1
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Zhuo W, Chen J, Jiang S, Zheng J, Huang H, Xie P, Li W, Lei M, Yin J, Gao Y, Liu Z. Proteomic profiling of eIF3a conditional knockout mice. Front Mol Biosci 2023; 10:1160063. [PMID: 37152897 PMCID: PMC10154561 DOI: 10.3389/fmolb.2023.1160063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/30/2023] [Indexed: 05/09/2023] Open
Abstract
Eukaryotic translation initiation factor 3 subunit A (eIF3a) is the largest subunit of the eukaryotic translation initiation factor 3 (eIF3). eIF3a plays an integral role in protein biosynthesis, hence impacting the onset, development, and treatment of tumors. The proteins regulated by eIF3a are still being explored in vivo. In this study, a Cre-loxP system was used to generate eIF3a conditional knockout mice. Tandem mass tag (TMT) labeling with LC-MS/MS analysis was used to identify differentially expressed proteins (DEPs) in fat, lungs, skin, and spleen tissue of the eIF3a knockout mice and controls. Bioinformatics analysis was then used to explore the functions and molecular signaling pathways of these protein landscapes. It was observed that eIF3a is essential for life sustenance. Abnormal tissue pathology was found in the lungs, fat, skin, spleen, and thymus. In total, 588, 210, 324, and 944 DEPs were quantified in the lungs, fat, skin, and spleen, respectively, of the eIF3a knockout mice as compared to the control. The quantified differentially expressed proteins were tissue-specific, except for eight proteins shared by the four tissues. A broad range of functions for eIF3a, including cellular signaling pathway, immune response, metabolism, defense response, phagocytes, and DNA replication, has been revealed using bioinformatics analysis. Herein, several pathways related to oxidative stress in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, including nitrogen metabolism, peroxisome, cytochrome P450 drug metabolism, pyruvate metabolism, PPAR signaling pathway, phospholipase D signaling pathway, B-cell receptor signaling pathway, ferroptosis, and focal adhesion, have been identified. Collectively, this study shows that eIF3a is an essential gene for sustaining life, and its downstream proteins are involved in diverse novel functions beyond mRNA translational regulation.
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Affiliation(s)
- Wei Zhuo
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Juan Chen
- Departments of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Shilong Jiang
- Departments of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Juyan Zheng
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Hanxue Huang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Pan Xie
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Wei Li
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Mengrong Lei
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Jiye Yin
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Ying Gao
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Departments of Gerontology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Zhaoqian Liu, ; Ying Gao,
| | - Zhaoqian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
- *Correspondence: Zhaoqian Liu, ; Ying Gao,
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2
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Ma S, Dong Z, Huang Y, Liu JY, Zhang JT. Translation initiation factor eIF3a regulates glucose metabolism and cell proliferation via promoting small GTPase Rheb synthesis and AMPK activation. J Biol Chem 2022; 298:102044. [PMID: 35595099 PMCID: PMC9207673 DOI: 10.1016/j.jbc.2022.102044] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/05/2022] Open
Abstract
Eukaryotic translation initiation factor 3 subunit A (eIF3a), the largest subunit of the eIF3 complex, has been shown to be overexpressed in malignant cancer cells, potentially making it a proto-oncogene. eIF3a overexpression can drive cancer cell proliferation but contributes to better prognosis. While its contribution to prognosis was previously shown to be due to its function in suppressing synthesis of DNA damage repair proteins, it remains unclear how eIF3a regulates cancer cell proliferation. In this study, we show using genetic approaches that eIF3a controls cell proliferation by regulating glucose metabolism via the phosphorylation and activation of AMP-activated protein kinase alpha (AMPKα) at Thr172 in its kinase activation loop. We demonstrate that eIF3a regulates AMPK activation mainly by controlling synthesis of the small GTPase Rheb, largely independent of the well-known AMPK upstream liver kinase B1 and Ca2+/calmodulin-dependent protein kinase kinase 2, and also independent of mammalian target of rapamycin signaling and glucose levels. Our findings suggest that glucose metabolism in and proliferation of cancer cells may be translationally regulated via a novel eIF3a–Rheb–AMPK signaling axis.
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Affiliation(s)
- Shijie Ma
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Zizheng Dong
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Yanfei Huang
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Jing-Yuan Liu
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Jian-Ting Zhang
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA.
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3
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Powell P, Bhardwaj U, Goss D. Eukaryotic initiation factor 4F promotes a reorientation of eukaryotic initiation factor 3 binding on the 5' and the 3' UTRs of barley yellow dwarf virus mRNA. Nucleic Acids Res 2022; 50:4988-4999. [PMID: 35446425 PMCID: PMC9122605 DOI: 10.1093/nar/gkac284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/14/2022] Open
Abstract
Viral mRNAs that lack a 5′ m7GTP cap and a 3′ poly-A tail rely on structural elements in their untranslated regions (UTRs) to form unique RNA-protein complexes that regulate viral translation. Recent studies of the barley yellow dwarf virus (BYDV) have revealed eukaryotic initiation factor 3 (eIF3) plays a significant role in facilitating communication between its 5′ and 3′ UTRs by binding both UTRs simultaneously. This report uses in vitro translation assays, fluorescence anisotropy binding assays, and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) footprinting to identify secondary structures that are selectively interacting with eIF3. SHAPE data also show that eIF3 alters its interaction with BYDV structures when another factor crucial for BYDV translation, eIF4F, is introduced by the 3′ BYDV translational enhancer (BTE). The observed BTE and eIF4F-induced shift of eIF3 position on the 5’ UTR and the translational effects of altering eIF3-binding structures (SLC and SLII) support a new model for BYDV translation initiation that requires the reorientation of eIF3 on BYDV UTRs. This eIF3 function in BYDV translation initiation is both reminiscent of and distinct from eIF3–RNA interactions found in other non-canonically translating mRNAs (e.g. HCV). This characterization of a new role in translation initiation expands the known functionality of eIF3 and may be broadly applicable to other non-canonically translating mRNAs.
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Affiliation(s)
- Paul Powell
- Department of Chemistry, Hunter College, CUNY, New York, NY 10065, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Usha Bhardwaj
- Department of Chemistry, Hunter College, CUNY, New York, NY 10065, USA
| | - Dixie Goss
- Department of Chemistry, Hunter College, CUNY, New York, NY 10065, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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4
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eIF3a regulation of mTOR signaling and translational control via HuR in cellular response to DNA damage. Oncogene 2022; 41:2431-2443. [PMID: 35279705 PMCID: PMC9035104 DOI: 10.1038/s41388-022-02262-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 01/29/2023]
Abstract
eIF3a (eukaryotic translation initiation factor 3a), a subunit of the eIF3 complex, has been suggested to play a regulatory role in protein synthesis and in cellular response to DNA-damaging treatments. S6K1 is an effector and a mediator of mTOR complex 1 (mTORC1) in regulating protein synthesis and integrating diverse signals into control of cell growth and response to stress. Here, we show that eIF3a regulates S6K1 activity by inhibiting mTORC1 kinase via regulating Raptor synthesis. The regulation of Raptor synthesis is via eIF3a interaction with HuR (human antigen R) and binding of the eIF3a-HuR complex to the 5'-UTR of Raptor mRNA. Furthermore, mTORC1 may mediate eIF3a function in cellular response to cisplatin by regulating synthesis of NER proteins and NER activity. Taken together, we conclude that the mTOR signaling pathway may also be regulated by translational control and mediate eIF3a regulation of cancer cell response to cisplatin by regulating NER protein synthesis.
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5
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Ma S, Dong Z, Cui Q, Liu JY, Zhang JT. eIF3i regulation of protein synthesis, cell proliferation, cell cycle progression, and tumorigenesis. Cancer Lett 2020; 500:11-20. [PMID: 33301799 DOI: 10.1016/j.canlet.2020.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/22/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023]
Abstract
eIF3i, a 36-kDa protein, is a putative subunit of the eIF3 complex important for translation initiation of mRNAs. It is a WD40 domain-containing protein with seven WD40 repeats that forms a β-propeller structure with an important function in pre-initiation complex formation and mRNA translation initiation. In addition to participating in the eIF3 complex formation for global translational control, eIF3i may bind to specific mRNAs and regulate their translation individually. Furthermore, eIF3i has been shown to bind to TGF-β type II receptor and participate in TGF-β signaling. It may also participate in and regulate other signaling pathways including Wnt/β-catenin pathway via translational regulation of COX-2 synthesis. These multiple canonical and noncanonical functions of eIF3i in translational control and in regulating signal transduction pathways may be responsible for its role in cell differentiation, cell cycle regulation, proliferation, and tumorigenesis. In this review, we will critically evaluate recent progresses and assess future prospects in studying eIF3i.
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Affiliation(s)
- Shijie Ma
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, 510095, China.
| | - Zizheng Dong
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA
| | - Qingbin Cui
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA
| | - Jing-Yuan Liu
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA.
| | - Jian-Ting Zhang
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, 43614, USA.
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6
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Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R. A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. EMBO J 2020; 40:e105179. [PMID: 33289941 PMCID: PMC7780240 DOI: 10.15252/embj.2020105179] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/21/2020] [Accepted: 09/29/2020] [Indexed: 11/24/2022] Open
Abstract
In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub‐complexes. These comprise/include the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP‐binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of the next 43S pre‐initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1‐containing pre‐initiation complexes by cryo‐EM. We found that ABCE1 was mostly associated with early 43S, but also with later 48S phases of initiation. It adopted a novel hybrid conformation of its nucleotide‐binding domains, while interacting with the N‐terminus of eIF3j. Further, eIF3j occupied the mRNA entry channel via its ultimate C‐terminus providing a structural explanation for its antagonistic role with respect to mRNA binding. Overall, the native human samples provide a near‐complete molecular picture of the architecture and sophisticated interaction network of the 43S‐bound eIF3 complex and the eIF2 ternary complex containing the initiator tRNA.
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Affiliation(s)
- Hanna Kratzat
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Timur Mackens-Kiani
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Michael Ameismeier
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Mia Potocnjak
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Jingdong Cheng
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Estelle Dacheux
- Génétique des Interactions Macromoléculaires, UMR3525 CNRS, Institut Pasteur, Paris, France
| | - Abdelkader Namane
- Génétique des Interactions Macromoléculaires, UMR3525 CNRS, Institut Pasteur, Paris, France
| | - Otto Berninghausen
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Franz Herzog
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | | | - Thomas Becker
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
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7
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Translational regulation of Chk1 expression by eIF3a via interaction with the RNA-binding protein HuR. Biochem J 2020; 477:1939-1950. [PMID: 32391557 DOI: 10.1042/bcj20200025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 01/10/2023]
Abstract
eIF3a is a putative subunit of the eukaryotic translation initiation factor 3 complex. Accumulating evidence suggests that eIF3a may have a translational regulatory function by suppressing translation of a subset of mRNAs while accelerating that of other mRNAs. Albeit the suppression of mRNA translation may derive from eIF3a binding to the 5'-UTRs of target mRNAs, how eIF3a may accelerate mRNA translation remains unknown. In this study, we show that eIF3a up-regulates translation of Chk1 but not Chk2 mRNA by interacting with HuR, which binds directly to the 3'-UTR of Chk1 mRNA. The interaction between eIF3a and HuR occurs at the 10-amino-acid repeat domain of eIF3a and the RNA recognition motif domain of HuR. This interaction may effectively circularize Chk1 mRNA to form an end-to-end complex that has recently been suggested to accelerate mRNA translation. Together with previous findings, we conclude that eIF3a may regulate mRNA translation by directly binding to the 5'-UTR to suppress or by interacting with RNA-binding proteins at 3'-UTRs to accelerate mRNA translation.
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8
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Tumia R, Wang CJ, Dong T, Ma S, Beebe J, Chen J, Dong Z, Liu JY, Zhang JT. eIF3a Regulation of NHEJ Repair Protein Synthesis and Cellular Response to Ionizing Radiation. Front Cell Dev Biol 2020; 8:753. [PMID: 32974334 PMCID: PMC7466773 DOI: 10.3389/fcell.2020.00753] [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: 05/27/2020] [Accepted: 07/20/2020] [Indexed: 11/21/2022] Open
Abstract
Translation initiation in protein synthesis regulated by eukaryotic initiation factors (eIFs) is a crucial step in controlling gene expression. eIF3a has been shown to regulate protein synthesis and cellular response to treatments by anticancer agents including cisplatin by regulating nucleotide excision repair. In this study, we tested the hypothesis that eIF3a regulates the synthesis of proteins important for the repair of double-strand DNA breaks induced by ionizing radiation (IR). We found that eIF3a upregulation sensitized cellular response to IR while its downregulation caused resistance to IR. eIF3a increases IR-induced DNA damages and decreases non-homologous end joining (NHEJ) activity by suppressing the synthesis of NHEJ repair proteins. Furthermore, analysis of existing patient database shows that eIF3a expression associates with better overall survival of breast, gastric, lung, and ovarian cancer patients. These findings together suggest that eIF3a plays an important role in cellular response to DNA-damaging treatments by regulating the synthesis of DNA repair proteins and, thus, eIIF3a likely contributes to the outcome of cancer patients treated with DNA-damaging strategies including IR.
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Affiliation(s)
- Rima Tumia
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Chao J Wang
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Tianhan Dong
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Shijie Ma
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Jenny Beebe
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Juan Chen
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Zizheng Dong
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Jing-Yuan Liu
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Jian-Ting Zhang
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
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9
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Herrmannová A, Prilepskaja T, Wagner S, Šikrová D, Zeman J, Poncová K, Valášek LS. Adapted formaldehyde gradient cross-linking protocol implicates human eIF3d and eIF3c, k and l subunits in the 43S and 48S pre-initiation complex assembly, respectively. Nucleic Acids Res 2020; 48:1969-1984. [PMID: 31863585 PMCID: PMC7039009 DOI: 10.1093/nar/gkz1185] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 12/18/2022] Open
Abstract
One of the key roles of the 12-subunit eukaryotic translation initiation factor 3 (eIF3) is to promote the formation of the 43S and 48S pre-initiation complexes (PICs). However, particular contributions of its individual subunits to these two critical initiation reactions remained obscure. Here, we adapted formaldehyde gradient cross-linking protocol to translation studies and investigated the efficiency of the 43S and 48S PIC assembly in knockdowns of individual subunits of human eIF3 known to produce various partial subcomplexes. We revealed that eIF3d constitutes an important intermolecular bridge between eIF3 and the 40S subunit as its elimination from the eIF3 holocomplex severely compromised the 43S PIC assembly. Similarly, subunits eIF3a, c and e were found to represent an important binding force driving eIF3 binding to the 40S subunit. In addition, we demonstrated that eIF3c, and eIF3k and l subunits alter the efficiency of mRNA recruitment to 43S PICs in an opposite manner. Whereas the eIF3c knockdown reduces it, downregulation of eIF3k or eIF3l increases mRNA recruitment, suggesting that the latter subunits possess a regulatory potential. Altogether this study provides new insights into the role of human eIF3 in the initial assembly steps of the translational machinery.
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Affiliation(s)
- Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Terezie Prilepskaja
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Darina Šikrová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Kristýna Poncová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, the Czech Republic
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10
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Roobol A, Roobol J, Smith ME, Carden MJ, Hershey JWB, Willis AE, Smales CM. Engineered transient and stable overexpression of translation factors eIF3i and eIF3c in CHOK1 and HEK293 cells gives enhanced cell growth associated with increased c-Myc expression and increased recombinant protein synthesis. Metab Eng 2020; 59:98-105. [PMID: 32061967 PMCID: PMC7118365 DOI: 10.1016/j.ymben.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/31/2020] [Accepted: 02/09/2020] [Indexed: 01/23/2023]
Abstract
There is a desire to engineer mammalian host cell lines to improve cell growth/biomass accumulation and recombinant biopharmaceutical protein production in industrially relevant cell lines such as the CHOK1 and HEK293 cell lines. The over-expression of individual subunits of the eukaryotic translation factor eIF3 in mammalian cells has previously been shown to result in oncogenic properties being imparted on cells, including increased cell proliferation and growth and enhanced global protein synthesis rates. Here we report on the engineering of CHOK1 and HEK cells to over-express the eIF3i and eIF3c subunits of the eIF3 complex and the resultant impact on cell growth and a reporter of exogenous recombinant protein production. Transient over-expression of eIF3i in HEK293 and CHOK1 cells resulted in a modest increase in total eIF3i amounts (maximum 40% increase above control) and an approximate 10% increase in global protein synthesis rates in CHOK1 cells. Stable over-expression of eIF3i in CHOK1 cells was not achievable, most likely due to the already high levels of eIF3i in CHO cells compared to HEK293 cells, but was achieved in HEK293 cells. HEK293 cells engineered to over-express eIF3i had faster growth that was associated with increased c-Myc expression, achieved higher cell biomass and gave enhanced yields of a reporter of recombinant protein production. Whilst CHOK1 cells could not be engineered to over-express eIF3i directly, they could be engineered to over-express eIF3c, which resulted in a subsequent increase in eIF3i amounts and c-Myc expression. The CHOK1 eIF3c engineered cells grew to higher cell numbers and had enhanced cap- and IRES-dependent recombinant protein synthesis. Collectively these data show that engineering of subunits of the eIF3 complex can enhance cell growth and recombinant protein synthesis in mammalian cells in a cell specific manner that has implications for the engineering or selection of fast growing or high producing cells for production of recombinant proteins. We have engineered the overexpression of eIF3i and eIF3c in CHOK1 and HEK293 cells. HEK293 cells overexpressing eIF3i had faster growth and increased c-Myc expression. Direct stable overexpression of eIF3i in CHOK1 cells was not achievable. Overexpression of eIF3c in CHOK1 cells resulted in an increase in eIF3i. eIF3c overexpressing CHOK1 cells had enhanced recombinant protein synthesis.
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Affiliation(s)
- Anne Roobol
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Joanne Roobol
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Matthew E Smith
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Martin J Carden
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - John W B Hershey
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA, 95616, USA
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Lancaster Rd, Leicester, LE1 9HN, UK.
| | - C Mark Smales
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
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11
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Zhang W, Yang Y, Dong Z, Shi Z, Zhang JT. Single-nucleotide polymorphisms in a short basic motif in the ABC transporter ABCG2 disable its trafficking out of endoplasmic reticulum and reduce cell resistance to anticancer drugs. J Biol Chem 2019; 294:20222-20232. [PMID: 31719146 DOI: 10.1074/jbc.ra119.008347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 08/14/2019] [Indexed: 12/14/2022] Open
Abstract
ATP-binding cassette (ABC) subfamily G member 2 (ABCG2) belongs to the ABC transporter superfamily and has been implicated in multidrug resistance of cancers. Although the structure and function of ABCG2 have been extensively studied, little is known about its biogenesis and the regulation thereof. In this study, using mutagenesis and several biochemical analyses, we show that the positive charges in the vicinity of the RKR motif downstream of the ABC signature drive trafficking of nascent ABCG2 out of the endoplasmic reticulum (ER) onto plasma membranes. Substitutions of and naturally occurring single-nucleotide polymorphisms within these positively charged residues disabled the trafficking of ABCG2 out of the ER. A representative ABCG2 variant in which the RKR motif had been altered underwent increased ER stress-associated degradation. We also found that unlike WT ABCG2, genetic ABCG2 RKR variants have disrupted normal maturation and do not reduce accumulation of the anticancer drug mitoxantrone and no longer confer resistance to the drug. We conclude that the positive charges downstream of the ABC signature motif critically regulate ABCG2 trafficking and maturation. We propose that single-nucleotide polymorphisms of these residues reduce ABCG2 expression via ER stress-associated degradation pathway and may contribute to reduced cancer drug resistance, improving the success of cancer chemotherapy.
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Affiliation(s)
- Wenji Zhang
- Department of Pharmacology and Toxicology and Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202.,Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China
| | - Yang Yang
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China
| | - Zizheng Dong
- Department of Pharmacology and Toxicology and Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202.,Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614
| | - Zhi Shi
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China
| | - Jian-Ting Zhang
- Department of Pharmacology and Toxicology and Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202 .,Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614
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12
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Valášek LS, Zeman J, Wagner S, Beznosková P, Pavlíková Z, Mohammad MP, Hronová V, Herrmannová A, Hashem Y, Gunišová S. Embraced by eIF3: structural and functional insights into the roles of eIF3 across the translation cycle. Nucleic Acids Res 2017; 45:10948-10968. [PMID: 28981723 PMCID: PMC5737393 DOI: 10.1093/nar/gkx805] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/31/2017] [Indexed: 12/31/2022] Open
Abstract
Protein synthesis is mediated via numerous molecules including the ribosome, mRNA, tRNAs, as well as translation initiation, elongation and release factors. Some of these factors play several roles throughout the entire process to ensure proper assembly of the preinitiation complex on the right mRNA, accurate selection of the initiation codon, errorless production of the encoded polypeptide and its proper termination. Perhaps, the most intriguing of these multitasking factors is the eukaryotic initiation factor eIF3. Recent evidence strongly suggests that this factor, which coordinates the progress of most of the initiation steps, does not come off the initiation complex upon subunit joining, but instead it remains bound to 80S ribosomes and gradually falls off during the first few elongation cycles to: (1) promote resumption of scanning on the same mRNA molecule for reinitiation downstream—in case of translation of upstream ORFs short enough to preserve eIF3 bound; or (2) come back during termination on long ORFs to fine tune its fidelity or, if signaled, promote programmed stop codon readthrough. Here, we unite recent structural views of the eIF3–40S complex and discus all known eIF3 roles to provide a broad picture of the eIF3’s impact on translational control in eukaryotic cells.
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Affiliation(s)
- Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Zuzana Pavlíková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Mahabub Pasha Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Yaser Hashem
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
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13
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Abstract
The eukaryotic initiation factor 3 (eIF3) is one of the most complex translation initiation factors in mammalian cells, consisting of several subunits (eIF3a to eIF3m). It is crucial in translation initiation and termination, and in ribosomal recycling. Accordingly, deregulated eIF3 expression is associated with different pathological conditions, including cancer. In this manuscript, we discuss the interactome and function of each subunit of the human eIF3 complex. Furthermore, we review how altered levels of eIF3 subunits correlate with neurodegenerative disorders and cancer onset and development; in addition, we evaluate how such misregulation may also trigger infection cascades. A deep understanding of the molecular mechanisms underlying eIF3 role in human disease is essential to develop new eIF3-targeted therapeutic approaches and thus, overcome such conditions.
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Affiliation(s)
- Andreia Gomes-Duarte
- a Department of Human Genetics , Instituto Nacional de Saúde Doutor Ricardo Jorge , Lisbon , Portugal.,b Gene Expression and Regulation Group, Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências , Universidade de Lisboa , Lisbon , Portugal
| | - Rafaela Lacerda
- a Department of Human Genetics , Instituto Nacional de Saúde Doutor Ricardo Jorge , Lisbon , Portugal.,b Gene Expression and Regulation Group, Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências , Universidade de Lisboa , Lisbon , Portugal
| | - Juliane Menezes
- a Department of Human Genetics , Instituto Nacional de Saúde Doutor Ricardo Jorge , Lisbon , Portugal.,b Gene Expression and Regulation Group, Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências , Universidade de Lisboa , Lisbon , Portugal
| | - Luísa Romão
- a Department of Human Genetics , Instituto Nacional de Saúde Doutor Ricardo Jorge , Lisbon , Portugal.,b Gene Expression and Regulation Group, Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências , Universidade de Lisboa , Lisbon , Portugal
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14
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Yin JY, Zhang JT, Zhang W, Zhou HH, Liu ZQ. eIF3a: A new anticancer drug target in the eIF family. Cancer Lett 2017; 412:81-87. [PMID: 29031564 DOI: 10.1016/j.canlet.2017.09.055] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/12/2017] [Accepted: 09/25/2017] [Indexed: 02/04/2023]
Abstract
eIF3a is the largest subunit of eIF3, which is a key player in all steps of translation initiation. During the past years, eIF3a is recognized as a proto-oncogene, which is an important discovery in this field. It is widely reported to be correlated with cancer occurrence, metastasis, prognosis, and therapeutic response. Recently, the mechanisms of eIF3a action in the carcinogenesis are unveiled gradually. A number of cellular, physiological, and pathological processes involving eIF3a are identified. Most importantly, it is emerging as a new potential drug target in the eIF family, and some small molecule inhibitors are being developed. Thus, we perform a critical review of recent advances in understanding eIF3a physiological and pathological functions, with specific focus on its role in cancer and anticancer drug targets.
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Affiliation(s)
- Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China.
| | - Jian-Ting Zhang
- Department of Pharmacology & Toxicology and IU Cancer Center, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, PR China.
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15
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Hinnebusch AG. Structural Insights into the Mechanism of Scanning and Start Codon Recognition in Eukaryotic Translation Initiation. Trends Biochem Sci 2017; 42:589-611. [PMID: 28442192 DOI: 10.1016/j.tibs.2017.03.004] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/12/2017] [Accepted: 03/20/2017] [Indexed: 12/21/2022]
Abstract
Initiation of translation on eukaryotic mRNAs generally follows the scanning mechanism, wherein a preinitiation complex (PIC) assembled on the small (40S) ribosomal subunit and containing initiator methionyl tRNAi (Met-tRNAi) scans the mRNA leader for an AUG codon. In a current model, the scanning PIC adopts an open conformation and rearranges to a closed state, with fully accommodated Met-tRNAi, upon AUG recognition. Evidence from recent high-resolution structures of PICs assembled with different ligands supports this model and illuminates the molecular functions of eukaryotic initiation factors eIF1, eIF1A, and eIF2 in restricting to AUG codons the transition to the closed conformation. They also reveal that the eIF3 complex interacts with multiple functional sites in the PIC, rationalizing its participation in numerous steps of initiation.
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Affiliation(s)
- Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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16
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Li K, Zhou S, Guo Q, Chen X, Lai DH, Lun ZR, Guo X. The eIF3 complex of Trypanosoma brucei: composition conservation does not imply the conservation of structural assembly and subunits function. RNA (NEW YORK, N.Y.) 2017; 23:333-345. [PMID: 27932584 PMCID: PMC5311491 DOI: 10.1261/rna.058651.116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 11/24/2016] [Indexed: 05/03/2023]
Abstract
The multisubunit eukaryotic initiation factor 3 (eIF3) plays multiple roles in translation but is poorly understood in trypanosomes. The putative subunits eIF3a and eIF3f of Trypanosoma brucei (TbIF3a and TbIF3f) were overexpressed and purified, and 11 subunits were identified, TbIF3a through l minus j, which form a tight complex. Both TbIF3a and TbIF3f are essential for the viability of T. brucei RNAi knockdown of either of them severely reduced total translation and the ratio of the polysome/80S peak area. TbIF3f and TbIF3a RNAi cell lines were modified to express tagged-TbIF3a and -TbIF3f, respectively. RNAi in combination with affinity purification assays indicated that both subunits are variably required for TbIF3 stability and integrity. The relative abundance of other subunits in the TbIF3f-tag complex changed little upon TbIF3a depletion; while only subunits TbIF3b, i, and e copurified comparably with TbIF3a-tag upon TbIF3f depletion. A genome-wide UV-crosslinking assay showed that several TbIF3 subunits have direct RNA-binding activity, with TbIF3c showing the strongest signal. In addition, CrPV IRES, but neither EMCV IRES nor HCV IRES, was found to mediate translation in T. brucei These results together imply that the structure of TbIF3 and the subunits function have trypanosome-specific features, although the composition is evolutionarily conserved.
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Affiliation(s)
- Kunrao Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
| | - Shuru Zhou
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
| | - Qixuan Guo
- Chengde Nursing Vocational College, Chengde 067000, China
| | - Xin Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
| | - De-Hua Lai
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhao-Rong Lun
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xuemin Guo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
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17
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Wagner S, Herrmannová A, Šikrová D, Valášek LS. Human eIF3b and eIF3a serve as the nucleation core for the assembly of eIF3 into two interconnected modules: the yeast-like core and the octamer. Nucleic Acids Res 2016; 44:10772-10788. [PMID: 27924037 PMCID: PMC5159561 DOI: 10.1093/nar/gkw972] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 12/05/2022] Open
Abstract
The 12-subunit mammalian eIF3 is the largest and most complex translation initiation factor and has been implicated in numerous steps of translation initiation, termination and ribosomal recycling. Imbalanced eIF3 expression levels are observed in various types of cancer and developmental disorders, but the consequences of altered eIF3 subunit expression on its overall structure and composition, and on translation in general, remain unclear. We present the first complete in vivo study monitoring the effects of RNAi knockdown of each subunit of human eIF3 on its function, subunit balance and integrity. We show that the eIF3b and octameric eIF3a subunits serve as the nucleation core around which other subunits assemble in an ordered way into two interconnected modules: the yeast-like core and the octamer, respectively. In the absence of eIF3b neither module forms in vivo, whereas eIF3d knock-down results in severe proliferation defects with no impact on eIF3 integrity. Disrupting the octamer produces an array of subcomplexes with potential roles in translational regulation. This study, outlining the mechanism of eIF3 assembly and illustrating how imbalanced expression of eIF3 subunits impacts the factor's overall expression profile, thus provides a comprehensive guide to the human eIF3 complex and to the relationship between eIF3 misregulation and cancer.
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Affiliation(s)
- Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Darina Šikrová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague, 142 20, the Czech Republic
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18
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Assembly of eIF3 Mediated by Mutually Dependent Subunit Insertion. Structure 2016; 24:886-96. [PMID: 27210288 DOI: 10.1016/j.str.2016.02.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 02/19/2016] [Accepted: 02/21/2016] [Indexed: 02/05/2023]
Abstract
Eukaryotic initiation factor 3 (eIF3), an essential multi-protein complex involved in translation initiation, is composed of 12 tightly associated subunits in humans. While the overall structure of eIF3 is known, the mechanism of its assembly and structural consequences of dysregulation of eIF3 subunit expression seen in many cancers is largely unknown. Here we show that subunits in eIF3 assemble into eIF3 in an interdependent manner. Assembly of eIF3 is governed primarily by formation of a helical bundle, composed of helices extending C-terminally from PCI-MPN domains in eight subunits. We propose that, while the minimal subcomplex of human-like eIF3 functional for translation initiation in cells consists of subunits a, b, c, f, g, i, and m, numerous other eIF3 subcomplexes exist under circumstances of subunit over- or underexpression. Thus, eIF3 subcomplexes formed or "released" due to dysregulated subunit expression may be determining factors contributing to eIF3-related cancers.
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19
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Toompuu M, Kärblane K, Pata P, Truve E, Sarmiento C. ABCE1 is essential for S phase progression in human cells. Cell Cycle 2016; 15:1234-47. [PMID: 26985706 DOI: 10.1080/15384101.2016.1160972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
ABCE1 is a highly conserved protein universally present in eukaryotes and archaea, which is crucial for the viability of different organisms. First identified as RNase L inhibitor, ABCE1 is currently recognized as an essential translation factor involved in several stages of eukaryotic translation and ribosome biogenesis. The nature of vital functions of ABCE1, however, remains unexplained. Here, we study the role of ABCE1 in human cell proliferation and its possible connection to translation. We show that ABCE1 depletion by siRNA results in a decreased rate of cell growth due to accumulation of cells in S phase, which is accompanied by inefficient DNA synthesis and reduced histone mRNA and protein levels. We infer that in addition to the role in general translation, ABCE1 is involved in histone biosynthesis and DNA replication and therefore is essential for normal S phase progression. In addition, we analyze whether ABCE1 is implicated in transcript-specific translation via its association with the eIF3 complex subunits known to control the synthesis of cell proliferation-related proteins. The expression levels of a few such targets regulated by eIF3A, however, were not consistently affected by ABCE1 depletion.
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Affiliation(s)
- Marina Toompuu
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Kairi Kärblane
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Pille Pata
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Erkki Truve
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Cecilia Sarmiento
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
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20
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des Georges A, Dhote V, Kuhn L, Hellen CUT, Pestova TV, Frank J, Hashem Y. Structure of mammalian eIF3 in the context of the 43S preinitiation complex. Nature 2015; 525:491-5. [PMID: 26344199 DOI: 10.1038/nature14891] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 07/06/2015] [Indexed: 12/11/2022]
Abstract
During eukaryotic translation initiation, 43S complexes, comprising a 40S ribosomal subunit, initiator transfer RNA and initiation factors (eIF) 2, 3, 1 and 1A, attach to the 5'-terminal region of messenger RNA and scan along it to the initiation codon. Scanning on structured mRNAs also requires the DExH-box protein DHX29. Mammalian eIF3 contains 13 subunits and participates in nearly all steps of translation initiation. Eight subunits having PCI (proteasome, COP9 signalosome, eIF3) or MPN (Mpr1, Pad1, amino-terminal) domains constitute the structural core of eIF3, to which five peripheral subunits are flexibly linked. Here we present a cryo-electron microscopy structure of eIF3 in the context of the DHX29-bound 43S complex, showing the PCI/MPN core at ∼6 Å resolution. It reveals the organization of the individual subunits and their interactions with components of the 43S complex. We were able to build near-complete polyalanine-level models of the eIF3 PCI/MPN core and of two peripheral subunits. The implications for understanding mRNA ribosomal attachment and scanning are discussed.
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Affiliation(s)
- Amedee des Georges
- HHMI, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Vidya Dhote
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Lauriane Kuhn
- CNRS, Proteomic Platform Strasbourg - Esplanade, Strasbourg 67084, France
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Joachim Frank
- HHMI, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.,Department of Biological Sciences, Columbia University, New York, New York 10032, USA
| | - Yaser Hashem
- CNRS, Architecture et Réactivité de l'ARN, Université de Strasbourg, Strasbourg 67084, France
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21
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Llácer JL, Hussain T, Marler L, Aitken CE, Thakur A, Lorsch JR, Hinnebusch AG, Ramakrishnan V. Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex. Mol Cell 2015. [PMID: 26212456 PMCID: PMC4534855 DOI: 10.1016/j.molcel.2015.06.033] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5′ end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition. Structures of eukaryotic translation initiation complexes in open and closed states In the open complex the 40S head moves upward to open the mRNA entry channel latch Transition to closed state locks initiator tRNA in the P site base-paired with AUG The structures show how eIF3 contacts eIF2 and eIF1 on the 40S subunit interface
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Affiliation(s)
- Jose L Llácer
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Laura Marler
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Colin Echeverría Aitken
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anil Thakur
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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22
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Structure of a yeast 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex. Nat Struct Mol Biol 2015; 22:269-71. [PMID: 25664723 DOI: 10.1038/nsmb.2963] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/24/2014] [Indexed: 11/09/2022]
Abstract
Eukaryotic translation initiation requires cooperative assembly of a large protein complex at the 40S ribosomal subunit. We have resolved a budding yeast initiation complex by cryo-EM, allowing placement of prior structures of eIF1, eIF1A, eIF3a, eIF3b and eIF3c. Our structure highlights differences in initiation-complex binding to the ribosome compared to that of mammalian eIF3, demonstrates a direct contact between eIF3j and eIF1A and reveals the network of interactions between eIF3 subunits.
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23
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Rezende AM, Assis LA, Nunes EC, da Costa Lima TD, Marchini FK, Freire ER, Reis CRS, de Melo Neto OP. The translation initiation complex eIF3 in trypanosomatids and other pathogenic excavates--identification of conserved and divergent features based on orthologue analysis. BMC Genomics 2014; 15:1175. [PMID: 25539953 PMCID: PMC4320536 DOI: 10.1186/1471-2164-15-1175] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/16/2014] [Indexed: 12/24/2022] Open
Abstract
Background The initiation of translation in eukaryotes is supported by the action of several eukaryotic Initiation Factors (eIFs). The largest of these is eIF3, comprising of up to thirteen polypeptides (eIF3a through eIF3m), involved in multiple stages of the initiation process. eIF3 has been better characterized from model organisms, but is poorly known from more diverged groups, including unicellular lineages represented by known human pathogens. These include the trypanosomatids (Trypanosoma and Leishmania) and other protists belonging to the taxonomic supergroup Excavata (Trichomonas and Giardia sp.). Results An in depth bioinformatic search was carried out to recover the full content of eIF3 subunits from the available genomes of L. major, T. brucei, T. vaginalis and G. duodenalis. The protein sequences recovered were then submitted to homology analysis and alignments comparing them with orthologues from representative eukaryotes. Eleven putative eIF3 subunits were found from both trypanosomatids whilst only five and four subunits were identified from T. vaginalis and G. duodenalis, respectively. Only three subunits were found in all eukaryotes investigated, eIF3b, eIF3c and eIF3i. The single subunit found to have a related Archaean homologue was eIF3i, the most conserved of the eIF3 subunits. The sequence alignments revealed several strongly conserved residues/region within various eIF3 subunits of possible functional relevance. Subsequent biochemical characterization of the Leishmania eIF3 complex validated the bioinformatic search and yielded a twelfth eIF3 subunit in trypanosomatids, eIF3f (the single unidentified subunit in trypanosomatids was then eIF3m). The biochemical data indicates a lack of association of the eIF3j subunit to the complex whilst highlighting the strong interaction between eIF3 and eIF1. Conclusions The presence of most eIF3 subunits in trypanosomatids is consistent with an early evolution of a fully functional complex. Simplified versions in other excavates might indicate a primordial complex or secondary loss of selected subunits, as seen for some fungal lineages. The conservation in eIF3i sequence might indicate critical functions within eIF3 which have been overlooked. The identification of eIF3 subunits from distantly related eukaryotes provides then a basis for the study of conserved/divergent aspects of eIF3 function, leading to a better understanding of eukaryotic translation initiation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1175) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Osvaldo P de Melo Neto
- Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Avenida Professor Moraes Rego s/n, Cidade Universitária, Recife, PE 50670-420, Brazil.
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24
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Hershey JWB. The role of eIF3 and its individual subunits in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:792-800. [PMID: 25450521 DOI: 10.1016/j.bbagrm.2014.10.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/28/2014] [Accepted: 10/28/2014] [Indexed: 12/15/2022]
Abstract
Specific individual subunits of eIF3 are elevated or reduced in numerous human tumors, and their ectopic overexpression in immortal cells can result in malignant transformation. The structure and assembly of eIF3 and its role in promoting mRNA and methionyl-tRNAi binding to the ribosome during the initiation phase of protein synthesis are described. Methods employed to detect altered levels of eIF3 subunits in cancers are critically evaluated in order to conclude rigorously that such subunits may cause malignant transformation. Strong evidence is presented that the individual overexpression of eIF3 subunits 3a, 3b, 3c, 3h, 3i and 3m may cause malignant transformation, whereas underexpression of subunits 3e and 3f may cause a similar outcome. Possible mechanisms to explain the malignant phenotypes are examined. The involvement of eIF3 in cancer reinforces the view that translational control plays an important role in the regulation of cell proliferation, and provides new targets for the development of therapeutic agents. This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- John W B Hershey
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, United States.
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25
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Yue MM, Lv K, Meredith SC, Martindale JL, Gorospe M, Schuger L. Novel RNA-binding protein P311 binds eukaryotic translation initiation factor 3 subunit b (eIF3b) to promote translation of transforming growth factor β1-3 (TGF-β1-3). J Biol Chem 2014; 289:33971-83. [PMID: 25336651 DOI: 10.1074/jbc.m114.609495] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
P311, a conserved 8-kDa intracellular protein expressed in brain, smooth muscle, regenerating tissues, and malignant glioblastomas, represents the first documented stimulator of TGF-β1-3 translation in vitro and in vivo. Here we initiated efforts to define the mechanism underlying P311 function. PONDR® (Predictor Of Naturally Disordered Regions) analysis suggested and CD confirmed that P311 is an intrinsically disordered protein, therefore requiring an interacting partner to acquire tertiary structure and function. Immunoprecipitation coupled with mass spectroscopy identified eIF3 subunit b (eIF3b) as a novel P311 binding partner. Immunohistochemical colocalization, GST pulldown, and surface plasmon resonance studies revealed that P311-eIF3b interaction is direct and has a Kd of 1.26 μm. Binding sites were mapped to the non-canonical RNA recognition motif of eIF3b and a central 11-amino acid-long region of P311, here referred to as eIF3b binding motif. Disruption of P311-eIF3b binding inhibited translation of TGF-β1, 2, and 3, as indicated by luciferase reporter assays, polysome fractionation studies, and Western blot analysis. RNA precipitation assays after UV cross-linking and RNA-protein EMSA demonstrated that P311 binds directly to TGF-β 5'UTRs mRNAs through a previously unidentified RNA recognition motif-like motif. Our results demonstrate that P311 is a novel RNA-binding protein that, by interacting with TGF-βs 5'UTRs and eIF3b, stimulates the translation of TGF-β1, 2, and 3.
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Affiliation(s)
| | | | - Stephen C Meredith
- From the Departments of Pathology and Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637 and
| | - Jennifer L Martindale
- the Laboratory of Genetics, NIA, National Institutes of Health, Baltimore, Maryland 21224
| | - Myriam Gorospe
- the Laboratory of Genetics, NIA, National Institutes of Health, Baltimore, Maryland 21224
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26
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Wagner S, Herrmannová A, Malík R, Peclinovská L, Valášek LS. Functional and biochemical characterization of human eukaryotic translation initiation factor 3 in living cells. Mol Cell Biol 2014; 34:3041-52. [PMID: 24912683 PMCID: PMC4135593 DOI: 10.1128/mcb.00663-14] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 06/04/2014] [Indexed: 11/20/2022] Open
Abstract
The main role of the translation initiation factor 3 (eIF3) is to orchestrate formation of 43S-48S preinitiation complexes (PICs). Until now, most of our knowledge on eIF3 functional contribution to regulation of gene expression comes from yeast studies. Hence, here we developed several novel in vivo assays to monitor the integrity of the 13-subunit human eIF3 complex, defects in assembly of 43S PICs, efficiency of mRNA recruitment, and postassembly events such as AUG recognition. We knocked down expression of the PCI domain-containing eIF3c and eIF3a subunits and of eIF3j in human HeLa and HEK293 cells and analyzed the functional consequences. Whereas eIF3j downregulation had barely any effect and eIF3a knockdown disintegrated the entire eIF3 complex, eIF3c knockdown produced a separate assembly of the a, b, g, and i subunits (closely resembling the yeast evolutionary conserved eIF3 core), which preserved relatively high 40S binding affinity and an ability to promote mRNA recruitment to 40S subunits and displayed defects in AUG recognition. Both eIF3c and eIF3a knockdowns also severely reduced protein but not mRNA levels of many other eIF3 subunits and indeed shut off translation. We propose that eIF3a and eIF3c control abundance and assembly of the entire eIF3 and thus represent its crucial scaffolding elements critically required for formation of PICs.
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Affiliation(s)
- Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska, Prague, Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska, Prague, Czech Republic
| | - Radek Malík
- Laboratory of Epigenetic Regulations, Institute of Molecular Genetics ASCR, Videnska, Prague, Czech Republic
| | - Lucie Peclinovská
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska, Prague, Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska, Prague, Czech Republic
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