-University, 60590 Frankfurt am Main, Germany
| | - Fabrice A C Klein
- Translational Medicine and Neurogenetics Department, Institut de Génétique et Biologie Moléculaire et Cellulaire, UMR7104-CNRS/U964-INSERM/UDS, BP10142, 67404 Illkirch Cédex, France
| | - Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, One Jimmy Fund Way, Boston, MA 02115, USA
| | - Georg Auburger
- Section of Molecular Neurogenetics, Dept. of Neurology, Building 89, 3rd floor, Goethe University Medical School, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany.
| |
Collapse
|
17
|
Kinsella E, Dora N, Mellis D, Lettice L, Deveney P, Hill R, Ditzel M. Use of a Conditional Ubr5 Mutant Allele to Investigate the Role of an N-End Rule Ubiquitin-Protein Ligase in Hedgehog Signalling and Embryonic Limb Development. PLoS One 2016; 11:e0157079. [PMID: 27299863 PMCID: PMC4907512 DOI: 10.1371/journal.pone.0157079] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 05/24/2016] [Indexed: 01/16/2023] Open
Abstract
Hedgehog (Hh) signalling is a potent regulator of cell fate and function. While much is known about the events within a Hh-stimulated cell, far less is known about the regulation of Hh-ligand production. Drosophila Hyperplastic Discs (Hyd), a ubiquitin-protein ligase, represents one of the few non-transcription factors that independently regulates both hh mRNA expression and pathway activity. Using a murine embryonic stem cell system, we revealed that shRNAi of the mammalian homologue of hyd, Ubr5, effectively prevented retinoic-acid-induced Sonic hedgehog (Shh) expression. We next investigated the UBR5:Hh signalling relationship in vivo by generating and validating a mouse bearing a conditional Ubr5 loss-of-function allele. Conditionally deleting Ubr5 in the early embryonic limb-bud mesenchyme resulted in a transient decrease in Indian hedgehog ligand expression and decreased Hh pathway activity, around E13.5. Although Ubr5-deficient limbs and digits were, on average, shorter than control limbs, the effects were not statistically significant. Hence, while loss of UBR5 perturbed Hedgehog signalling in the developing limb, there were no obvious morphological defects. In summary, we report the first conditional Ubr5 mutant mouse and provide evidence for a role for UBR5 in influencing Hh signalling, but are uncertain to whether the effects on Hedgehog signaling were direct (cell autonomous) or indirect (non-cell-autonomous). Elaboration of the cellular/molecular mechanism(s) involved may help our understanding on diseases and developmental disorders associated with aberrant Hh signalling.
Collapse
Affiliation(s)
- Elaine Kinsella
- Edinburgh CRUK Cancer Research Centre, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Natalie Dora
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - David Mellis
- Edinburgh CRUK Cancer Research Centre, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Laura Lettice
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Paul Deveney
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Robert Hill
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Mark Ditzel
- Edinburgh CRUK Cancer Research Centre, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| |
Collapse
|
18
|
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: 56] [Impact Index Per Article: 7.0] [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.
Collapse
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
| |
Collapse
|
19
|
Shearer RF, Iconomou M, Watts CKW, Saunders DN. Functional Roles of the E3 Ubiquitin Ligase UBR5 in Cancer. Mol Cancer Res 2015; 13:1523-32. [PMID: 26464214 DOI: 10.1158/1541-7786.mcr-15-0383] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/06/2015] [Indexed: 11/16/2022]
Abstract
The Ubiquitin-Proteasome System (UPS) is an important regulator of cell signaling and proteostasis, which are essential to a variety of cellular processes. The UPS is disrupted in many diseases including cancer, and targeting the UPS for cancer therapy is gaining wide interest. E3 ubiquitin ligases occupy a key position in the hierarchical UPS enzymatic cascade, largely responsible for determining substrate specificity and ubiquitin (Ub) chain topology. The E3 ligase UBR5 (aka EDD1) is emerging as a key regulator of the UPS in cancer and development. UBR5 expression is deregulated in many cancer types and UBR5 is frequently mutated in mantle cell lymphoma. UBR5 is highly conserved in metazoans, has unique structural features, and has been implicated in regulation of DNA damage response, metabolism, transcription, and apoptosis. Hence, UBR5 is a key regulator of cell signaling relevant to broad areas of cancer biology. However, the mechanism by which UBR5 may contribute to tumor initiation and progression remains poorly defined. This review synthesizes emerging insights from genetics, biochemistry, and cell biology to inform our understanding of UBR5 in cancer. These molecular insights indicate a role for UBR5 in integrating/coordinating various cellular signaling pathways. Finally, we discuss outstanding questions in UBR5 biology and highlight the need to systematically characterize substrates, and address limitations in current animal models, to better define the role of UBR5 in cancer.
Collapse
Affiliation(s)
- Robert F Shearer
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Mary Iconomou
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Colin K W Watts
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Darren N Saunders
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia.
| |
Collapse
|
20
|
Moncrieff S, Moncan M, Scialpi F, Ditzel M. Regulation of hedgehog Ligand Expression by the N-End Rule Ubiquitin-Protein Ligase Hyperplastic Discs and the Drosophila GSK3β Homologue, Shaggy. PLoS One 2015; 10:e0136760. [PMID: 26334301 PMCID: PMC4559392 DOI: 10.1371/journal.pone.0136760] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/07/2015] [Indexed: 12/11/2022] Open
Abstract
Hedgehog (Hh) morphogen signalling plays an essential role in tissue development and homeostasis. While much is known about the Hh signal transduction pathway, far less is known about the molecules that regulate the expression of the hedgehog (hh) ligand itself. Here we reveal that Shaggy (Sgg), the Drosophila melanogaster orthologue of GSK3β, and the N-end Rule Ubiquitin-protein ligase Hyperplastic Discs (Hyd) act together to co-ordinate Hedgehog signalling through regulating hh ligand expression and Cubitus interruptus (Ci) expression. Increased hh and Ci expression within hyd mutant clones was effectively suppressed by sgg RNAi, placing sgg downstream of hyd. Functionally, sgg RNAi also rescued the adult hyd mutant head phenotype. Consistent with the genetic interactions, we found Hyd to physically interact with Sgg and Ci. Taken together we propose that Hyd and Sgg function to co-ordinate hh ligand and Ci expression, which in turn influences important developmental signalling pathways during imaginal disc development. These findings are important as tight temporal/spatial regulation of hh ligand expression underlies its important roles in animal development and tissue homeostasis. When deregulated, hh ligand family misexpression underlies numerous human diseases (e.g., colorectal, lung, pancreatic and haematological cancers) and developmental defects (e.g., cyclopia and polydactyly). In summary, our Drosophila-based findings highlight an apical role for Hyd and Sgg in initiating Hedgehog signalling, which could also be evolutionarily conserved in mammals.
Collapse
Affiliation(s)
- Sophie Moncrieff
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
| | - Matthieu Moncan
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
| | - Flavia Scialpi
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
| | - Mark Ditzel
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
- * E-mail:
| |
Collapse
|
21
|
Muñoz-Escobar J, Matta-Camacho E, Kozlov G, Gehring K. The MLLE domain of the ubiquitin ligase UBR5 binds to its catalytic domain to regulate substrate binding. J Biol Chem 2015. [PMID: 26224628 DOI: 10.1074/jbc.m115.672246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
E3 ubiquitin ligases catalyze the transfer of ubiquitin from an E2-conjugating enzyme to a substrate. UBR5, homologous to the E6AP C terminus (HECT)-type E3 ligase, mediates the ubiquitination of proteins involved in translation regulation, DNA damage response, and gluconeogenesis. In addition, UBR5 functions in a ligase-independent manner by prompting protein/protein interactions without ubiquitination of the binding partner. Despite recent functional studies, the mechanisms involved in substrate recognition and selective ubiquitination of its binding partners remain elusive. The C terminus of UBR5 harbors the HECT catalytic domain and an adjacent MLLE domain. MLLE domains mediate protein/protein interactions through the binding of a conserved peptide motif, termed PAM2. Here, we characterize the binding properties of the UBR5 MLLE domain to PAM2 peptides from Paip1 and GW182. The crystal structure with a Paip1 PAM2 peptide reveals the network of hydrophobic and ionic interactions that drive binding. In addition, we identify a novel interaction of the MLLE domain with the adjacent HECT domain mediated by a PAM2-like sequence. Our results confirm the role of the MLLE domain of UBR5 in substrate recruitment and suggest a potential role in regulating UBR5 ligase activity.
Collapse
Affiliation(s)
- Juliana Muñoz-Escobar
- From the Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Edna Matta-Camacho
- From the Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Guennadi Kozlov
- From the Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Kalle Gehring
- From the Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G 0B1, Canada
| |
Collapse
|
22
|
Eliseeva IA, Lyabin DN, Ovchinnikov LP. Poly(A)-binding proteins: structure, domain organization, and activity regulation. BIOCHEMISTRY (MOSCOW) 2014; 78:1377-91. [PMID: 24490729 DOI: 10.1134/s0006297913130014] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA-binding proteins are of vital importance for mRNA functioning. Among these, poly(A)-binding proteins (PABPs) are of special interest due to their participation in virtually all mRNA-dependent events that is caused by their high affinity for A-rich mRNA sequences. Apart from mRNAs, PABPs interact with many proteins, thus promoting their involvement in cellular events. In the nucleus, PABPs play a role in polyadenylation, determine the length of the poly(A) tail, and may be involved in mRNA export. In the cytoplasm, they participate in regulation of translation initiation and either protect mRNAs from decay through binding to their poly(A) tails or stimulate this decay by promoting mRNA interactions with deadenylase complex proteins. This review presents modern notions of the role of PABPs in mRNA-dependent events; peculiarities of regulation of PABP amount in the cell and activities are also discussed.
Collapse
Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | | | | |
Collapse
|
23
|
The "tale" of poly(A) binding protein: the MLLE domain and PAM2-containing proteins. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1062-8. [PMID: 25120199 DOI: 10.1016/j.bbagrm.2014.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/11/2014] [Accepted: 08/04/2014] [Indexed: 11/21/2022]
Abstract
The cytoplasmic poly(A) binding protein 1 (PABPC1) is an essential eukaryotic translational initiation factor first described over 40 years ago. Most studies of PABPC1 have focused on its N-terminal RRM domains, which bind the mRNA 3' poly(A) tail and 5' translation complex eIF4F via eIF4G; however, the protein also contains a C-terminal MLLE domain that binds a peptide motif, termed PAM2, found in many proteins involved in translation regulation and mRNA metabolism. Studies over the past decade have revealed additional functions of PAM2-containing proteins (PACs) in neurodegenerative diseases, circadian rhythms, innate defense, and ubiquitin-mediated protein degradation. Here, we summarize functional and structural studies of the MLLE/PAM2 interaction and discuss the diverse roles of PACs.
Collapse
|
24
|
A functional genomic approach reveals the transcriptional role of EDD in the expression and function of angiogenesis regulator ACVRL1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1309-19. [PMID: 24189493 DOI: 10.1016/j.bbagrm.2013.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 10/18/2013] [Accepted: 10/28/2013] [Indexed: 11/22/2022]
Abstract
EDD (E3 isolated by differential display) was initially isolated as a progestin-regulated gene in breast cancer cells, and represents the human ortholog of the Drosophila melanogaster hyperplastic discs gene (hyd). It encodes a highly conserved and predominantly nuclear ubiquitin E3 ligase of the HECT family, with potential multifunctional roles in development and tumorigenesis. In this study, we further examined the largely uncharacterized role of EDD in transcriptional regulation by uncovering the spectrum of its direct target genes at a genome-wide level. Use of a systematic approach that integrates gene expression and chromatin binding profiling identified several candidate EDD-target genes, one of which is ACVRL1, a TGF-β receptor with functional implications in blood vessel development. Further characterization revealed a negative regulation of ACVRL1 gene expression by EDD that is exerted at the promoter. Consistent with the aberrant upregulation of ACVRL1 and downstream Smad signaling, abrogation of EDD led to deregulated vessel development and endothelial cell motility. Collectively, these results extended the known cellular roles of EDD to critical functions in transcriptional regulation as well as angiogenesis, and may provide mechanistic explanations for EDD's tumorigenic and developmental roles.
Collapse
|
25
|
Merret R, Martino L, Bousquet-Antonelli C, Fneich S, Descombin J, Billey É, Conte MR, Deragon JM. The association of a La module with the PABP-interacting motif PAM2 is a recurrent evolutionary process that led to the neofunctionalization of La-related proteins. RNA (NEW YORK, N.Y.) 2013; 19:36-50. [PMID: 23148093 PMCID: PMC3527725 DOI: 10.1261/rna.035469.112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/12/2012] [Indexed: 05/27/2023]
Abstract
La-related proteins (LARPs) are largely uncharacterized factors, well conserved throughout evolution. Recent reports on the function of human LARP4 and LARP6 suggest that these proteins fulfill key functions in mRNA metabolism and/or translation. We report here a detailed evolutionary history of the LARP4 and 6 families in eukaryotes. Genes coding for LARP4 and 6 were duplicated in the common ancestor of the vertebrate lineage, but one LARP6 gene was subsequently lost in the common ancestor of the eutherian lineage. The LARP6 gene was also independently duplicated several times in the vascular plant lineage. We observed that vertebrate LARP4 and plant LARP6 duplication events were correlated with the acquisition of a PABP-interacting motif 2 (PAM2) and with a significant reorganization of their RNA-binding modules. Using isothermal titration calorimetry (ITC) and immunoprecipitation methods, we show that the two plant PAM2-containing LARP6s (LARP6b and c) can, indeed, interact with the major plant poly(A)-binding protein (PAB2), while the third plant LARP6 (LARP6a) is unable to do so. We also analyzed the RNA-binding properties and the subcellular localizations of the two types of plant LARP6 proteins and found that they display nonredundant characteristics. As a whole, our results support a model in which the acquisition by LARP4 and LARP6 of a PAM2 allowed their targeting to mRNA 3' UTRs and led to their neofunctionalization.
Collapse
Affiliation(s)
- Rémy Merret
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, United Kingdom
| | - Cécile Bousquet-Antonelli
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Sara Fneich
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Julie Descombin
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Élodie Billey
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London SE1 1UL, United Kingdom
| | - Jean-Marc Deragon
- Université de Perpignan Via Domitia, UMR5096 LGDP, 66860 Perpignan Cedex, France
- CNRS, UMR5096 LGDP, 66860 Perpignan Cedex, France
| |
Collapse
|
26
|
Evidence providing new insights into TOB-promoted deadenylation and supporting a link between TOB's deadenylation-enhancing and antiproliferative activities. Mol Cell Biol 2012; 32:1089-98. [PMID: 22252318 DOI: 10.1128/mcb.06370-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The mammalian TOB1 and TOB2 proteins have emerged as key players in repressing cell proliferation. Accumulating evidence indicates that TOBs regulate mRNA deadenylation. A recruitment model was proposed in which TOBs promote deadenylation by recruiting CAF1-CCR4 deadenylase complex to the 3' end of mRNAs by simultaneously binding CAF1 and PABP. However, the exact molecular mechanism underlying TOB-promoted deadenylation remains unclear. It is also unclear whether TOBs' antiproliferative and deadenylation-promoting activities are connected. Here, we combine biochemical analyses with a functional assay directly monitoring deadenylation and mRNA decay to characterize the effects of tethering TOBs or their mutant derivatives to mRNAs. The results provide direct evidence supporting the recruitment model and reveal a link between TOBs' antiproliferative and deadenylation-promoting activities. We also find that TOBs' actions in deadenylation are independent of the phosphorylation state of three serines known to regulate antiproliferative actions, suggesting that TOBs arrest cell growth through at least two different mechanisms. TOB1 and TOB2 were interchangeable in the properties tested here, indicating considerable functional redundancy between the two proteins. We propose that their multiple modes of modulating mRNA turnover and arresting cell growth permit the TOB proteins to coordinate their diverse roles in controlling cell growth and differentiation.
Collapse
|
27
|
Su H, Meng S, Lu Y, Trombly MI, Chen J, Lin C, Turk A, Wang X. Mammalian hyperplastic discs homolog EDD regulates miRNA-mediated gene silencing. Mol Cell 2011; 43:97-109. [PMID: 21726813 DOI: 10.1016/j.molcel.2011.06.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 03/16/2011] [Accepted: 06/10/2011] [Indexed: 01/10/2023]
Abstract
MicroRNAs (miRNAs) regulate gene expression through translation repression and mRNA destabilization. However, the molecular mechanisms of miRNA silencing are still not well defined. Using a genetic screen in mouse embryonic stem (ES) cells, we identify mammalian hyperplastic discs protein EDD, a known E3 ubiquitin ligase, as a key component of the miRNA silencing pathway. ES cells deficient for EDD are defective in miRNA function and exhibit growth defects. We demonstrate that E3 ubiquitin ligase activity is dispensable for EDD function in miRNA silencing. Instead, EDD interacts with GW182 family proteins in the Argonaute-miRNA complexes. The PABC domain of EDD is essential for its silencing function. Through the PABC domain, EDD participates in miRNA silencing by recruiting downstream effectors. Among the PABC-interactors, DDX6 and Tob1/2 are both required and sufficient for silencing mRNA targets. Taken together, these data demonstrate a critical function for EDD in miRNA silencing.
Collapse
Affiliation(s)
- Hong Su
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Yang R, Gaidamakov SA, Xie J, Lee J, Martino L, Kozlov G, Crawford AK, Russo AN, Conte MR, Gehring K, Maraia RJ. La-related protein 4 binds poly(A), interacts with the poly(A)-binding protein MLLE domain via a variant PAM2w motif, and can promote mRNA stability. Mol Cell Biol 2011; 31:542-56. [PMID: 21098120 PMCID: PMC3028612 DOI: 10.1128/mcb.01162-10] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 11/05/2010] [Accepted: 11/12/2010] [Indexed: 12/19/2022] Open
Abstract
The conserved RNA binding protein La recognizes UUU-3'OH on its small nuclear RNA ligands and stabilizes them against 3'-end-mediated decay. We report that newly described La-related protein 4 (LARP4) is a factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). Yeast two-hybrid analysis and reciprocal immunoprecipitations (IPs) from HeLa cells revealed that LARP4 interacts with RACK1, a 40S ribosome- and mRNA-associated protein. LARP4 cosediments with 40S ribosome subunits and polyribosomes, and its knockdown decreases translation. Mutagenesis of the RNA binding or PABP interaction motifs decrease LARP4 association with polysomes. Several translation and mRNA metabolism-related proteins use a PAM2 sequence containing a critical invariant phenylalanine to make direct contact with the MLLE domain of PABP, and their competition for the MLLE is thought to regulate mRNA homeostasis. Unlike all ∼150 previously analyzed PAM2 sequences, LARP4 contains a variant PAM2 (PAM2w) with tryptophan in place of the phenylalanine. Binding and nuclear magnetic resonance (NMR) studies have shown that a peptide representing LARP4 PAM2w interacts with the MLLE of PABP within the affinity range measured for other PAM2 motif peptides. A cocrystal of PABC bound to LARP4 PAM2w shows tryptophan in the pocket in PABC-MLLE otherwise occupied by phenylalanine. We present evidence that LARP4 expression stimulates luciferase reporter activity by promoting mRNA stability, as shown by mRNA decay analysis of luciferase and cellular mRNAs. We propose that LARP4 activity is integrated with other PAM2 protein activities by PABP as part of mRNA homeostasis.
Collapse
Affiliation(s)
- Ruiqing Yang
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Sergei A. Gaidamakov
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Jingwei Xie
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Joowon Lee
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Luigi Martino
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Guennadi Kozlov
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Amanda K. Crawford
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Amy N. Russo
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Maria R. Conte
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Kalle Gehring
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| | - Richard J. Maraia
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom, Department of Biochemistry, McGill University, Montreal, QC, Canada, Commissioned Corps, U.S. Public Health Service, Washington, DC
| |
Collapse
|
29
|
Kozlov G, Gehring K. Molecular basis of eRF3 recognition by the MLLE domain of poly(A)-binding protein. PLoS One 2010; 5:e10169. [PMID: 20418951 PMCID: PMC2854688 DOI: 10.1371/journal.pone.0010169] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2010] [Accepted: 03/26/2010] [Indexed: 12/29/2022] Open
Abstract
PABPC1 (cytosolic poly(A)-binding protein 1) is an RNA-binding protein that binds to the poly(A) tail of mRNAs to promote translation and mRNA turnover. In addition to RNA-binding domains, PABPC1 contains a unique protein-protein interaction domain, MLLE (also known as PABC) that binds regulatory proteins and translation factors that contain a conserved 12 amino acid peptide motif termed PAM2. Eukaryotic Release Factor 3 (eRF3/GSPT1) contains two overlapping PAM2 sequences, which are required for its activity. Here, we determined the crystal structures of the MLLE domain from PABPC1 in complex with the two PAM2 regions of eRF3. The structures reveal a mechanism of cooperativity between the two PAM2 sites that increases the binding affinity but prevents the binding of more than one molecule of eRF3 to PABPC1. Relative to previous structures, the high-resolution crystal structures force a re-evaluation of the PAM2 motif and improve our understanding of the molecular basis of MLLE peptide recognition.
Collapse
Affiliation(s)
- Guennadi Kozlov
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Groupe de recherche axé sur la structure des protéines, Montréal, Québec, Canada
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Groupe de recherche axé sur la structure des protéines, Montréal, Québec, Canada
- * E-mail:
| |
Collapse
|
30
|
Kozlov G, Safaee N, Rosenauer A, Gehring K. Structural basis of binding of P-body-associated proteins GW182 and ataxin-2 by the Mlle domain of poly(A)-binding protein. J Biol Chem 2010; 285:13599-606. [PMID: 20181956 DOI: 10.1074/jbc.m109.089540] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Poly(A)-binding protein (PABPC1) is involved in multiple aspects of mRNA processing and translation. It is a component of RNA stress granules and binds the RNA-induced silencing complex to promote degradation of silenced mRNAs. Here, we report the crystal structures of the C-terminal Mlle (or PABC) domain in complex with peptides from GW182 (TNRC6C) and Ataxin-2. The structures reveal overlapping binding sites but with unexpected diversity in the peptide conformation and residues involved in binding. The mutagenesis and binding studies show low to submicromolar binding affinity with overlapping but distinct specificity determinants. These results rationalize the role of the Mlle domain of PABPC1 in microRNA-mediated mRNA deadenylation and suggest a more general function in the assembly of cytoplasmic RNA granules.
Collapse
Affiliation(s)
- Guennadi Kozlov
- Department of Biochemistry and Groupe de Recherche axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G1Y6, Canada
| | | | | | | |
Collapse
|
31
|
Kozlov G, Ménade M, Rosenauer A, Nguyen L, Gehring K. Molecular determinants of PAM2 recognition by the MLLE domain of poly(A)-binding protein. J Mol Biol 2010; 397:397-407. [PMID: 20096703 DOI: 10.1016/j.jmb.2010.01.032] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 01/13/2010] [Accepted: 01/14/2010] [Indexed: 10/19/2022]
Abstract
MLLE (previously known as PABC) is a peptide-binding domain that is found in poly(A)-binding protein (PABP) and EDD (E3 isolated by differential display), a HECT E3 ubiquitin ligase also known as HYD (hyperplastic discs tumor suppressor) or UBR5. The MLLE domain from PABP recruits various regulatory proteins and translation factors to poly(A) mRNAs through binding of a conserved 12 amino acid peptide motif called PAM2 (for PABP-interacting motif 2). Here, we determined crystal structures of the MLLE domain from PABP alone and in complex with PAM2 peptides from PABP-interacting protein 2. The structures provide a detailed view of hydrophobic determinants of the MLLE binding coded by PAM2 positions 3, 5, 7, 10, and 12 and reveal novel intermolecular polar contacts. In particular, the side chain of the invariant MLLE residue K580 forms hydrogen bonds with the backbone of PAM2 residues 5 and 7. The structures also show that peptide residues outside of the conserved PAM2 motif contribute to binding. Altogether, the structures provide a significant advance in understanding the molecular basis for the binding of PABP by PAM2-containing proteins involved in translational control, mRNA deadenylation, and other cellular processes.
Collapse
Affiliation(s)
- Guennadi Kozlov
- Department of Biochemistry, Groupe de recherche axé sur la structure des protéines, McGill University, 3655 Promenade Sir William Osler, Montréal, Québec, Canada H3G 1Y6
| | | | | | | | | |
Collapse
|
32
|
Mauxion F, Chen CYA, Séraphin B, Shyu AB. BTG/TOB factors impact deadenylases. Trends Biochem Sci 2009; 34:640-7. [PMID: 19828319 DOI: 10.1016/j.tibs.2009.07.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 07/19/2009] [Accepted: 07/21/2009] [Indexed: 10/20/2022]
Abstract
BTG/TOB factors are a family of antiproliferative proteins whose expression is altered in numerous cancers. They have been implicated in cell differentiation, development and apoptosis. Although proposed to affect transcriptional regulation, these factors interact with CAF1, a subunit of the main eukaryotic deadenylase, and with poly(A)-binding-proteins, strongly suggesting a role in post-transcriptional regulation of gene expression. The recent determination of the structures of BTG2, TOB1 N-terminal domain (TOB1N138) and TOB1N138-CAF1 complexes support a role for BTG/TOB proteins in mRNA deadenylation, a function corroborated by recently published functional characterizations. We highlight molecular mechanisms by which BTG/TOB proteins influence deadenylation and discuss the need for a better understanding of BTG/TOB physiological functions.
Collapse
Affiliation(s)
- Fabienne Mauxion
- Equipe Labellisée La Ligue, Centre de Génétique Moléculaire, CNRS FRE3144, Gif-sur-Yvette, France
| | | | | | | |
Collapse
|
33
|
Unal EB, Gursoy A, Erman B. Conformational energies and entropies of peptides, and the peptide–protein binding problem. Phys Biol 2009; 6:036014. [DOI: 10.1088/1478-3975/6/3/036014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
34
|
Brook M, Smith JWS, Gray NK. The DAZL and PABP families: RNA-binding proteins with interrelated roles in translational control in oocytes. Reproduction 2009; 137:595-617. [DOI: 10.1530/rep-08-0524] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Gametogenesis is a highly complex process that requires the exquisite temporal, spatial and amplitudinal regulation of gene expression at multiple levels. Translational regulation is important in a wide variety of cell types but may be even more prevalent in germ cells, where periods of transcriptional quiescence necessitate the use of post-transcriptional mechanisms to effect changes in gene expression. Consistent with this, studies in multiple animal models have revealed an essential role for mRNA translation in the establishment and maintenance of reproductive competence. While studies in humans are less advanced, emerging evidence suggests that translational regulation plays a similarly important role in human germ cells and fertility. This review highlights specific mechanisms of translational regulation that play critical roles in oogenesis by activating subsets of mRNAs. These mRNAs are activated in a strictly determined temporal manner via elements located within their 3′UTR, which serve as binding sites fortrans-acting factors. While we concentrate on oogenesis, these regulatory events also play important roles during spermatogenesis. In particular, we focus on the deleted in azoospermia-like (DAZL) family of proteins, recently implicated in the translational control of specific mRNAs in germ cells; their relationship with the general translation initiation factor poly(A)-binding protein (PABP) and the process of cytoplasmic mRNA polyadenylation.
Collapse
|
35
|
De Crescenzo G, Boucher C, Durocher Y, Jolicoeur M. Kinetic Characterization by Surface Plasmon Resonance-Based Biosensors: Principle and Emerging Trends. Cell Mol Bioeng 2008. [DOI: 10.1007/s12195-008-0035-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
36
|
De Crescenzo G, Woodward L, Srinivasan B. Online optimization of surface plasmon resonance‐based biosensor experiments for improved throughput and confidence. J Mol Recognit 2008; 21:256-66. [DOI: 10.1002/jmr.894] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
37
|
Mauxion F, Faux C, Séraphin B. The BTG2 protein is a general activator of mRNA deadenylation. EMBO J 2008; 27:1039-48. [PMID: 18337750 DOI: 10.1038/emboj.2008.43] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 02/18/2008] [Indexed: 12/11/2022] Open
Abstract
BTG2 is a prototype member of the BTG/Tob family of antiproliferative proteins, originally identified as a primary response gene induced by growth factors and tumour promoters. Its expression has been linked to diverse cellular processes such as cell-cycle progression, differentiation or apoptosis. BTG2 has also been shown to interact with the Pop2/Caf1 deadenylase. Here, we demonstrate that BTG2 is a general activator of mRNA decay, thereby contributing to gene expression control. Detailed characterizations of BTG2 show that it enhances deadenylation of all transcripts tested. Our results demonstrate that Caf1 nuclease activity is required for efficient deadenylation in mammalian cells and that the deadenylase activities of both Caf1 and its Ccr4 partner are required for Btg2-induced poly(A) degradation. General activation of deadenylation may represent a new mode of global regulation of gene expression, which could be important to allow rapid resetting of protein production during development or after specific stresses. This may constitute a common function for BTG/Tob family members.
Collapse
Affiliation(s)
- Fabienne Mauxion
- CNRS, Equipe Labellisée La Ligue, Centre de Génétique Moléculaire, UPR 2167, Gif-sur-Yvette, France.
| | | | | |
Collapse
|
38
|
Roth G, Freund S, Möhrle B, Wöllner K, Brünjes J, Gauglitz G, Wiesmüller KH, Jung G. Ubiquitin binds to a short peptide segment of hydrolase UCH-L3: a study by FCS, RIfS, ITC and NMR. Chembiochem 2008; 8:323-31. [PMID: 17211910 DOI: 10.1002/cbic.200600254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Screening for small peptidic affinity tags for the detection of ubiquitin and ubiquitinated proteins yielded the dodecapeptide amide DPDELRFNAIAL-NH(2) as a specific ubiquitin-interacting ligand. A peptide collection--based on crystal structures with ubiquitin-interacting proteins--was designed and confirmed by sequence comparison of ubiquitin-interacting motifs. Four independent physical detection methods demonstrated that the peptide binds to monomeric ubiquitin with an affinity of about 10 muM and with fast on and off rates. Fluorescence correlation spectroscopy with fluorescent peptides showed specific interaction with ubiquitin. Reflectometric interference spectroscopy with surface-immobilized peptides and isothermal calorimetry measurements confirmed the specific binding of ubiquitin and fast rate constants. (1)H,(15)N heteronuclear NMR localised the interaction site across the beta sheet of ubiquitin. The peptide aligns well with the ubiquitin-interacting motif and represents a lead structure for the rational design of high-affinity tags for targeting ubiquitinated protein in vitro and in vivo.
Collapse
Affiliation(s)
- Günter Roth
- Institut für Organische Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Mechanism of mRNA deadenylation: evidence for a molecular interplay between translation termination factor eRF3 and mRNA deadenylases. Genes Dev 2008; 21:3135-48. [PMID: 18056425 DOI: 10.1101/gad.1597707] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In eukaryotes, shortening of the 3'-poly(A) tail is the rate-limiting step in the degradation of most mRNAs, and two major mRNA deadenylase complexes--Caf1-Ccr4 and Pan2-Pan3--play central roles in this process, referred to as deadenylation. However, the molecular mechanism triggering deadenylation remains elusive. Previously, we demonstrated that eukaryotic releasing factor eRF3 mediates deadenylation and decay of mRNA in a manner coupled to translation termination. Here, we report the mechanism of mRNA deadenylation. The eRF3-mediated deadenylation is catalyzed by both Caf1-Ccr4 and Pan2-Pan3. Interestingly, translation termination complexes eRF1-eRF3, Pan2-Pan3, and Caf1-Ccr4 competitively interact with polyadenylate-binding protein PABPC1. In each complex, eRF3, Pan3, and Tob, respectively, mediate PABPC1 binding, and a combination of a PAM2 motif and a PABC domain is commonly utilized for their contacts. A translation-dependent exchange of eRF1-eRF3 for the deadenylase occurs on PABPC1. Consequently, PABPC1 binding leads to the activation of Pan2-Pan3 and Caf1-Ccr4. From these results, we suggest a mechanism of mRNA deadenylation by Pan2-Pan3 and Caf1-Ccr4 in cooperation with eRF3 and PABPC1.
Collapse
|
40
|
Okhrimenko O, Jelesarov I. A survey of the year 2006 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:1-19. [DOI: 10.1002/jmr.859] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
41
|
Ezzeddine N, Chang TC, Zhu W, Yamashita A, Chen CYA, Zhong Z, Yamashita Y, Zheng D, Shyu AB. Human TOB, an antiproliferative transcription factor, is a poly(A)-binding protein-dependent positive regulator of cytoplasmic mRNA deadenylation. Mol Cell Biol 2007; 27:7791-801. [PMID: 17785442 PMCID: PMC2169145 DOI: 10.1128/mcb.01254-07] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In mammalian cells, mRNA decay begins with deadenylation, which involves two consecutive phases mediated by the PAN2-PAN3 and the CCR4-CAF1 complexes, respectively. The regulation of the critical deadenylation step and its relationship with RNA-processing bodies (P-bodies), which are thought to be a site where poly(A)-shortened mRNAs get degraded, are poorly understood. Using the Tet-Off transcriptional pulsing approach to investigate mRNA decay in mouse NIH 3T3 fibroblasts, we found that TOB, an antiproliferative transcription factor, enhances mRNA deadenylation in vivo. Results from glutathione S-transferase pull-down and coimmunoprecipitation experiments indicate that TOB can simultaneously interact with the poly(A) nuclease complex CCR4-CAF1 and the cytoplasmic poly(A)-binding protein, PABPC1. Combining these findings with those from mutagenesis studies, we further identified the protein motifs on TOB and PABPC1 that are necessary for their interaction and found that interaction with PABPC1 is necessary for TOB's deadenylation-enhancing effect. Moreover, our immunofluorescence microscopy results revealed that TOB colocalizes with P-bodies, suggesting a role of TOB in linking deadenylation to the P-bodies. Our findings reveal a new mechanism by which the fate of mammalian mRNA is modulated at the deadenylation step by a protein that recruits poly(A) nuclease(s) to the 3' poly(A) tail-PABP complex.
Collapse
Affiliation(s)
- Nader Ezzeddine
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Siddiqui N, Mangus DA, Chang TC, Palermino JM, Shyu AB, Gehring K. Poly(A) nuclease interacts with the C-terminal domain of polyadenylate-binding protein domain from poly(A)-binding protein. J Biol Chem 2007; 282:25067-75. [PMID: 17595167 DOI: 10.1074/jbc.m701256200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The poly(A)-binding protein (PABP) is an essential protein found in all eukaryotes and is involved in an extensive range of cellular functions, including translation, mRNA metabolism, and mRNA export. Its C-terminal region contains a peptide-interacting PABC domain that recruits proteins containing a highly specific PAM-2 sequence motif to the messenger ribonucleoprotein complex. In humans, these proteins, including Paip1, Paip2, eRF3 (eukaryotic release factor 3), Ataxin-2, and Tob2, are all found to regulate translation through varying mechanisms. The following reports poly(A) nuclease (PAN) as a PABC-interacting partner in both yeast and humans. Their interaction is mediated by a PAM-2 motif identified within the PAN3 subunit. This site was identified in various fungal and animal species suggesting that the interaction is conserved throughout evolution. Our results indicate that PABP is directly involved in recruiting a deadenylase to the messenger ribonucleoprotein complex. This demonstrates a novel role for the PABC domain in mRNA metabolic processes and gives further insight into the function of PABP in mRNA maturation, export, and turnover.
Collapse
Affiliation(s)
- Nadeem Siddiqui
- Department of Biochemistry, McGill University, Montréal, Quebec H3G 1Y6, Canada
| | | | | | | | | | | |
Collapse
|
43
|
Nonhoff U, Ralser M, Welzel F, Piccini I, Balzereit D, Yaspo ML, Lehrach H, Krobitsch S. Ataxin-2 interacts with the DEAD/H-box RNA helicase DDX6 and interferes with P-bodies and stress granules. Mol Biol Cell 2007; 18:1385-96. [PMID: 17392519 PMCID: PMC1838996 DOI: 10.1091/mbc.e06-12-1120] [Citation(s) in RCA: 260] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Tight control of translation is fundamental for eukaryotic cells, and deregulation of proteins implicated contributes to numerous human diseases. The neurodegenerative disorder spinocerebellar ataxia type 2 is caused by a trinucleotide expansion in the SCA2 gene encoding a lengthened polyglutamine stretch in the gene product ataxin-2, which seems to be implicated in cellular RNA-processing pathways and translational regulation. Here, we substantiate a function of ataxin-2 in such pathways by demonstrating that ataxin-2 interacts with the DEAD/H-box RNA helicase DDX6, a component of P-bodies and stress granules, representing cellular structures of mRNA triage. We discovered that altered ataxin-2 levels interfere with the assembly of stress granules and cellular P-body structures. Moreover, ataxin-2 regulates the intracellular concentration of its interaction partner, the poly(A)-binding protein, another stress granule component and a key factor for translational control. Thus, our data imply that the cellular ataxin-2 concentration is important for the assembly of stress granules and P-bodies, which are main compartments for regulating and controlling mRNA degradation, stability, and translation.
Collapse
Affiliation(s)
- Ute Nonhoff
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Markus Ralser
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Franziska Welzel
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ilaria Piccini
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | | | | | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sylvia Krobitsch
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| |
Collapse
|
44
|
Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
45
|
Karim MM, Svitkin YV, Kahvejian A, De Crescenzo G, Costa-Mattioli M, Sonenberg N. A mechanism of translational repression by competition of Paip2 with eIF4G for poly(A) binding protein (PABP) binding. Proc Natl Acad Sci U S A 2006; 103:9494-9. [PMID: 16772376 PMCID: PMC1480435 DOI: 10.1073/pnas.0603701103] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The eukaryotic mRNA 3' poly(A) tail and the 5' cap cooperate to synergistically enhance translation. This interaction is mediated by the cap-binding protein eIF4E, the poly(A) binding protein (PABP), and eIF4G, a scaffolding protein that bridges between eIF4E and PABP to bring about the circularization of the mRNA. The translational repressor, Paip2 (PABP-interacting protein 2), inhibits translation by promoting the dissociation of PABP from poly(A). Here we report on the existence of an alternative mechanism by which Paip2 inhibits translation by competing with eIF4G for binding to PABP. We demonstrate that Paip2 can abrogate the translational activity of PABP, which is tethered to the 3' end of the mRNA. Thus, Paip2 can inhibit translation by a previously unrecognized mechanism, which is independent of its ability to disrupt PABP-poly(A) interaction.
Collapse
Affiliation(s)
- Muhammad M. Karim
- *Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, QC, Canada H3G 1Y6; and
| | - Yuri V. Svitkin
- *Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, QC, Canada H3G 1Y6; and
| | - Avak Kahvejian
- *Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, QC, Canada H3G 1Y6; and
| | - Gregory De Crescenzo
- Department of Chemical Engineering, Bio-P2 Unit, École Polytechnique de Montréal, Montreal, QC, Canada H3T 1J4
| | - Mauro Costa-Mattioli
- *Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, QC, Canada H3G 1Y6; and
| | - Nahum Sonenberg
- *Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, QC, Canada H3G 1Y6; and
- To whom correspondence should be addressed at:
Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC, Canada H3G 1Y6. E-mail:
| |
Collapse
|