1
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Ide NA, Gentry RC, Rudbach MA, Yoo K, Velez PK, Comunale VM, Hartwick EW, Kinz-Thompson CD, Gonzalez RL, Aitken CE. A dynamic compositional equilibrium governs mRNA recognition by eIF3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.581977. [PMID: 38712078 PMCID: PMC11071631 DOI: 10.1101/2024.04.25.581977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Eukaryotic translation initiation factor (eIF) 3 is a multi-subunit protein complex that binds both ribosomes and messenger RNAs (mRNAs) in order to drive a diverse set of mechanistic steps during translation. Despite its importance, a unifying framework explaining how eIF3 performs these numerous activities is lacking. Using single-molecule light scattering microscopy, we demonstrate that Saccharomyces cerevisiae eIF3 is an equilibrium mixture of the full complex, subcomplexes, and subunits. By extending our microscopy approach to an in vitro reconstituted eIF3 and complementing it with biochemical assays, we define the subspecies comprising this equilibrium and show that, rather than being driven by the full complex, mRNA binding by eIF3 is instead driven by the eIF3a subunit within eIF3a-containing subcomplexes. Our findings provide a mechanistic model for the role of eIF3 in the mRNA recruitment step of translation initiation and establish a mechanistic framework for explaining and investigating the other activities of eIF3.
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2
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Pan Q, Yu F, Jin H, Zhang P, Huang X, Peng J, Xie X, Li X, Ma N, Wei Y, Wen W, Zhang J, Zhang B, Yu H, Xiao Y, Liu R, Liu Q, Meng X, Lee M. eIF3f Mediates SGOC Pathway Reprogramming by Enhancing Deubiquitinating Activity in Colorectal Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300759. [PMID: 37544925 PMCID: PMC10520677 DOI: 10.1002/advs.202300759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/25/2023] [Indexed: 08/08/2023]
Abstract
Numerous studies have demonstrated that individual proteins can moonlight. Eukaryotic Initiation translation factor 3, f subunit (eIF3f) is involved in critical biological functions; however, its role independent of protein translation in regulating colorectal cancer (CRC) is not characterized. Here, it is demonstrated that eIF3f is upregulated in CRC tumor tissues and that both Wnt and EGF signaling pathways are participating in eIF3f's oncogenic impact on targeting phosphoglycerate dehydrogenase (PHGDH) during CRC development. Mechanistically, EGF blocks FBXW7β-mediated PHGDH ubiquitination through GSK3β deactivation, and eIF3f antagonizes FBXW7β-mediated PHGDH ubiquitination through its deubiquitinating activity. Additionally, Wnt signals transcriptionally activate the expression of eIF3f, which also exerts its deubiquitinating activity toward MYC, thereby increasing MYC-mediated PHGDH transcription. Thereby, both impacts allow eIF3f to elevate the expression of PHGDH, enhancing Serine-Glycine-One-Carbon (SGOC) signaling pathway to facilitate CRC development. In summary, the study uncovers the intrinsic role and underlying molecular mechanism of eIF3f in SGOC signaling, providing novel insight into the strategies to target eIF3f-PHGDH axis in CRC.
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Affiliation(s)
- Qihao Pan
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Department of Obstetrics and GynecologyThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Fenghai Yu
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Huilin Jin
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Peng Zhang
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Xiaoling Huang
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Jingxuan Peng
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Xiaoshan Xie
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Xiangli Li
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Ning Ma
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Yue Wei
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Weijie Wen
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Jieping Zhang
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Boyu Zhang
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Hongyan Yu
- Department of Clinical Biological Resource BankGuangzhou Institute of PediatricsGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhou510623China
| | - Yuanxun Xiao
- Burn Plastic SurgeryYue bei People's HospitalWujiang512099China
| | - Ran‐yi Liu
- State Key Laboratory of Oncology in South China & Collaborative Innovation Center of Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Qingxin Liu
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Xiangqi Meng
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
| | - Mong‐Hong Lee
- Department of General SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
- Department of OncologyThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhou510655China
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3
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Abaeva IS, Arhab Y, Miścicka A, Hellen CUT, Pestova TV. In vitro reconstitution of SARS-CoV-2 Nsp1-induced mRNA cleavage reveals the key roles of the N-terminal domain of Nsp1 and the RRM domain of eIF3g. Genes Dev 2023; 37:844-860. [PMID: 37821106 PMCID: PMC10620056 DOI: 10.1101/gad.350829.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
SARS CoV-2 nonstructural protein 1 (Nsp1) is the major pathogenesis factor that inhibits host translation using a dual strategy of impairing initiation and inducing endonucleolytic cleavage of cellular mRNAs. To investigate the mechanism of cleavage, we reconstituted it in vitro on β-globin, EMCV IRES, and CrPV IRES mRNAs that use unrelated initiation mechanisms. In all instances, cleavage required Nsp1 and only canonical translational components (40S subunits and initiation factors), arguing against involvement of a putative cellular RNA endonuclease. Requirements for initiation factors differed for these mRNAs, reflecting their requirements for ribosomal attachment. Cleavage of CrPV IRES mRNA was supported by a minimal set of components consisting of 40S subunits and eIF3g's RRM domain. The cleavage site was located in the coding region 18 nt downstream from the mRNA entrance, indicating that cleavage occurs on the solvent side of the 40S subunit. Mutational analysis identified a positively charged surface on Nsp1's N-terminal domain (NTD) and a surface above the mRNA-binding channel on eIF3g's RRM domain that contain residues essential for cleavage. These residues were required for cleavage on all three mRNAs, highlighting general roles of the Nsp1 NTD and eIF3g's RRM domain in cleavage per se, irrespective of the mode of ribosomal attachment.
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Affiliation(s)
- Irina S Abaeva
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Yani Arhab
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Anna Miścicka
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
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4
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Abaeva IS, Arhab Y, Miścicka A, Hellen CUT, Pestova TV. In vitro reconstitution of SARS CoV-2 Nsp1-induced mRNA cleavage reveals the key roles of the N-terminal domain of Nsp1 and the RRM domain of eIF3g. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542379. [PMID: 37292671 PMCID: PMC10245999 DOI: 10.1101/2023.05.25.542379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
SARS CoV-2 nonstructural protein 1 (Nsp1) is the major pathogenesis factor that inhibits host translation using a dual strategy of impairing initiation and inducing endonucleolytic cleavage of cellular mRNAs. To investigate the mechanism of cleavage, we reconstituted it in vitro on β-globin, EMCV IRES and CrPV IRES mRNAs that use unrelated initiation mechanisms. In all instances, cleavage required Nsp1 and only canonical translational components (40S subunits and initiation factors), arguing against involvement of a putative cellular RNA endonuclease. Requirements for initiation factors differed for these mRNAs, reflecting their requirements for ribosomal attachment. Cleavage of CrPV IRES mRNA was supported by a minimal set of components consisting of 40S subunits and eIF3g's RRM domain. The cleavage site was located in the coding region 18 nucleotides downstream from the mRNA entrance indicating that cleavage occurs on the solvent side of the 40S subunit. Mutational analysis identified a positively charged surface on Nsp1's N-terminal domain (NTD) and a surface above the mRNA-binding channel on eIF3g's RRM domain that contain residues essential for cleavage. These residues were required for cleavage on all three mRNAs, highlighting general roles of Nsp1-NTD and eIF3g's RRM domain in cleavage per se, irrespective of the mode of ribosomal attachment.
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Affiliation(s)
- Irina S. Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Yani Arhab
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Anna Miścicka
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | | | - Tatyana V. Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
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5
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Li Y, Gao Z, Lu J, Wei X, Qi M, Yin Z, Li T. SlSnRK2.3 interacts with SlSUI1 to modulate high temperature tolerance via Abscisic acid (ABA) controlling stomatal movement in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111305. [PMID: 35696906 DOI: 10.1016/j.plantsci.2022.111305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/02/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Tomato is often exposed to high temperature stress during summer cultivation. Stomatal movement plays important roles in photosynthesis and transpiration which restricts the quality and yield of tomato under environmental stress. To elucidate the mechanism of stomatal movement in high temperature tolerance, SlSnRK2s (sucrose non-fermenting 1-related protein kinases) silenced plants were generated in tomato with CRISPR-Cas 9 gene editing techniques. Through the observation of stomatal parameters, SlSnRK2.3 regulated stomatal closure which was responded to ABA (abscisic acid) and activated signaling pathway of ROS (reactive oxygen species) in high temperature stress. Based on the positive functions of SlSnRK2.3, the cDNA library was generated to investigate interaction proteins of SlSnRK2s. The interaction between SlSnRK2.3 and SlSUI1 (protein translation factor SUI1 homolog) was employed by Yeast two hybrid assay (Y2H), Luciferase (LUC), and Bimolecular fluorescence complementation (BiFC). Finally, the specific interactive sites between SlSnRK2.3 and SlSUI1 were verified by site-directed mutagenesis. The consistent mechanism of SlSnRK2.3 and SlSUI1 in stomatal movement, indicating that SlSUI1 interacted with SlSnRK2.3 through ABA-dependent signaling pathway in high temperature stress. Our results provided evidence for improving the photosynthetic capacity of tomato under high temperature stress, and support the breeding and genetic engineering of tomato over summer facility cultivation.
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Affiliation(s)
- Yangyang Li
- Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, 110866, PR China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), No. 120 Dongling Road, Shenhe District, 110866, PR China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, No. 120 Dongling Road, Shenhe District, 110866, PR China
| | - Zhenhua Gao
- Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, 110866, PR China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), No. 120 Dongling Road, Shenhe District, 110866, PR China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, No. 120 Dongling Road, Shenhe District, 110866, PR China
| | - Jiazhi Lu
- Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, 110866, PR China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), No. 120 Dongling Road, Shenhe District, 110866, PR China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, No. 120 Dongling Road, Shenhe District, 110866, PR China
| | - Xueying Wei
- Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, 110866, PR China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), No. 120 Dongling Road, Shenhe District, 110866, PR China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, No. 120 Dongling Road, Shenhe District, 110866, PR China
| | - Mingfang Qi
- Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, 110866, PR China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), No. 120 Dongling Road, Shenhe District, 110866, PR China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, No. 120 Dongling Road, Shenhe District, 110866, PR China
| | - Zepeng Yin
- Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, 110866, PR China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, No. 120 Dongling Road, Shenhe District, 110866, PR China; Key Laboratory of Fruit Postharvest Biology of Liaoning Province, No. 120 Dongling Road, Shenhe District, 110866, PR China.
| | - Tianlai Li
- Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, 110866, PR China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), No. 120 Dongling Road, Shenhe District, 110866, PR China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, No. 120 Dongling Road, Shenhe District, 110866, PR China.
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6
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Stanciu A, Luo J, Funes L, Galbokke Hewage S, Kulkarni SD, Aitken CE. eIF3 and Its mRNA-Entry-Channel Arm Contribute to the Recruitment of mRNAs With Long 5′-Untranslated Regions. Front Mol Biosci 2022; 8:787664. [PMID: 35087868 PMCID: PMC8787345 DOI: 10.3389/fmolb.2021.787664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/13/2021] [Indexed: 01/21/2023] Open
Abstract
Translation initiation in eukaryotes is a multi-step pathway and the most regulated phase of translation. Eukaryotic initiation factor 3 (eIF3) is the largest and most complex of the translation initiation factors, and it contributes to events throughout the initiation pathway. In particular, eIF3 appears to play critical roles in mRNA recruitment. More recently, eIF3 has been implicated in driving the selective translation of specific classes of mRNAs. However, unraveling the mechanism of these diverse contributions—and disentangling the roles of the individual subunits of the eIF3 complex—remains challenging. We employed ribosome profiling of budding yeast cells expressing two distinct mutations targeting the eIF3 complex. These mutations either disrupt the entire complex or subunits positioned near the mRNA-entry channel of the ribosome and which appear to relocate during or in response to mRNA binding and start-codon recognition. Disruption of either the entire eIF3 complex or specific targeting of these subunits affects mRNAs with long 5′-untranslated regions and whose translation is more dependent on eIF4A, eIF4B, and Ded1 but less dependent on eIF4G, eIF4E, and PABP. Disruption of the entire eIF3 complex further affects mRNAs involved in mitochondrial processes and with structured 5′-untranslated regions. Comparison of the suite of mRNAs most sensitive to both mutations with those uniquely sensitive to disruption of the entire complex sheds new light on the specific roles of individual subunits of the eIF3 complex.
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Affiliation(s)
- Andrei Stanciu
- Computer Science Department, Vassar College, Poughkeepsie, NY, United States
| | - Juncheng Luo
- Biochemistry Program, Vassar College, Poughkeepsie, NY, United States
| | - Lucy Funes
- Biology Department, Vassar College, Poughkeepsie, NY, United States
| | | | - Shardul D. Kulkarni
- Department of Biochemistry and Molecular Biology, Penn State Eberly College of Medicine, University Park, PA, United States
| | - Colin Echeverría Aitken
- Biochemistry Program, Vassar College, Poughkeepsie, NY, United States
- Biology Department, Vassar College, Poughkeepsie, NY, United States
- *Correspondence: Colin Echeverría Aitken,
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7
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Llácer JL, Hussain T, Dong J, Villamayor L, Gordiyenko Y, Hinnebusch AG. Large-scale movement of eIF3 domains during translation initiation modulate start codon selection. Nucleic Acids Res 2021; 49:11491-11511. [PMID: 34648019 PMCID: PMC8599844 DOI: 10.1093/nar/gkab908] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single particle electron cryomicroscopy (cryo-EM) reconstruction of yeast 48S ribosomal preinitiation complex (PIC) in an open conformation conducive to scanning, with core subunit eIF3b bound on the 40S interface near the decoding center in contact with the ternary complex eIF2·GTP·initiator tRNA. eIF3b is relocated together with eIF3i from their solvent interface locations observed in other PIC structures, with eIF3i lacking 40S contacts. Re-processing of micrographs of our previous 48S PIC in a closed state also suggests relocation of the entire eIF3b-3i-3g-3a-Cter module during the course of initiation. Genetic analysis indicates that high fidelity initiation depends on eIF3b interactions at the 40S subunit interface that promote the closed PIC conformation, or facilitate the relocation of eIF3b/eIF3i to the solvent interface, on start codon selection.
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Affiliation(s)
- Jose L Llácer
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia 46010, Spain.,Centro para Investigación Biomédica en Red sobre Enfermedades Raras CIBERER-ISCIII, Valencia, Spain
| | - Tanweer Hussain
- Molecular Reproduction, Development and Genetics (MRDG), Biological Sciences Building, Indian Institute of Science, Bangalore 560012, India
| | - Jinsheng Dong
- 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
| | - Laura Villamayor
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia 46010, Spain
| | | | - 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
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8
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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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9
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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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10
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Pechmann S. Programmed Trade-offs in Protein Folding Networks. Structure 2020; 28:1361-1375.e4. [PMID: 33053320 DOI: 10.1016/j.str.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/25/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
Molecular chaperones as specialized protein quality control enzymes form the core of cellular protein homeostasis. How chaperones selectively interact with their substrate proteins thus allocate their overall limited capacity remains poorly understood. Here, I present an integrated analysis of sequence and structural determinants that define interactions of protein domains as the basic protein folding unit with the Saccharomyces cerevisiae Hsp70 Ssb. Structural homologs of single-domain proteins that differentially interact with Ssb for de novo folding were found to systematically differ in complexity of their folding landscapes, selective use of nonoptimal codons, and presence of short discriminative sequences, thus highlighting pervasive trade-offs in chaperone-assisted protein folding landscapes. However, short discriminative sequences were found to contribute by far the strongest signal toward explaining Ssb interactions. This observation suggested that some chaperone interactions may be directly programmed in the amino acid sequences rather than responding to folding challenges, possibly for regulatory advantages.
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Affiliation(s)
- Sebastian Pechmann
- Département de biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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11
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Poncová K, Wagner S, Jansen ME, Beznosková P, Gunišová S, Herrmannová A, Zeman J, Dong J, Valášek LS. uS3/Rps3 controls fidelity of translation termination and programmed stop codon readthrough in co-operation with eIF3. Nucleic Acids Res 2020; 47:11326-11343. [PMID: 31642471 PMCID: PMC6868437 DOI: 10.1093/nar/gkz929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/03/2019] [Accepted: 10/07/2019] [Indexed: 12/27/2022] Open
Abstract
Ribosome was long considered as a critical yet passive player in protein synthesis. Only recently the role of its basic components, ribosomal RNAs and proteins, in translational control has begun to emerge. Here we examined function of the small ribosomal protein uS3/Rps3, earlier shown to interact with eukaryotic translation initiation factor eIF3, in termination. We identified two residues in consecutive helices occurring in the mRNA entry pore, whose mutations to the opposite charge either reduced (K108E) or increased (R116D) stop codon readthrough. Whereas the latter increased overall levels of eIF3-containing terminating ribosomes in heavy polysomes in vivo indicating slower termination rates, the former specifically reduced eIF3 amounts in termination complexes. Combining these two mutations with the readthrough-reducing mutations at the extreme C-terminus of the a/Tif32 subunit of eIF3 either suppressed (R116D) or exacerbated (K108E) the readthrough phenotypes, and partially corrected or exacerbated the defects in the composition of termination complexes. In addition, we found that K108 affects efficiency of termination in the termination context-specific manner by promoting incorporation of readthrough-inducing tRNAs. Together with the multiple binding sites that we identified between these two proteins, we suggest that Rps3 and eIF3 closely co-operate to control translation termination and stop codon readthrough.
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Affiliation(s)
- Kristýna Poncová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, the Czech Republic.,Charles University, Faculty of Science, Prague, the Czech Republic
| | - Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, the Czech Republic
| | - Myrte Esmeralda Jansen
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, the Czech Republic
| | - Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, the Czech Republic
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, the Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, the Czech Republic
| | - Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, the Czech Republic
| | - Jinsheng Dong
- 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
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, the Czech Republic
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12
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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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13
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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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14
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Zeman J, Itoh Y, Kukačka Z, Rosůlek M, Kavan D, Kouba T, Jansen ME, Mohammad MP, Novák P, Valášek LS. Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes. Nucleic Acids Res 2019; 47:8282-8300. [PMID: 31291455 PMCID: PMC6735954 DOI: 10.1093/nar/gkz570] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/12/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
eIF3 is a large multiprotein complex serving as an essential scaffold promoting binding of other eIFs to the 40S subunit, where it coordinates their actions during translation initiation. Perhaps due to a high degree of flexibility of multiple eIF3 subunits, a high-resolution structure of free eIF3 from any organism has never been solved. Employing genetics and biochemistry, we previously built a 2D interaction map of all five yeast eIF3 subunits. Here we further improved the previously reported in vitro reconstitution protocol of yeast eIF3, which we cross-linked and trypsin-digested to determine its overall shape in 3D by advanced mass-spectrometry. The obtained cross-links support our 2D subunit interaction map and reveal that eIF3 is tightly packed with its WD40 and RRM domains exposed. This contrasts with reported cryo-EM structures depicting eIF3 as a molecular embracer of the 40S subunit. Since the binding of eIF1 and eIF5 further fortified the compact architecture of eIF3, we suggest that its initial contact with the 40S solvent-exposed side makes eIF3 to open up and wrap around the 40S head with its extended arms. In addition, we mapped the position of eIF5 to the region below the P- and E-sites of the 40S subunit.
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Affiliation(s)
- 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
| | - Yuzuru Itoh
- Institute of Genetics and Molecular and Cellular Biology, CNRS UMR7104, INSERM UMR964, Illkirch, France
| | - Zdeněk Kukačka
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Michal Rosůlek
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Daniel Kavan
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Tomáš Kouba
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Myrte E Jansen
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Mahabub P Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Leoš S 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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15
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Raabe K, Honys D, Michailidis C. The role of eukaryotic initiation factor 3 in plant translation regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:75-83. [PMID: 31665669 DOI: 10.1016/j.plaphy.2019.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Regulation of translation represents a critical step in the regulation of gene expression. In plants, the translation regulation plays an important role at all stages of development and, during stress responses, functions as a fast and flexible tool which not only modulates the global translation rate but also controls the production of specific proteins. Regulation of translation is mostly focused on the initiation phase. There, one of essential initiation factors is the large multisubunit protein complex of eukaryotic translation initiation factor 3 (eIF3). In all eukaryotes, the general eIF3 function is to scaffold the formation of the translation initiation complex and to enhance the accuracy of scanning mechanism for start codon selection. Over the past decades, additional eIF3 functions were described as necessary for development in various eukaryotic organisms, including plants. The importance of the eIF3 complex lies not only at the global level of initiation event, but also in the precise translation regulation of specific transcripts. This review gathers the available information on functions of the plant eIF3 complex.
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Affiliation(s)
- Karel Raabe
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic
| | - David Honys
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic
| | - Christos Michailidis
- Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, 165 02, Praha 6, Czech Republic.
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16
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Xiong H, Hu M, Huang H, Gong J, Wu J, Zhang H. Eukaryotic translation initiation factor 3B downregulation inhibits cell proliferation and promotes cell apoptosis through negatively regulating tumor necrosis factor receptor superfamily member 21 in gastric cancer. Transl Cancer Res 2019; 8:2242-2251. [PMID: 35116977 PMCID: PMC8797879 DOI: 10.21037/tcr.2019.09.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 08/27/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND This study aimed to detect eukaryotic translation initiation factor 3B (EIF3B) expression in gastric cancer (GC) cell lines, and further explore the effect of EIF3B downregulation on GC cell proliferation and apoptosis. METHODS EIF3B mRNA expression and protein expression in human GC cell lines (NCI-N87, AGS, HGC-27, BGC-823 and MGC80-3) and human gastric mucosal epithelial cell line (GES-1) were detected. Control siRNA (Si-NC group) and EIF3B siRNA (Si-EIF3B group) were transfected into NCI-N87 cells. Rescue experiment was performed by transfection of EIF3B siRNA (Si-EIF3B group) and EIF3B siRNA plus tumor necrosis factor receptor superfamily member 21 (TNFRSF21) siRNA (Si-EIF3B & Si-TNFRSF21 group) into NCI-N87 cells. Besides, cell proliferation, apoptosis, TNFRSF21 expression and TRAF1 expression were assessed. RESULTS EIF3B mRNA expression and protein expression were elevated in NCI-N87, AGS, HGC-27 and BGC-823 cell lines compared to GES-1 cell line. In NCI-N87 cells, proliferation was reduced in Si-EIF3B group compared to Si-NC group. For cell apoptosis, its rate and apoptotic marker C-Caspase 3 expression were increased but anti-apoptosis marker Bcl-2 expression was reduced in Si-EIF3B group compared to Si-NC group. Moreover, mRNA expression and protein expression of TNFRSF21 were increased in Si-EIF3B group compared to Si-NC group, while mRNA expression and protein expression of TRAF1 were reduced in Si-EIF3B group compared to Si-NC group. In rescue experiment, cell proliferation was increased but apoptosis was decreased in Si-EIF3B & Si-TNFRSF21 group compared to Si-EIF3B group. CONCLUSIONS EIF3B is overexpressed in GC cell lines, and its downregulation inhibits cell proliferation while promotes apoptosis through negatively regulating TNFRSF21 in GC.
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Affiliation(s)
- Huiling Xiong
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Mei Hu
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Hui Huang
- Department of Gastrointestinal Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Jing Gong
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Jie Wu
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Heng Zhang
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
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17
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Back S, Gorman AW, Vogel C, Silva GM. Site-Specific K63 Ubiquitinomics Provides Insights into Translation Regulation under Stress. J Proteome Res 2018; 18:309-318. [PMID: 30489083 DOI: 10.1021/acs.jproteome.8b00623] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
During oxidative stress, K63-linked polyubiquitin chains modify a variety of proteins including ribosomes. Knowledge of the precise sites of K63 ubiquitin is key to understand its function during the response to stress. To identify the sites of K63 ubiquitin, we developed a new mass spectrometry based method that quantified >1100 K63 ubiquitination sites in yeast that responded to oxidative stress induced by H2O2. We determined that under stress, K63 ubiquitin-modified proteins were involved in several cellular functions including ion transport, protein trafficking, and translation. The most abundant ubiquitin sites localized to the head of the 40S subunit of the ribosome, modified assembled polysomes, and affected the binding of translation factors. The results suggested a new pathway of post-initiation control of translation during oxidative stress and illustrated the importance of high-resolution mapping of noncanonical ubiquitination events.
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Affiliation(s)
- Songhee Back
- Center for Genomics and Systems Biology , New York University , 12 Waverly Place , New York , New York 10003 , United States
| | - Andrew W Gorman
- Department of Biology , Duke University , 130 Science Drive , Durham , North Carolina 27708 , United States
| | - Christine Vogel
- Center for Genomics and Systems Biology , New York University , 12 Waverly Place , New York , New York 10003 , United States
| | - Gustavo M Silva
- Department of Biology , Duke University , 130 Science Drive , Durham , North Carolina 27708 , United States
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18
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Chen YC, Chang YW, Huang YS. Dysregulated Translation in Neurodevelopmental Disorders: An Overview of Autism-Risk Genes Involved in Translation. Dev Neurobiol 2018; 79:60-74. [PMID: 30430754 DOI: 10.1002/dneu.22653] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/17/2018] [Accepted: 10/25/2018] [Indexed: 01/08/2023]
Abstract
Regulated local translation-whereby specific mRNAs are transported and localized in subcellular domains where they are translated in response to regional signals-allows for remote control of gene expression to concentrate proteins in subcellular compartments. Neurons are highly polarized cells with unique features favoring local control for axonal pathfinding and synaptic plasticity, which are key processes involved in constructing functional circuits in the developing brain. Neurodevelopmental disorders are caused by genetic or environmental factors that disturb the nervous system's development during prenatal and early childhood periods. The growing list of genetic mutations that affect mRNA translation raises the question of whether aberrant translatomes in individuals with neurodevelopmental disorders share common molecular features underlying their stereotypical phenotypes and, vice versa, cause a certain degree of phenotypic heterogeneity. Here, we briefly give an overview of the role of local translation during neuronal development. We take the autism-risk gene list and discuss the molecules that (perhaps) are involved in mRNA transport and translation. Both exaggerated and suppressed translation caused by mutations in those genes have been identified or suggested. Finally, we discuss some proof-of-principle regimens for use in autism mouse models to correct dysregulated translation.
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Affiliation(s)
- Yan-Chu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Wei Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
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19
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Vlachakis D, Labrou NE, Iliopoulos C, Hardy J, Lewis PA, Rideout H, Trabzuni D. Insights into the Influence of Specific Splicing Events on the Structural Organization of LRRK2. Int J Mol Sci 2018; 19:ijms19092784. [PMID: 30223621 PMCID: PMC6165039 DOI: 10.3390/ijms19092784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/17/2022] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large protein of unclear function. Rare mutations in the LRRK2 gene cause familial Parkinson's disease (PD) and inflammatory bowel disease. Genome-wide association studies (GWAS) have revealed significant association of the abovementioned diseases at the LRRK2 locus. Cell and systems biology research has led to potential roles that LRRK2 may have in PD pathogenesis, especially the kinase domain (KIN). Previous human expression studies showed evidence of mRNA expression and splicing patterns that may contribute to our understanding of the function of LRRK2. In this work, we investigate and identified significant regional differences in LRRK2 expression at the mRNA level, including a number of splicing events in the Ras of complex protein (Roc) and C-terminal of Roc domain (COR) of LRRK2, in the substantia nigra (SN) and occipital cortex (OCTX). Our findings indicate that the predominant form of LRRK2 mRNA is full length, with shorter isoforms present at a lower copy number. Our molecular modelling study suggests that splicing events in the ROC/COR domains will have major consequences on the enzymatic function and dimer formation of LRRK2. The implications of these are highly relevant to the broader effort to understand the biology and physiological functions of LRRK2, and to better characterize the role(s) of LRRK2 in the underlying mechanism leading to PD.
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Affiliation(s)
- Dimitrios Vlachakis
- Genetics Laboratory, Department of Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, 11855 Athens, Greece.
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, 11855 Athens, Greece.
| | - Costas Iliopoulos
- Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, Strand, London WC2R 2LS, UK.
| | - John Hardy
- Department of Neurodegenerative disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| | - Patrick A Lewis
- Department of Neurodegenerative disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
- School of Pharmacy, University of Reading, Whiteknights, Reading RG6 6AP, UK.
| | - Hardy Rideout
- Division of Basic Neurosciences; Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece.
| | - Daniah Trabzuni
- Department of Neurodegenerative disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia.
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20
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Feng X, Li J, Liu P. The Biological Roles of Translation Initiation Factor 3b. Int J Biol Sci 2018; 14:1630-1635. [PMID: 30416377 PMCID: PMC6216031 DOI: 10.7150/ijbs.26932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/05/2018] [Indexed: 11/12/2022] Open
Abstract
Translation has important roles in almost all physiological and pathological processes, and translation initiation factors are particularly relevant to the translation initiation step, which is the most important step in translation regulation. Translation initiation factor 3b (eIF3b), a key subunit of the largest translation initiation factor 3 (eIF3), is widely considered a scaffold protein that acts to ensure the accuracy of translation initiation. A series of recent finds has revealed that eIF3 is closely related to oncogenesis. However, the concrete mechanism by which eIF3b is involve in carcinogenesis remains elusive. Here, we summarize a series of research findings regarding the relationship between eIF3b, translation and cancer.
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Affiliation(s)
- Xuefei Feng
- Center for Translational Medicine, the First Affiliated Hospital of Xi'an Jiaotong University.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi'an Jiaotong University
| | - Juan Li
- Center for Translational Medicine, the First Affiliated Hospital of Xi'an Jiaotong University.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi'an Jiaotong University
| | - Peijun Liu
- Center for Translational Medicine, the First Affiliated Hospital of Xi'an Jiaotong University.,Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi'an Jiaotong University
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21
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Chen Y, George A. TRIP-1 Promotes the Assembly of an ECM That Contains Extracellular Vesicles and Factors That Modulate Angiogenesis. Front Physiol 2018; 9:1092. [PMID: 30158875 PMCID: PMC6104305 DOI: 10.3389/fphys.2018.01092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/23/2018] [Indexed: 01/14/2023] Open
Abstract
Transforming growth factor beta receptor II interacting protein-1 (TRIP-1) was recently localized in the mineralized matrices of bone and dentin. The function of TRIP-1 in the ECM is enigmatic, as it is known to function as an intracellular endoplasmic reticulum protein during protein synthesis. Based on its localization pattern in bones and teeth, we posited that TRIP-1 must function as a regulatory protein with multiple functions during mineralization. In this study, we determined the in vivo function of TRIP-1 by an implantation assay performed using recombinant TRIP-1 and TRIP-1 overexpressing and knocked down cells embedded in a 3D biomimetic scaffold. After 4 weeks, the subcutaneous tissues from TRIP-1 overexpressing cells and scaffolds containing recombinant TRIP-1 showed higher expression levels of several ECM proteins such as fibronectin and collagen I. Picrosirius red and polarized microscopy was used to identify the birefringence of the collagen fibrils in the extracellular matrix (ECM). Interestingly, knockdown of TRIP-1 resulted in lower fibronectin and downregulation of the activation of the ERK MAP kinase. We further demonstrate that TRIP-1 overexpression leads to higher expression of pro-angiogenic marker VEGF and downregulation of anti-angiogenic factors such as pigment epithelium-derived factor and thrombospondin. Field emission scanning electron microscope results demonstrated that TRIP-1 overexpressing cells released large amount of extracellular microvesicles which were localized on the fibrillar matrix in the ECM. Overall, this study demonstrates that TRIP-1 can promote secretion of extracellular vesicles, synthesis of key osteogenic ECM matrix proteins and promote angiogenesis.
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Affiliation(s)
- Yinghua Chen
- Brodie Tooth Development Genetics and Regenerative Medicine Research Laboratory, Department of Oral Biology, University of Illinois at Chicago, Chicago, IL, United States
| | - Anne George
- Brodie Tooth Development Genetics and Regenerative Medicine Research Laboratory, Department of Oral Biology, University of Illinois at Chicago, Chicago, IL, United States
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22
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Hashem Y, Frank J. The Jigsaw Puzzle of mRNA Translation Initiation in Eukaryotes: A Decade of Structures Unraveling the Mechanics of the Process. Annu Rev Biophys 2018; 47:125-151. [PMID: 29494255 DOI: 10.1146/annurev-biophys-070816-034034] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Translation initiation in eukaryotes is a highly regulated and rate-limiting process. It results in the assembly and disassembly of numerous transient and intermediate complexes involving over a dozen eukaryotic initiation factors (eIFs). This process culminates in the accommodation of a start codon marking the beginning of an open reading frame at the appropriate ribosomal site. Although this process has been extensively studied by hundreds of groups for nearly half a century, it has been only recently, especially during the last decade, that we have gained deeper insight into the mechanics of the eukaryotic translation initiation process. This advance in knowledge is due in part to the contributions of structural biology, which have shed light on the molecular mechanics underlying the different functions of various eukaryotic initiation factors. In this review, we focus exclusively on the contribution of structural biology to the understanding of the eukaryotic initiation process, a long-standing jigsaw puzzle that is just starting to yield the bigger picture.
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Affiliation(s)
- Yaser Hashem
- INSERM U1212, Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France;
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY 10032, USA;
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23
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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: 80] [Impact Index Per Article: 11.4] [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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24
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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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25
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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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26
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Yadav DK, Lukavsky PJ. NMR solution structure determination of large RNA-protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:57-81. [PMID: 27888840 DOI: 10.1016/j.pnmrs.2016.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems. The new combination of NMR measurements with MD simulations and its potential will also be discussed. Application and combination of these various methods for structure determination of large RNPs will be illustrated with three large RNA-protein complexes (>40kDa) and other interesting complexes determined in the past six and a half years.
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Affiliation(s)
- Deepak Kumar Yadav
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Peter J Lukavsky
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic.
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27
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Aitken CE, Beznosková P, Vlčkova V, Chiu WL, Zhou F, Valášek LS, Hinnebusch AG, Lorsch JR. Eukaryotic translation initiation factor 3 plays distinct roles at the mRNA entry and exit channels of the ribosomal preinitiation complex. eLife 2016; 5. [PMID: 27782884 PMCID: PMC5153249 DOI: 10.7554/elife.20934] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/25/2016] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic translation initiation factor 3 (eIF3) is a central player in recruitment of the pre-initiation complex (PIC) to mRNA. We probed the effects on mRNA recruitment of a library of S. cerevisiae eIF3 functional variants spanning its 5 essential subunits using an in vitro-reconstituted system. Mutations throughout eIF3 disrupt its interaction with the PIC and diminish its ability to accelerate recruitment to a native yeast mRNA. Alterations to the eIF3a CTD and eIF3b/i/g significantly slow mRNA recruitment, and mutations within eIF3b/i/g destabilize eIF2•GTP•Met-tRNAi binding to the PIC. Using model mRNAs lacking contacts with the 40S entry or exit channels, we uncovered a critical role for eIF3 requiring the eIF3a NTD, in stabilizing mRNA interactions at the exit channel, and an ancillary role at the entry channel requiring residues of the eIF3a CTD. These functions are redundant: defects at each channel can be rescued by filling the other channel with mRNA. DOI:http://dx.doi.org/10.7554/eLife.20934.001 Cells use the genetic information stored within genes to build proteins, which are largely responsible for performing the molecular tasks essential for life. The ribosome is the molecular machine that translates the information within genes to assemble proteins in all cells, from bacteria to humans. To make a protein, the corresponding gene is first copied to make molecules of messenger ribonucleic acid (or mRNA for short). Then the ribosome binds to the mRNA in a process called translation initiation. Cells tightly regulate translation initiation so that they can decide which proteins to make, according to their needs and in response to changes in the environment. In fact, regulation of translation initiation is often disrupted during viral infections, cancer and other human diseases. A set of proteins called translation initiation factors drive translation initiation; the largest and least understood of these is called eIF3. Cells are unable to load the mRNA onto the ribosome without eIF3, which has two “arms” that sit near where the mRNA enters and exits the ribosome. Aitken et al. used mutant forms of eIF3 from genetically modified yeast to investigate how the arms of the protein work, and if they help the ribosome hold onto the mRNA. These experiments show that the two arms of eIF3 have unique roles. One arm sits near where mRNA exits the ribosome and is important for holding onto the mRNA. The other arm – which is near where mRNA enters the ribosome – helps hold the ribosome and other components of the translation machinery together. This arm may also help to open and close the channel through which messenger RNA enters the ribosome. The next challenges are to find out the precise role this arm plays in translation – in particular, how it helps to open and close the channel in the ribosome, and whether this helps the ribosome load the messenger RNA or even move along it. DOI:http://dx.doi.org/10.7554/eLife.20934.002
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Affiliation(s)
- Colin Echeverría Aitken
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Prague, Czech Republic
| | - Vladislava Vlčkova
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Prague, Czech Republic
| | - Wen-Ling Chiu
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Fujun Zhou
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Prague, Czech Republic
| | - 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, United States
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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28
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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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29
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Simonetti A, Brito Querido J, Myasnikov AG, Mancera-Martinez E, Renaud A, Kuhn L, Hashem Y. eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition. Mol Cell 2016; 63:206-217. [PMID: 27373335 DOI: 10.1016/j.molcel.2016.05.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/07/2016] [Accepted: 05/23/2016] [Indexed: 11/30/2022]
Abstract
mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal 40S subunit, mRNA scanning for start codon, and accommodation of initiator tRNA at the 40S P site. eIF3, composed of 13 subunits, 8 core (a, c, e, f, h, l, k, and m) and 5 peripheral (b, d, g, i, and j), plays a central role during this process. Here we report a cryo-electron microscopy structure of a mammalian 48S initiation complex at 5.8 Å resolution. It shows the relocation of subunits eIF3i and eIF3g to the 40S intersubunit face on the GTPase binding site, at a late stage in initiation. On the basis of a previous study, we demonstrate the relocation of eIF3b to the 40S intersubunit face, binding below the eIF2-Met-tRNAi(Met) ternary complex upon mRNA attachment. Our analysis reveals the deep rearrangement of eIF3 and unravels the molecular mechanism underlying eIF3 function in mRNA scanning and timing of ribosomal subunit joining.
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Affiliation(s)
- Angelita Simonetti
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France.
| | - Jailson Brito Querido
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France
| | | | - Eder Mancera-Martinez
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Adeline Renaud
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Lauriane Kuhn
- CNRS, Proteomic Platform Strasbourg - Esplanade, 67084 Strasbourg, France
| | - Yaser Hashem
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France.
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30
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Zhou JW, Li Y, Yue LX, Luo CL, Chen Y, Zhang JY. Autoantibody response to Sui1 and its tissue-specific expression in hepatocellular carcinoma. Tumour Biol 2015; 37:2547-53. [DOI: 10.1007/s13277-015-4074-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/13/2015] [Indexed: 01/09/2023] Open
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31
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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: 174] [Impact Index Per Article: 19.3] [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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32
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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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33
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Beznosková P, Wagner S, Jansen ME, von der Haar T, Valášek LS. Translation initiation factor eIF3 promotes programmed stop codon readthrough. Nucleic Acids Res 2015; 43:5099-111. [PMID: 25925566 PMCID: PMC4446449 DOI: 10.1093/nar/gkv421] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/18/2015] [Indexed: 12/21/2022] Open
Abstract
Programmed stop codon readthrough is a post-transcription regulatory mechanism specifically increasing proteome diversity by creating a pool of C-terminally extended proteins. During this process, the stop codon is decoded as a sense codon by a near-cognate tRNA, which programs the ribosome to continue elongation. The efficiency of competition for the stop codon between release factors (eRFs) and near-cognate tRNAs is largely dependent on its nucleotide context; however, the molecular mechanism underlying this process is unknown. Here, we show that it is the translation initiation (not termination) factor, namely eIF3, which critically promotes programmed readthrough on all three stop codons. In order to do so, eIF3 must associate with pre-termination complexes where it interferes with the eRF1 decoding of the third/wobble position of the stop codon set in the unfavorable termination context, thus allowing incorporation of near-cognate tRNAs with a mismatch at the same position. We clearly demonstrate that efficient readthrough is enabled by near-cognate tRNAs with a mismatch only at the third/wobble position. Importantly, the eIF3 role in programmed readthrough is conserved between yeast and humans.
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Affiliation(s)
- Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic Faculty of Science, Charles University, Vinicna 5, Prague 128 44, the Czech Republic
| | - Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, Prague 142 20, the Czech Republic
| | - Myrte Esmeralda Jansen
- 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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Wilson BT, Omer M, Hellens SW, Zwolinski SA, Yates LM, Lynch SA. Microdeletion 1p35.2: a recognizable facial phenotype with developmental delay. Am J Med Genet A 2015; 167A:1916-20. [PMID: 25900906 DOI: 10.1002/ajmg.a.37114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/02/2015] [Indexed: 11/08/2022]
Abstract
We describe two patients with microdeletion 1p35.2, intrauterine growth retardation, small stature, hypermetropia, hearing impairment and developmental delay. Both patients have long, myopathic facies, with fine eyebrows, small mouths and micrognathia. We postulate a role for the histone deacetylase HDAC1 in the facial phenotype and suggest that deletion of KPNA6 may prevent transmission of the 1p35.2 deletion from affected girls to any offspring through impaired zygotic genome activation.
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Affiliation(s)
- Brian T Wilson
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK.,Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, International Centre for Life, Newcastle upon Tyne, UK
| | - Murwan Omer
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Stephen W Hellens
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, International Centre for Life, Newcastle upon Tyne, UK
| | - Simon A Zwolinski
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, International Centre for Life, Newcastle upon Tyne, UK
| | - Laura M Yates
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK.,Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, International Centre for Life, Newcastle upon Tyne, UK
| | - Sally Ann Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
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35
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Yan X, Xie J, Li J, Shuanghu C, Wu Z, Jian J. Screening and analysis on the protein interaction of the protein VP7 in grass carp reovirus. Virus Genes 2015; 50:425-33. [PMID: 25860999 DOI: 10.1007/s11262-015-1193-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 11/06/2014] [Indexed: 12/26/2022]
Abstract
Grass carp reovirus (GCRV) has caused serious economic losses for several decades in China. The protein VP7 is one of the important structural proteins in GCRV. Recent studies indicated that the protein VP7 had the commendable antigenicity and immunogenicity. The protein VP7 cooperated with VP5 could change the conformation of the cell membrane and facilitate entry of GCRV into host cells. We speculated that the protein VP7 should play an important role in the pathogenesis of GCRV. In order to explore the function of the protein VP7, the bait protein expression plasmid pGBKT7-vp7 and the cDNA library of CIK cells were constructed. By yeast two-hybrid system, after multiple screening with the high screening rate medium, rotary verification, sequencing and bioinformatics analysis, the interactions of the protein VP7 with ribosomal protein S20 (RPS20) and eukaryotic translation initiation factor 3 subunit b (eIF3b) in CIK cells were identified. RPS20 played the important roles in the generation of influenza B virus and a variety of diseases. eIF3b was relative to the infection of some viruses. This study suggested that the protein VP7 played the role in viral replication and most likely interacted with host proteins by RPS20 and eIF3b. The interaction mechanisms of the protein VP7 with RPS20 and eIF3b, and the subsequent effector mechanisms needed to be further studied. The corresponding protein interaction of the protein VP7 was not acquired in bioinformatics. The protein VP7 and its untranslated region may have the unknown special function. This study laid the foundation for deeply exploring the function of the protein VP7 in GCRV and had the important scientific significance for exploring the pathogenic mechanism of GCRV.
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Affiliation(s)
- Xiuying Yan
- Guangdong Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Ocean University, Huguangyan East, Zhanjiang, 524088, China,
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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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37
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Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex. Cell 2015; 158:1123-1135. [PMID: 25171412 PMCID: PMC4151992 DOI: 10.1016/j.cell.2014.07.044] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/29/2014] [Accepted: 07/29/2014] [Indexed: 11/25/2022]
Abstract
Eukaryotic translation initiation requires the recruitment of the large, multiprotein eIF3 complex to the 40S ribosomal subunit. We present X-ray structures of all major components of the minimal, six-subunit Saccharomyces cerevisiae eIF3 core. These structures, together with electron microscopy reconstructions, cross-linking coupled to mass spectrometry, and integrative structure modeling, allowed us to position and orient all eIF3 components on the 40S⋅eIF1 complex, revealing an extended, modular arrangement of eIF3 subunits. Yeast eIF3 engages 40S in a clamp-like manner, fully encircling 40S to position key initiation factors on opposite ends of the mRNA channel, providing a platform for the recruitment, assembly, and regulation of the translation initiation machinery. The structures of eIF3 components reported here also have implications for understanding the architecture of the mammalian 43S preinitiation complex and the complex of eIF3, 40S, and the hepatitis C internal ribosomal entry site RNA. X-ray structures of major yeast eIF3 components and subcomplexes Crosslinking coupled to mass-spectrometry analysis of 40S⋅eIF1⋅eIF3 complex Integrative modeling reveals architecture of 40S⋅eIF1⋅eIF3 complex
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Affiliation(s)
- Jan P Erzberger
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
| | - Florian Stengel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, UCSF MC 2552, Byers Hall Room 503B, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Suyang Zhang
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Tanja Schaefer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Christopher H S Aylett
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Peter Cimermančič
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, UCSF MC 2552, Byers Hall Room 503B, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, UCSF MC 2552, Byers Hall Room 503B, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
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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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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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40
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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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41
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Qi J, Dong Z, Liu J, Zhang JT. EIF3i promotes colon oncogenesis by regulating COX-2 protein synthesis and β-catenin activation. Oncogene 2014; 33:4156-63. [PMID: 24056964 PMCID: PMC3962800 DOI: 10.1038/onc.2013.397] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 12/21/2022]
Abstract
Translational control of gene expression has recently been recognized as an important mechanism controlling cell proliferation and oncogenesis, and it mainly occurs in the initiation step of protein synthesis that involves multiple eukaryotic initiation factors (eIFs). Many eIFs have been found to have aberrant expression in human tumors and the aberrant expression may contribute to oncogenesis. However, how these previously considered house-keeping proteins are potentially oncogenic remains elusive. In this study, we investigated the expression of eIF3i in human colon cancers, tested its contribution to colon oncogenesis and determined the mechanism of eIF3i action in colon oncogenesis. We found that eIF3i expression was upregulated in both human colon adenocarcinoma and adenoma polyps as well as in model inducible colon tumorigenic cell lines. Overexpression of ectopic eIF3i in intestinal epithelial cells causes oncogenesis by directly upregulating the synthesis of cyclooxygenase-2 (COX-2) protein and activates the β-catenin/T-cell factor 4 signaling pathway that mediates the oncogenic function of eIF3i. Together, we conclude that eIF3i is a proto-oncogene that drives colon oncogenesis by translationally upregulating COX-2 and activating the β-catenin signaling pathway. These findings imply that proto-oncogenic eIFs likely exert their tumorigenic function by regulating/altering the synthesis level of downstream tumor suppressor or oncogenes.
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Affiliation(s)
- J Qi
- Department of Pharmacology and Toxicology and IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Z Dong
- Department of Pharmacology and Toxicology and IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - J Liu
- Department of Pharmacology and Toxicology and IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - J-T Zhang
- Department of Pharmacology and Toxicology and IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
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42
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Translation initiation factor eIF3b contains a nine-bladed β-propeller and interacts with the 40S ribosomal subunit. Structure 2014; 22:923-30. [PMID: 24768115 DOI: 10.1016/j.str.2014.03.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/13/2014] [Accepted: 03/21/2014] [Indexed: 11/20/2022]
Abstract
The multisubunit eukaryotic translation initiation factor 3, among which the subunit b (eIF3b) is a major scaffold protein, plays essential roles in protein synthesis. Here, we report the crystal structure of the WD40 domain of Chaetomium thermophilum eIF3b, revealing a nine-bladed β-propeller fold. Sequence analysis indicates that this propeller architecture is common to all eIF3b orthologs. Revisiting the cryoelectron microscopy (cryo-EM) map of the 43S preinitiation complex suggests an interaction of the eIF3b with the 40S ribosomal subunit involving the ribosomal protein S9e and the 18S rRNA. This model is strongly supported by the direct binding of eIF3b to 40S ribosomes and to the isolated ribosomal protein rpS9e in vitro.
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43
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The chaperonin CCT interacts with and mediates the correct folding and activity of three subunits of translation initiation factor eIF3: b, i and h. Biochem J 2014; 458:213-24. [PMID: 24320561 DOI: 10.1042/bj20130979] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
eIF3 (eukaryotic initiation factor 3) is the largest and most complex eukaryotic mRNA translation factor in terms of the number of protein components or subunits. In mammals, eIF3 is composed of 13 different polypeptide subunits, of which five, i.e. a, b, c, g and i, are conserved and essential in vivo from yeasts to mammals. In the present study, we show that the eukaryotic cytosolic chaperonin CCT [chaperonin containing TCP-1 (tailless complex polypeptide 1)] binds to newly synthesized eIF3b and promotes the correct folding of eIF3h and eIF3i. Interestingly, overexpression of these last two subunits is associated with enhanced translation of specific mRNAs over and above the general enhancement of global translation. In agreement with this, our data show that, as CCT is required for the correct folding of eIF3h and eIF3i subunits, it indirectly influences gene expression with eIF3i overexpression enhancing both cap- and IRES (internal ribosome entry segment)-dependent translation initiation, whereas eIF3h overexpression selectively increases IRES-dependent translation initiation. Importantly, these studies demonstrate the requirement of the chaperonin machinery for the correct folding of essential components of the translational machinery and provide further evidence of the close interplay between the cell environment, cell signalling, cell proliferation, the chaperone machinery and translational apparatus.
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Wei Q, Huang H, Yang L, Yuan J, Yang X, Liu Y, Zhuang Z. Hydrogen peroxide induces adaptive response and differential gene expression in human embryo lung fibroblast cells. ENVIRONMENTAL TOXICOLOGY 2014; 29:478-485. [PMID: 22489041 DOI: 10.1002/tox.21775] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 05/31/2023]
Abstract
Hydrogen peroxide (H2 O2 ), a substance involved in cellular oxidative stress, has been observed to induce an adaptive response, which is characterized by a protection against the toxic effect of H2 O2 at higher concentrations. However, the molecular mechanism for the adaptive response remains unclear. In particular, the existing reports on H2 O2 -induced adaptive response are limited to animal cells and human tumor cells, and relatively normal human cells have never been observed for an adaptive response to H2 O2 . In this study, a human embryo lung fibroblast (MRC-5) cell line was used to model an adaptive response to H2 O2 , and the relevant differential gene expressions by using fluoro mRNA differential display RT-PCR. The results showed significant suppression of cytotoxicity of H2 O2 (1100 μM, 1 h) after pretreatment of the cells with H2 O2 at lower concentrations (0.088-8.8 μM, 24 h), as indicated by cell survival, lactate dehydrogenase release, and the rate of apoptotic cells. Totally 60 mRNA components were differentially expressed compared to untreated cells, and five of them (sizing 400-600 bp) which demonstrated the greatest increase in expression were cloned and sequenced. They showed identity with known genes, such as BCL-2, eIF3S5, NDUFS4, and RPS10. Real time RT-PCR analysis of the five genes displayed a pattern of differential expression consistent with that by the last method. These five genes may be involved in the induction of adaptive response by H2 O2 in human cells, at least in this particular cell type.
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Affiliation(s)
- Qinzhi Wei
- Department of Toxicology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, People's Republic of China; Department of Toxicology, Faculty of Preventive Medicine, School of Public Health, Sun Yat-Sen University, Guangzhou 510080, People's Republic of China; Toxicology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, 21 TianBei 1st Road, Shenzhen 518020, Guangdong Province, People's Republic of China
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Abstract
In eukaryotes, the translation initiation codon is generally identified by the scanning mechanism, wherein every triplet in the messenger RNA leader is inspected for complementarity to the anticodon of methionyl initiator transfer RNA (Met-tRNAi). Binding of Met-tRNAi to the small (40S) ribosomal subunit, in a ternary complex (TC) with eIF2-GTP, is stimulated by eukaryotic initiation factor 1 (eIF1), eIF1A, eIF3, and eIF5, and the resulting preinitiation complex (PIC) joins the 5' end of mRNA preactivated by eIF4F and poly(A)-binding protein. RNA helicases remove secondary structures that impede ribosome attachment and subsequent scanning. Hydrolysis of eIF2-bound GTP is stimulated by eIF5 in the scanning PIC, but completion of the reaction is impeded at non-AUG triplets. Although eIF1 and eIF1A promote scanning, eIF1 and possibly the C-terminal tail of eIF1A must be displaced from the P decoding site to permit base-pairing between Met-tRNAi and the AUG codon, as well as to allow subsequent phosphate release from eIF2-GDP. A second GTPase, eIF5B, catalyzes the joining of the 60S subunit to produce an 80S initiation complex that is competent for elongation.
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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, Maryland 20892;
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Khoshnevis S, Gunišová S, Vlčková V, Kouba T, Neumann P, Beznosková P, Ficner R, Valášek LS. Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes. Nucleic Acids Res 2014; 42:4123-39. [PMID: 24423867 PMCID: PMC3973348 DOI: 10.1093/nar/gkt1369] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Transfer of genetic information from genes into proteins is mediated by messenger RNA (mRNA) that must be first recruited to ribosomal pre-initiation complexes (PICs) by a mechanism that is still poorly understood. Recent studies showed that besides eIF4F and poly(A)-binding protein, eIF3 also plays a critical role in this process, yet the molecular mechanism of its action is unknown. We showed previously that the PCI domain of the eIF3c/NIP1 subunit of yeast eIF3 is involved in RNA binding. To assess the role of the second PCI domain of eIF3 present in eIF3a/TIF32, we performed its mutational analysis and identified a 10-Ala-substitution (Box37) that severely reduces amounts of model mRNA in the 43–48S PICs in vivo as the major, if not the only, detectable defect. Crystal structure analysis of the a/TIF32-PCI domain at 2.65-Å resolution showed that it is required for integrity of the eIF3 core and, similarly to the c/NIP1-PCI, is capable of RNA binding. The putative RNA-binding surface defined by positively charged areas contains two Box37 residues, R363 and K364. Their substitutions with alanines severely impair the mRNA recruitment step in vivo suggesting that a/TIF32-PCI represents one of the key domains ensuring stable and efficient mRNA delivery to the PICs.
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Affiliation(s)
- Sohail Khoshnevis
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, George-August University, Goettingen, Germany, 37077 and Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, 142 20 Prague, the Czech Republic
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47
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Beznosková P, Cuchalová L, Wagner S, Shoemaker CJ, Gunišová S, von der Haar T, Valášek LS. Translation initiation factors eIF3 and HCR1 control translation termination and stop codon read-through in yeast cells. PLoS Genet 2013; 9:e1003962. [PMID: 24278036 PMCID: PMC3836723 DOI: 10.1371/journal.pgen.1003962] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/01/2013] [Indexed: 11/19/2022] Open
Abstract
Translation is divided into initiation, elongation, termination and ribosome recycling. Earlier work implicated several eukaryotic initiation factors (eIFs) in ribosomal recycling in vitro. Here, we uncover roles for HCR1 and eIF3 in translation termination in vivo. A substantial proportion of eIF3, HCR1 and eukaryotic release factor 3 (eRF3) but not eIF5 (a well-defined "initiation-specific" binding partner of eIF3) specifically co-sediments with 80S couples isolated from RNase-treated heavy polysomes in an eRF1-dependent manner, indicating the presence of eIF3 and HCR1 on terminating ribosomes. eIF3 and HCR1 also occur in ribosome- and RNA-free complexes with both eRFs and the recycling factor ABCE1/RLI1. Several eIF3 mutations reduce rates of stop codon read-through and genetically interact with mutant eRFs. In contrast, a slow growing deletion of hcr1 increases read-through and accumulates eRF3 in heavy polysomes in a manner suppressible by overexpressed ABCE1/RLI1. Based on these and other findings we propose that upon stop codon recognition, HCR1 promotes eRF3·GDP ejection from the post-termination complexes to allow binding of its interacting partner ABCE1/RLI1. Furthermore, the fact that high dosage of ABCE1/RLI1 fully suppresses the slow growth phenotype of hcr1Δ as well as its termination but not initiation defects implies that the termination function of HCR1 is more critical for optimal proliferation than its function in translation initiation. Based on these and other observations we suggest that the assignment of HCR1 as a bona fide eIF3 subunit should be reconsidered. Together our work characterizes novel roles of eIF3 and HCR1 in stop codon recognition, defining a communication bridge between the initiation and termination/recycling phases of translation.
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Affiliation(s)
- Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska, Prague, the Czech Republic
| | - Lucie Cuchalová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska, Prague, the Czech Republic
| | - Susan Wagner
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska, Prague, the Czech Republic
| | - Christopher J. Shoemaker
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska, Prague, the Czech Republic
| | | | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska, Prague, the Czech Republic
- * E-mail:
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48
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Kim JT, Lee SJ, Kim BY, Lee CH, Yeom YI, Choe YK, Yoon DY, Chae SK, Kim JW, Yang Y, Lim JS, Lee HG. Caspase-mediated cleavage and DNase activity of the translation initiation factor 3, subunit G (eIF3g). FEBS Lett 2013; 587:3668-74. [DOI: 10.1016/j.febslet.2013.09.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/12/2013] [Accepted: 09/20/2013] [Indexed: 11/26/2022]
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49
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Hashem Y, des Georges A, Dhote V, Langlois R, Liao HY, Grassucci RA, Hellen CUT, Pestova TV, Frank J. Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29. Cell 2013; 153:1108-19. [PMID: 23706745 DOI: 10.1016/j.cell.2013.04.036] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/06/2013] [Accepted: 04/05/2013] [Indexed: 01/19/2023]
Abstract
Eukaryotic translation initiation begins with assembly of a 43S preinitiation complex. First, methionylated initiator methionine transfer RNA (Met-tRNAi(Met)), eukaryotic initiation factor (eIF) 2, and guanosine triphosphate form a ternary complex (TC). The TC, eIF3, eIF1, and eIF1A cooperatively bind to the 40S subunit, yielding the 43S preinitiation complex, which is ready to attach to messenger RNA (mRNA) and start scanning to the initiation codon. Scanning on structured mRNAs additionally requires DHX29, a DExH-box protein that also binds directly to the 40S subunit. Here, we present a cryo-electron microscopy structure of the mammalian DHX29-bound 43S complex at 11.6 Å resolution. It reveals that eIF2 interacts with the 40S subunit via its α subunit and supports Met-tRNAi(Met) in an unexpected P/I orientation (eP/I). The structural core of eIF3 resides on the back of the 40S subunit, establishing two principal points of contact, whereas DHX29 binds around helix 16. The structure provides insights into eukaryote-specific aspects of translation, including the mechanism of action of DHX29.
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Affiliation(s)
- Yaser Hashem
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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50
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Xia Z, Tong X, Liang F, Zhang Y, Kuok C, Zhang Y, Liu X, Zhu Z, Lin S, Zhang B. Eif3ba regulates cranial neural crest development by modulating p53 in zebrafish. Dev Biol 2013; 381:83-96. [PMID: 23791820 DOI: 10.1016/j.ydbio.2013.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 06/01/2013] [Accepted: 06/06/2013] [Indexed: 02/05/2023]
Abstract
Congenital diseases caused by abnormal development of the cranial neural crest usually present craniofacial malformations and heart defects while the precise mechanism is not fully understood. Here, we show that the zebrafish eif3ba mutant caused by pseudo-typed retrovirus insertion exhibited a similar phenotype due to the hypogenesis of cranial neural crest cells (NCCs). The derivatives of cranial NCCs, including the NCC-derived cell population of pharyngeal arches, craniofacial cartilage, pigment cells and the myocardium derived from cardiac NCCs, were affected in this mutant. The expression of several neural crest marker genes, including crestin, dlx2a and nrp2b, was specifically reduced in the cranial regions of the eif3ba mutant. Through fluorescence-tracing of the cranial NCC migration marker nrp2b, we observed reduced intensity of NCC-derived cells in the heart. In addition, p53 was markedly up-regulated in the eif3ba mutant embryos, which correlated with pronounced apoptosis in the cranial area as shown by TUNEL staining. These findings suggest a novel function of eif3ba during embryonic development and a novel level of regulation in the process of cranial NCC development, in addition to providing a potential animal model to mimic congenital diseases due to cranial NCC defects. Furthermore, we report the identification of a novel transgenic fish line Et(gata2a:EGFP)pku418 to trace the migration of cranial NCCs (including cardiac NCCs); this may serve as an invaluable tool for investigating the development and dynamics of cranial NCCs during zebrafish embryogenesis.
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Affiliation(s)
- Zhidan Xia
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, PR China
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