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Wang F, Holmes MJ, Hong HJ, Thaprawat P, Kannan G, Huynh MH, Schultz TL, Licon MH, Lourido S, Dong W, Querido JB, Sullivan WJ, O'Leary SE, Carruthers VB. Translation initiation factor eIF1.2 promotes Toxoplasma stage conversion by regulating levels of key differentiation factors. bioRxiv 2024:2023.11.03.565545. [PMID: 37961607 PMCID: PMC10635126 DOI: 10.1101/2023.11.03.565545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The parasite Toxoplasma gondii persists in its hosts by converting from replicating tachyzoites to latent bradyzoites housed in tissue cysts. The molecular mechanisms that mediate T. gondii differentiation remain poorly understood. Through a mutagenesis screen, we identified translation initiation factor eIF1.2 as a critical factor for T. gondii differentiation. A F97L mutation in eIF1.2 or the genetic ablation of eIF1.2 (Δ eif1.2 ) markedly impeded bradyzoite cyst formation in vitro and in vivo . We demonstrated, at single-molecule level, that the eIF1.2 F97L mutation impacts the scanning process of the ribosome preinitiation complex on a model mRNA. RNA sequencing and ribosome profiling experiments unveiled that Δ eif1.2 parasites are defective in upregulating bradyzoite induction factors BFD1 and BFD2 during stress-induced differentiation. Forced expression of BFD1 or BFD2 significantly restored differentiation in Δ eif1.2 parasites. Together, our findings suggest that eIF1.2 functions by regulating the translation of key differentiation factors necessary to establish chronic toxoplasmosis.
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2
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Brito Querido J, Sokabe M, Díaz-López I, Gordiyenko Y, Fraser CS, Ramakrishnan V. The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Nat Struct Mol Biol 2024; 31:455-464. [PMID: 38287194 PMCID: PMC10948362 DOI: 10.1038/s41594-023-01196-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 11/30/2023] [Indexed: 01/31/2024]
Abstract
Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), which then scans along the mRNA until the start codon is recognized. We have previously shown that eIF4F binds near the mRNA exit channel of the 43S, leaving open the question of how mRNA secondary structure is removed as it enters the mRNA channel on the other side of the 40S subunit. Here we report the structure of a human 48S that shows that, in addition to the eIF4A that is part of eIF4F, there is a second eIF4A helicase bound at the mRNA entry site, which could unwind RNA secondary structures as they enter the 48S. The structure also reveals conserved interactions between eIF4F and the 43S, probaby explaining how eIF4F can promote mRNA recruitment in all eukaryotes.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | | | | | - Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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3
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Brito Querido J, Díaz-López I, Ramakrishnan V. The molecular basis of translation initiation and its regulation in eukaryotes. Nat Rev Mol Cell Biol 2024; 25:168-186. [PMID: 38052923 DOI: 10.1038/s41580-023-00624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 12/07/2023]
Abstract
The regulation of gene expression is fundamental for life. Whereas the role of transcriptional regulation of gene expression has been studied for several decades, it has been clear over the past two decades that post-transcriptional regulation of gene expression, of which translation regulation is a major part, can be equally important. Translation can be divided into four main stages: initiation, elongation, termination and ribosome recycling. Translation is controlled mainly during its initiation, a process which culminates in a ribosome positioned with an initiator tRNA over the start codon and, thus, ready to begin elongation of the protein chain. mRNA translation has emerged as a powerful tool for the development of innovative therapies, yet the detailed mechanisms underlying the complex process of initiation remain unclear. Recent studies in yeast and mammals have started to shed light on some previously unclear aspects of this process. In this Review, we discuss the current state of knowledge on eukaryotic translation initiation and its regulation in health and disease. Specifically, we focus on recent advances in understanding the processes involved in assembling the 43S pre-initiation complex and its recruitment by the cap-binding complex eukaryotic translation initiation factor 4F (eIF4F) at the 5' end of mRNA. In addition, we discuss recent insights into ribosome scanning along the 5' untranslated region of mRNA and selection of the start codon, which culminates in joining of the 60S large subunit and formation of the 80S initiation complex.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Irene Díaz-López
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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4
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Tidu A, Martin F. The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes. Biochimie 2024; 217:20-30. [PMID: 37741547 DOI: 10.1016/j.biochi.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Translation initiation consists in the assembly of the small and large ribosomal subunits on the start codon. This important step directly modulates the general proteome in living cells. Recently, genome wide studies revealed unexpected translation initiation events from unsuspected novel open reading frames resulting in the synthesis of a so-called 'dark proteome'. Indeed, the identification of the start codon by the translation machinery is a critical step that defines the translational landscape of the cell. Therefore, translation initiation is a highly regulated process in all organisms. In this review, we focus on the various cis- and trans-acting factors that rule the regulation of translation initiation in eukaryotes. Recent discoveries have shown that the guidance of the translation machinery for the choice of the start codon require sophisticated molecular mechanisms. In particular, the 5'UTR and the coding sequences contain cis-acting elements that trigger the use of AUG codons but also non-AUG codons to initiate protein synthesis. The use of these alternative start codons is also largely influenced by numerous trans-acting elements that drive selective mRNA translation in response to environmental changes.
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Affiliation(s)
- Antonin Tidu
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France.
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5
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Jia W, Yuan J, Li S, Cheng B. The role of dysregulated mRNA translation machinery in cancer pathogenesis and therapeutic value of ribosome-inactivating proteins. Biochim Biophys Acta Rev Cancer 2023; 1878:189018. [PMID: 37944831 DOI: 10.1016/j.bbcan.2023.189018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/17/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Dysregulated protein synthesis is a hallmark of tumors. mRNA translation reprogramming contributes to tumorigenesis, which is fueled by abnormalities in ribosome formation, tRNA abundance and modification, and translation factors. Not only malignant cells but also stromal cells within tumor microenvironment can undergo transformation toward tumorigenic phenotypes during translational reprogramming. Ribosome-inactivating proteins (RIPs) have garnered interests for their ability to selectively inhibit protein synthesis and suppress tumor growth. This review summarizes the role of dysregulated translation machinery in tumor development and explores the potential of RIPs in cancer treatment.
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Affiliation(s)
- Wentao Jia
- Oncology Department of Traditional Chinese Medicine, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai 200043, China
| | - Jiaying Yuan
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China
| | - Shu Li
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, China.
| | - Binbin Cheng
- Oncology Department of Traditional Chinese Medicine, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai 200043, China.
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6
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Mao Y, Jia L, Dong L, Shu XE, Qian SB. Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation. Nat Struct Mol Biol 2023; 30:1816-1825. [PMID: 37957305 DOI: 10.1038/s41594-023-01119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/07/2023] [Indexed: 11/15/2023]
Abstract
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome profiling, here we report pervasive out-of-frame translation immediately from the start codon. Start codon-associated ribosomal frameshifting (SCARF) stems from the slippage of ribosomes during the transition from initiation to elongation. Using a massively paralleled reporter assay, we uncovered sequence elements acting as SCARF enhancers or repressors, implying that start codon recognition is coupled with reading frame fidelity. This finding explains thousands of mass spectrometry spectra that are unannotated in the human proteome. Mechanistically, we find that the eukaryotic initiation factor 5B (eIF5B) maintains the reading frame fidelity by stabilizing initiating ribosomes. Intriguingly, amino acid starvation induces SCARF by proteasomal degradation of eIF5B. The stress-induced SCARF protects cells from starvation by enabling amino acid recycling and selective mRNA translation. Our findings illustrate a beneficial effect of translational 'noise' in nutrient stress adaptation.
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Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Longfei Jia
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Leiming Dong
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA.
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7
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Fang JC, Liu MJ. Translation initiation at AUG and non-AUG triplets in plants. Plant Sci 2023; 335:111822. [PMID: 37574140 DOI: 10.1016/j.plantsci.2023.111822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/22/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
In plants and other eukaryotes, precise selection of translation initiation site (TIS) on mRNAs shapes the proteome in response to cellular events or environmental cues. The canonical translation of mRNAs initiates at a 5' proximal AUG codon in a favorable context. However, the coding and non-coding regions of plant genomes contain numerous unannotated alternative AUG and non-AUG TISs. Determining how and why these unexpected and prevalent TISs are activated in plants has emerged as an exciting research area. In this review, we focus on the selection of plant TISs and highlight studies that revealed previously unannotated TISs used in vivo via comparative genomics and genome-wide profiling of ribosome positioning and protein N-terminal ends. The biological signatures of non-AUG TIS-initiated open reading frames (ORFs) in plants are also discussed. We describe what is understood about cis-regulatory RNA elements and trans-acting eukaryotic initiation factors (eIFs) in the site selection for translation initiation by featuring the findings in plants along with supporting findings in non-plant species. The prevalent, unannotated TISs provide a hidden reservoir of ORFs that likely help reshape plant proteomes in response to developmental or environmental cues. These findings underscore the importance of understanding the mechanistic basis of TIS selection to functionally annotate plant genomes, especially for crops with large genomes.
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Affiliation(s)
- Jhen-Cheng Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan.
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8
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Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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9
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Mao Y, Jia L, Dong L, Shu XE, Qian SB. Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation. bioRxiv 2023:2023.02.15.528768. [PMID: 36824937 PMCID: PMC9949036 DOI: 10.1101/2023.02.15.528768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome profiling, here we report pervasive out-of-frame translation immediately from the start codon. The start codon-associated ribosome frameshifting (SCARF) stems from the slippage of ribosomes during the transition from initiation to elongation. Using a massively paralleled reporter assay, we uncovered sequence elements acting as SCARF enhancers or repressors, implying that start codon recognition is coupled with reading frame fidelity. This finding explains thousands of mass spectrometry spectra unannotated from human proteome. Mechanistically, we find that the eukaryotic initiation factor 5B (eIF5B) maintains the reading frame fidelity by stabilizing initiating ribosomes. Intriguingly, amino acid starvation induces SCARF by proteasomal degradation of eIF5B. The stress-induced SCARF protects cells from starvation by enabling amino acid recycling and selective mRNA translation. Our findings illustrate a beneficial effect of translational "noise" in nutrient stress adaptation.
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10
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:ijms24032976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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11
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Sehrawat U, Haimov O, Weiss B, Tamarkin-Ben Harush A, Ashkenazi S, Plotnikov A, Noiman T, Leshkowitz D, Stelzer G, Dikstein R. Inhibitors of eIF4G1-eIF1 uncover its regulatory role of ER/UPR stress-response genes independent of eIF2α-phosphorylation. Proc Natl Acad Sci U S A 2022; 119:e2120339119. [PMID: 35857873 DOI: 10.1073/pnas.2120339119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
During translation initiation, eIF4G1 dynamically interacts with eIF4E and eIF1. While the role of eIF4E-eIF4G1 is well established, the regulatory functions of eIF4G1-eIF1 are poorly understood. Here, we report the identification of the eIF4G1-eIF1 inhibitors i14G1-10 and i14G1-12. i14G1s directly bind eIF4G1 and inhibit translation in vitro and in the cell, and their effects on translation are dependent on eIF4G1 levels. Translatome analyses revealed that i14G1s mimic eIF1 and eIF4G1 perturbations on the stringency of start codon selection and the opposing roles of eIF1-eIF4G1 in scanning-dependent and scanning-independent short 5' untranslated region (UTR) translation. Remarkably, i14G1s activate ER/unfolded protein response (UPR) stress-response genes via enhanced ribosome loading, elevated 5'UTR translation at near-cognate AUGs, and unexpected concomitant up-regulation of coding-region translation. These effects are, at least in part, independent of eIF2α-phosphorylation. Interestingly, eIF4G1-eIF1 interaction itself is negatively regulated by ER stress and mTOR inhibition. Thus, i14G1s uncover an unknown mechanism of ER/UPR translational stress response and are valuable research tools and potential drugs against diseases exhibiting dysregulated translation.
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12
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Basu I, Gorai B, Chandran T, Maiti PK, Hussain T. Selection of start codon during mRNA scanning in eukaryotic translation initiation. Commun Biol 2022; 5:587. [PMID: 35705698 PMCID: PMC9200866 DOI: 10.1038/s42003-022-03534-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 05/25/2022] [Indexed: 11/24/2022] Open
Abstract
Accurate and high-speed scanning and subsequent selection of the correct start codon are important events in protein synthesis. Eukaryotic mRNAs have long 5′ UTRs that are inspected for the presence of a start codon by the ribosomal 48S pre-initiation complex (PIC). However, the conformational state of the 48S PIC required for inspecting every codon is not clearly understood. Here, atomistic molecular dynamics (MD) simulations and energy calculations suggest that the scanning conformation of 48S PIC may reject all but 4 (GUG, CUG, UUG and ACG) of the 63 non-AUG codons, and initiation factor eIF1 is crucial for this discrimination. We provide insights into the possible role of initiation factors eIF1, eIF1A, eIF2α and eIF2β in scanning. Overall, the study highlights how the scanning conformation of ribosomal 48S PIC acts as a coarse selectivity checkpoint for start codon selection and scans long 5′ UTRs in eukaryotic mRNAs with accuracy and high speed. Molecular simulations of start codon selection by the eukaryotic ribosome during mRNA scanning provide further insight into high speed of scanning and how initiation factors contribute toward codon-anticodon-ribosome network stability.
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Affiliation(s)
- Ipsita Basu
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Biswajit Gorai
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.,Department of Chemical Engineering, University of New Hampshire, Durham, NH-03824, USA
| | - Thyageshwar Chandran
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore, 560012, India.,Department of Biotechnology, National Institute of Technology-Warangal, Telangana, 506004, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore, 560012, India.
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13
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Sunavala-Dossabhoy G. Disorder at the Start: The Contribution of Dysregulated Translation Initiation to Cancer Therapy Resistance. Front Oral Health 2022; 2:765931. [PMID: 35048066 PMCID: PMC8757695 DOI: 10.3389/froh.2021.765931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/02/2021] [Indexed: 11/26/2022] Open
Abstract
Translation of cellular RNA to protein is an energy-intensive process through which synthesized proteins dictate cellular processes and function. Translation is regulated in response to extracellular effectors and availability of amino acids intracellularly. Most eukaryotic mRNA rely on the methyl 7-guanosine (m7G) nucleotide cap to recruit the translation machinery, and the uncoupling of translational control that occurs in tumorigenesis plays a significant role in cancer treatment response. This article provides an overview of the mammalian translation initiation process and the primary mechanisms by which it is regulated. An outline of how deregulation of initiation supports tumorigenesis and how initiation at a downstream open reading frame (ORF) of Tousled-like kinase 1 (TLK1) leads to treatment resistance is discussed.
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Affiliation(s)
- Gulshan Sunavala-Dossabhoy
- Department of Biochemistry and Molecular Biology, Louisiana State University Health and Feist Weiller Cancer Center, Shreveport, LA, United States
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14
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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: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Sonobe Y, Aburas J, Krishnan G, Fleming AC, Ghadge G, Islam P, Warren EC, Gu Y, Kankel MW, Brown AEX, Kiskinis E, Gendron TF, Gao FB, Roos RP, Kratsios P. A C. elegans model of C9orf72-associated ALS/FTD uncovers a conserved role for eIF2D in RAN translation. Nat Commun 2021; 12:6025. [PMID: 34654821 PMCID: PMC8519953 DOI: 10.1038/s41467-021-26303-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/28/2021] [Indexed: 12/31/2022] Open
Abstract
A hexanucleotide repeat expansion GGGGCC in the non-coding region of C9orf72 is the most common cause of inherited amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Toxic dipeptide repeats (DPRs) are synthesized from GGGGCC via repeat-associated non-AUG (RAN) translation. Here, we develop C. elegans models that express, either ubiquitously or exclusively in neurons, 75 GGGGCC repeats flanked by intronic C9orf72 sequence. The worms generate DPRs (poly-glycine-alanine [poly-GA], poly-glycine-proline [poly-GP]) and poly-glycine-arginine [poly-GR]), display neurodegeneration, and exhibit locomotor and lifespan defects. Mutation of a non-canonical translation-initiating codon (CUG) upstream of the repeats selectively reduces poly-GA steady-state levels and ameliorates disease, suggesting poly-GA is pathogenic. Importantly, loss-of-function mutations in the eukaryotic translation initiation factor 2D (eif-2D/eIF2D) reduce poly-GA and poly-GP levels, and increase lifespan in both C. elegans models. Our in vitro studies in mammalian cells yield similar results. Here, we show a conserved role for eif-2D/eIF2D in DPR expression.
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Affiliation(s)
- Yoshifumi Sonobe
- grid.412578.d0000 0000 8736 9513University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.412578.d0000 0000 8736 9513Department of Neurology, University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.170205.10000 0004 1936 7822The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, IL USA
| | - Jihad Aburas
- grid.412578.d0000 0000 8736 9513University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.170205.10000 0004 1936 7822The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, IL USA ,grid.170205.10000 0004 1936 7822Department of Neurobiology, University of Chicago, Chicago, IL USA
| | - Gopinath Krishnan
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Andrew C. Fleming
- grid.16753.360000 0001 2299 3507The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Ghanashyam Ghadge
- grid.412578.d0000 0000 8736 9513University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.412578.d0000 0000 8736 9513Department of Neurology, University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.170205.10000 0004 1936 7822The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, IL USA
| | - Priota Islam
- grid.14105.310000000122478951MRC London Institute of Medical Sciences, London, UK ,grid.7445.20000 0001 2113 8111Institute of Clinical Sciences, Imperial College London, London, UK
| | - Eleanor C. Warren
- grid.14105.310000000122478951MRC London Institute of Medical Sciences, London, UK ,grid.7445.20000 0001 2113 8111Institute of Clinical Sciences, Imperial College London, London, UK
| | - Yuanzheng Gu
- grid.417832.b0000 0004 0384 8146Neuromuscular & Movement Disorders, Biogen, Cambridge, MA 02142 USA
| | - Mark W. Kankel
- grid.417832.b0000 0004 0384 8146Neuromuscular & Movement Disorders, Biogen, Cambridge, MA 02142 USA
| | - André E. X. Brown
- grid.14105.310000000122478951MRC London Institute of Medical Sciences, London, UK ,grid.7445.20000 0001 2113 8111Institute of Clinical Sciences, Imperial College London, London, UK
| | - Evangelos Kiskinis
- grid.16753.360000 0001 2299 3507The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Tania F. Gendron
- grid.417467.70000 0004 0443 9942Department of Neuroscience, Mayo Clinic, Jacksonville, FL USA
| | - Fen-Biao Gao
- grid.168645.80000 0001 0742 0364Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Raymond P. Roos
- grid.412578.d0000 0000 8736 9513University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.412578.d0000 0000 8736 9513Department of Neurology, University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL 60637 USA ,grid.170205.10000 0004 1936 7822The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, IL USA
| | - Paschalis Kratsios
- University of Chicago Medical Center, 5841S. Maryland Avenue, Chicago, IL, 60637, USA. .,The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, IL, USA. .,Department of Neurobiology, University of Chicago, Chicago, IL, USA.
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16
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Rana A, Gupta N, Thakur A. Post-transcriptional and translational control of the morphology and virulence in human fungal pathogens. Mol Aspects Med 2021; 81:101017. [PMID: 34497025 DOI: 10.1016/j.mam.2021.101017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
Host-pathogen interactions at the molecular level are the key to fungal pathogenesis. Fungal pathogens utilize several mechanisms such as adhesion, invasion, phenotype switching and metabolic adaptations, to survive in the host environment and respond. Post-transcriptional and translational regulations have emerged as key regulatory mechanisms ensuring the virulence and survival of fungal pathogens. Through these regulations, fungal pathogens effectively alter their protein pool, respond to various stress, and undergo morphogenesis, leading to efficient and comprehensive changes in fungal physiology. The regulation of virulence through post-transcriptional and translational regulatory mechanisms is mediated through mRNA elements (cis factors) or effector molecules (trans factors). The untranslated regions upstream and downstream of the mRNA, as well as various RNA-binding proteins involved in translation initiation or circularization of the mRNA, play pivotal roles in the regulation of morphology and virulence by influencing protein synthesis, protein isoforms, and mRNA stability. Therefore, post-transcriptional and translational mechanisms regulating the morphology, virulence and drug-resistance processes in fungal pathogens can be the target for new therapeutics. With improved "omics" technologies, these regulatory mechanisms are increasingly coming to the forefront of basic biology and drug discovery. This review aims to discuss various modes of post-transcriptional and translation regulations, and how these mechanisms exert influence in the virulence and morphogenesis of fungal pathogens.
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Affiliation(s)
- Aishwarya Rana
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Nidhi Gupta
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Anil Thakur
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India.
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17
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Thakur A, Gaikwad S, Vijjamarri AK, Hinnebusch AG. eIF2α interactions with mRNA control accurate start codon selection by the translation preinitiation complex. Nucleic Acids Res 2020; 48:10280-10296. [PMID: 32955564 DOI: 10.1093/nar/gkaa761] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 11/13/2022] Open
Abstract
In translation initiation, AUG recognition triggers rearrangement of the 48S preinitiation complex (PIC) from an open conformation to a closed state with more tightly-bound Met-tRNAi. Cryo-EM structures have revealed interactions unique to the closed complex between arginines R55/R57 of eIF2α with mRNA, including the -3 nucleotide of the 'Kozak' context. We found that R55/R57 substitutions reduced recognition of a UUG start codon at HIS4 in Sui- cells (Ssu- phenotype); and in vitro, R55G-R57E accelerated dissociation of the eIF2·GTP·Met-tRNAi ternary complex (TC) from reconstituted PICs with a UUG start codon, indicating destabilization of the closed complex. R55/R57 substitutions also decreased usage of poor-context AUGs in SUI1 and GCN4 mRNAs in vivo. In contrast, eIF2α-R53 interacts with the rRNA backbone only in the open complex, and the R53E substitution enhanced initiation at a UUG codon (Sui- phenotype) and poor-context AUGs, while reducing the rate of TC loading (Gcd- phenotype) in vivo. Consistently, R53E slowed TC binding to the PIC while decreasing TC dissociation at UUG codons in vitro, indicating destabilization of the open complex. Thus, distinct interactions of eIF2α with rRNA or mRNA stabilize first the open, and then closed, conformation of the PIC to influence the accuracy of initiation in vivo.
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Affiliation(s)
- Anil Thakur
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.,Regional Centre for Biotechnology, 3rd milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Swati Gaikwad
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Anil K Vijjamarri
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
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18
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Zhou F, Zhang H, Kulkarni SD, Lorsch JR, Hinnebusch AG. eIF1 discriminates against suboptimal initiation sites to prevent excessive uORF translation genome-wide. RNA 2020; 26:419-438. [PMID: 31915290 PMCID: PMC7075259 DOI: 10.1261/rna.073536.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/06/2020] [Indexed: 05/22/2023]
Abstract
The translation preinitiation complex (PIC) scans the mRNA for an AUG codon in a favorable context. Previous findings suggest that the factor eIF1 discriminates against non-AUG start codons by impeding full accommodation of Met-tRNAi in the P site of the 40S ribosomal subunit, necessitating eIF1 dissociation for start codon selection. Consistent with this, yeast eIF1 substitutions that weaken its binding to the PIC increase initiation at UUG codons on a mutant his4 mRNA and particular synthetic mRNA reporters; and also at the AUG start codon of the mRNA for eIF1 itself owing to its poor Kozak context. It was not known however whether such eIF1 mutants increase initiation at suboptimal start codons genome-wide. By ribosome profiling, we show that the eIF1-L96P variant confers increased translation of numerous upstream open reading frames (uORFs) initiating with either near-cognate codons (NCCs) or AUGs in poor context. The increased uORF translation is frequently associated with the reduced translation of the downstream main coding sequences (CDS). Initiation is also elevated at certain NCCs initiating amino-terminal extensions, including those that direct mitochondrial localization of the GRS1 and ALA1 products, and at a small set of main CDS AUG codons with especially poor context, including that of eIF1 itself. Thus, eIF1 acts throughout the yeast translatome to discriminate against NCC start codons and AUGs in poor context; and impairing this function enhances the repressive effects of uORFs on CDS translation and alters the ratios of protein isoforms translated from near-cognate versus AUG start codons.
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Affiliation(s)
- Fujun Zhou
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hongen Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Shardul D Kulkarni
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jon R Lorsch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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19
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Wallace EWJ, Maufrais C, Sales-Lee J, Tuck LR, de Oliveira L, Feuerbach F, Moyrand F, Natarajan P, Madhani HD, Janbon G. Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom. Nucleic Acids Res 2020; 48:2312-2331. [PMID: 32020195 PMCID: PMC7049704 DOI: 10.1093/nar/gkaa060] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5' and 3' ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that quantitatively programs both the expression and the structures of proteins in diverse fungi.
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Affiliation(s)
- Edward W J Wallace
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, UK
| | - Corinne Maufrais
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
- Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015 Paris, France
| | - Jade Sales-Lee
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Laura R Tuck
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, UK
| | - Luciana de Oliveira
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| | - Frank Feuerbach
- Institut Pasteur, Unité Génétique des Interactions Macromoléculaire, Département Génome et Génétique, F-75015 Paris, France
| | - Frédérique Moyrand
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
| | - Prashanthi Natarajan
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Guilhem Janbon
- Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015 Paris, France
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20
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Thakur A, Marler L, Hinnebusch AG. A network of eIF2β interactions with eIF1 and Met-tRNAi promotes accurate start codon selection by the translation preinitiation complex. Nucleic Acids Res 2019; 47:2574-2593. [PMID: 30576497 PMCID: PMC6411837 DOI: 10.1093/nar/gky1274] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/07/2018] [Accepted: 12/15/2018] [Indexed: 11/14/2022] Open
Abstract
In translation initiation, a 43S preinitiation complex (PIC) containing eIF1 and a ternary complex (TC) of GTP-bound eIF2 and Met-RNAi scans the mRNA for the start codon. AUG recognition triggers eIF1 release and rearrangement from an open PIC conformation to a closed state with more tightly-bound Met-tRNAi (PIN state). Cryo-EM models reveal eIF2β contacts with eIF1 and Met-tRNAi exclusive to the open complex that should destabilize the closed state. eIF2β or eIF1 substitutions disrupting these contacts increase initiation at UUG codons, and compound substitutions also derepress translation of GCN4, indicating slower TC recruitment. The latter substitutions slow TC loading while stabilizing TC binding at UUG codons in reconstituted PICs, indicating a destabilized open complex and shift to the closed/PIN state. An eIF1 substitution that should strengthen the eIF2β:eIF1 interface has the opposite genetic and biochemical phenotypes. eIF2β is also predicted to restrict Met-tRNAi movement into the closed/PIN state, and substitutions that should diminish this clash increase UUG initiation in vivo and stabilize Met-tRNAi binding at UUG codons in vitro with little effect on TC loading. Thus, eIF2β anchors eIF1 and TC to the open complex, enhancing PIC assembly and scanning, while impeding rearrangement to the closed conformation at non-AUG codons.
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Affiliation(s)
- Anil Thakur
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Laura Marler
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
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21
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Monestier A, Lazennec-Schurdevin C, Coureux PD, Mechulam Y, Schmitt E. Role of aIF1 in Pyrococcus abyssi translation initiation. Nucleic Acids Res 2019; 46:11061-11074. [PMID: 30239976 PMCID: PMC6237735 DOI: 10.1093/nar/gky850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/11/2018] [Indexed: 01/06/2023] Open
Abstract
In archaeal translation initiation, a preinitiation complex (PIC) made up of aIF1, aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNAiMet) and mRNA bound to the small ribosomal subunit is responsible for start codon selection. Many archaeal mRNAs contain a Shine-Dalgarno (SD) sequence allowing the PIC to be prepositioned in the vicinity of the start codon. Nevertheless, cryo-EM studies have suggested local scanning to definitely establish base pairing of the start codon with the tRNA anticodon. Here, using fluorescence anisotropy, we show that aIF1 and mRNA have synergistic binding to the Pyrococcus abyssi 30S. Stability of 30S:mRNA:aIF1 strongly depends on the SD sequence. Further, toeprinting experiments show that aIF1-containing PICs display a dynamic conformation with the tRNA not firmly accommodated in the P site. AIF1-induced destabilization of the PIC is favorable for proofreading erroneous initiation complexes. After aIF1 departure, the stability of the PIC increases reflecting initiator tRNA fully base-paired to the start codon. Altogether, our data support the idea that some of the main events governing start codon selection in eukaryotes and archaea occur within a common structural and functional core. However, idiosyncratic features in loop 1 sequence involved in 30S:mRNA binding suggest adjustments of e/aIF1 functioning in the two domains.
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Affiliation(s)
- Auriane Monestier
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | | | - Pierre-Damien Coureux
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Yves Mechulam
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
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Gómez-Herranz M, Nekulova M, Faktor J, Hernychova L, Kote S, Sinclair EH, Nenutil R, Vojtesek B, Ball KL, Hupp TR. The effects of IFITM1 and IFITM3 gene deletion on IFNγ stimulated protein synthesis. Cell Signal 2019; 60:39-56. [PMID: 30951861 PMCID: PMC7111284 DOI: 10.1016/j.cellsig.2019.03.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/29/2019] [Accepted: 03/29/2019] [Indexed: 02/02/2023]
Abstract
Interferon-induced transmembrane proteins IFITM1 and IFITM3 (IFITM1/3) play a role in both RNA viral restriction and in human cancer progression. Using immunohistochemical staining of FFPE tissue, we identified subgroups of cervical cancer patients where IFITM1/3 protein expression is inversely related to metastasis. Guide RNA-CAS9 methods were used to develop an isogenic IFITM1/IFITM3 double null cervical cancer model in order to define dominant pathways triggered by presence or absence of IFITM1/3 signalling. A pulse SILAC methodology identified IRF1, HLA-B, and ISG15 as the most dominating IFNγ inducible proteins whose synthesis was attenuated in the IFITM1/IFITM3 double-null cells. Conversely, SWATH-IP mass spectrometry of ectopically expressed SBP-tagged IFITM1 identified ISG15 and HLA-B as dominant co-associated proteins. ISG15ylation was attenuated in IFNγ treated IFITM1/IFITM3 double-null cells. Proximity ligation assays indicated that HLA-B can interact with IFITM1/3 proteins in parental SiHa cells. Cell surface expression of HLA-B was attenuated in IFNγ treated IFITM1/IFITM3 double-null cells. SWATH-MS proteomic screens in cells treated with IFITM1-targeted siRNA cells resulted in the attenuation of an interferon regulated protein subpopulation including MHC Class I molecules as well as IFITM3, STAT1, B2M, and ISG15. These data have implications for the function of IFITM1/3 in mediating IFNγ stimulated protein synthesis including ISG15ylation and MHC Class I production in cancer cells. The data together suggest that pro-metastatic growth associated with IFITM1/3 negative cervical cancers relates to attenuated expression of MHC Class I molecules that would support tumor immune escape. IFITM1/3 expression in cervical cancers inversely correlates with metastases. Isogenic IFITM1 and IFITM3 null cervical cancer cells were developed. Pulse SILAC approaches were used to define IFITM1/3 dependent signalling pathways. The major IFITM1/3-interferon-γ dependent effectors are HLA-B and ISG15. IFITM1/3 loss would be predicted to reduce HLA expression and ISG15ylation in vivo.
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Affiliation(s)
- Maria Gómez-Herranz
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XR, United Kingdom
| | - Marta Nekulova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Jakub Faktor
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Lenka Hernychova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Sachin Kote
- University of Gdansk, International Centre for Cancer Vaccine Science, Department of Chemistry, Gdansk, Poland
| | - Elizabeth H Sinclair
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XR, United Kingdom
| | - Rudolf Nenutil
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Borivoj Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic.
| | - Kathryn L Ball
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XR, United Kingdom; Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic.
| | - Ted R Hupp
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XR, United Kingdom; Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; University of Gdansk, International Centre for Cancer Vaccine Science, Department of Chemistry, Gdansk, Poland.
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23
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Schmitt E, Coureux PD, Monestier A, Dubiez E, Mechulam Y. Start Codon Recognition in Eukaryotic and Archaeal Translation Initiation: A Common Structural Core. Int J Mol Sci 2019; 20:E939. [PMID: 30795538 DOI: 10.3390/ijms20040939] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 01/12/2023] Open
Abstract
Understanding molecular mechanisms of ribosomal translation sheds light on the emergence and evolution of protein synthesis in the three domains of life. Universally, ribosomal translation is described in three steps: initiation, elongation and termination. During initiation, a macromolecular complex assembled around the small ribosomal subunit selects the start codon on the mRNA and defines the open reading frame. In this review, we focus on the comparison of start codon selection mechanisms in eukaryotes and archaea. Eukaryotic translation initiation is a very complicated process, involving many initiation factors. The most widespread mechanism for the discovery of the start codon is the scanning of the mRNA by a pre-initiation complex until the first AUG codon in a correct context is found. In archaea, long-range scanning does not occur because of the presence of Shine-Dalgarno (SD) sequences or of short 5′ untranslated regions. However, archaeal and eukaryotic translation initiations have three initiation factors in common: e/aIF1, e/aIF1A and e/aIF2 are directly involved in the selection of the start codon. Therefore, the idea that these archaeal and eukaryotic factors fulfill similar functions within a common structural ribosomal core complex has emerged. A divergence between eukaryotic and archaeal factors allowed for the adaptation to the long-range scanning process versus the SD mediated prepositioning of the ribosome.
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Llácer JL, Hussain T, Saini AK, Nanda JS, Kaur S, Gordiyenko Y, Kumar R, Hinnebusch AG, Lorsch JR, Ramakrishnan V. Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition. eLife 2018; 7:e39273. [PMID: 30475211 PMCID: PMC6298780 DOI: 10.7554/elife.39273] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/21/2018] [Indexed: 12/22/2022] Open
Abstract
In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNAi in a 'PIN' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a yeast 48S pre-initiation complex (PIC), at an overall resolution of 3.0 Å, featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNAi. Substitutions of eIF5 residues involved in the eIF5-NTD/tRNAi interaction influenced initiation at near-cognate UUG codonsin vivo, and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection.
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Affiliation(s)
- Jose Luis Llácer
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
- Instituto de Biomedicina de Valencia (IBV-CSIC)ValenciaSpain
| | - Tanweer Hussain
- Department of Molecular Reproduction, Development and GeneticsIndian Institute of ScienceBangaloreIndia
| | - Adesh K Saini
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | - Jagpreet Singh Nanda
- Laboratory on the Mechanism and Regulation of Protein SynthesisEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Sukhvir Kaur
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | | | - Rakesh Kumar
- Shoolini University of Biotechnology and Management SciencesHimachal PradeshIndia
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and DevelopmentEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein SynthesisEunice K Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - V Ramakrishnan
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
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