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Grove DJ, Russell PJ, Kearse MG. To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1833. [PMID: 38433101 PMCID: PMC11260288 DOI: 10.1002/wrna.1833] [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: 10/31/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
Selection of the correct start codon is critical for high-fidelity protein synthesis. In eukaryotes, this is typically governed by a multitude of initiation factors (eIFs), including eIF2·GTP that directly delivers the initiator tRNA (Met-tRNAi Met ) to the P site of the ribosome. However, numerous reports, some dating back to the early 1970s, have described other initiation factors having high affinity for the initiator tRNA and the ability of delivering it to the ribosome, which has provided a foundation for further work demonstrating non-canonical initiation mechanisms using alternative initiation factors. Here we provide a critical analysis of current understanding of eIF2A, eIF2D, and the MCT-1·DENR dimer, the evidence surrounding their ability to initiate translation, their implications in human disease, and lay out important key questions for the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Mechanisms Translation > Regulation.
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Affiliation(s)
- Daisy J. Grove
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Paul J. Russell
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- The Cellular, Molecular, Biochemical Sciences Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Michael G. Kearse
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- The Cellular, Molecular, Biochemical Sciences Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
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2
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Alghoul F, Laure S, Eriani G, Martin F. Translation inhibitory elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition. eLife 2021; 10:e66369. [PMID: 34076576 PMCID: PMC8172242 DOI: 10.7554/elife.66369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/20/2021] [Indexed: 01/20/2023] Open
Abstract
During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5'UTR. First, an internal ribosome entry site (IRES) enables cap-independent translation. The second regulon is a translation inhibitory element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of mouse Hoxa3 and Hoxa11 TIEs. Both TIEs possess an upstream open reading frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In Hoxa3 TIE, we identify an uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of Hoxa11 TIE is different, it also contains an uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a 'start-stop'. The 'start-stop' sequence is species-specific and in mice, is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hoxa11 main ORF.
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Affiliation(s)
- Fatima Alghoul
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Schaeffer Laure
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Gilbert Eriani
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
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Vasudevan D, Neuman SD, Yang A, Lough L, Brown B, Bashirullah A, Cardozo T, Ryoo HD. Translational induction of ATF4 during integrated stress response requires noncanonical initiation factors eIF2D and DENR. Nat Commun 2020; 11:4677. [PMID: 32938929 PMCID: PMC7495428 DOI: 10.1038/s41467-020-18453-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 08/17/2020] [Indexed: 01/25/2023] Open
Abstract
The Integrated Stress Response (ISR) helps metazoan cells adapt to cellular stress by limiting the availability of initiator methionyl-tRNA for translation. Such limiting conditions paradoxically stimulate the translation of ATF4 mRNA through a regulatory 5' leader sequence with multiple upstream Open Reading Frames (uORFs), thereby activating stress-responsive gene expression. Here, we report the identification of two critical regulators of such ATF4 induction, the noncanonical initiation factors eIF2D and DENR. Loss of eIF2D and DENR in Drosophila results in increased vulnerability to amino acid deprivation, susceptibility to retinal degeneration caused by endoplasmic reticulum (ER) stress, and developmental defects similar to ATF4 mutants. eIF2D requires its RNA-binding motif for regulation of 5' leader-mediated ATF4 translation. Consistently, eIF2D and DENR deficient human cells show impaired ATF4 protein induction in response to ER stress. Altogether, our findings indicate that eIF2D and DENR are critical mediators of ATF4 translational induction and stress responses in vivo.
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Affiliation(s)
- Deepika Vasudevan
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Sarah D Neuman
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Amy Yang
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Lea Lough
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Brian Brown
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Arash Bashirullah
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Timothy Cardozo
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Hyung Don Ryoo
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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Renz PF, Valdivia-Francia F, Sendoel A. Some like it translated: small ORFs in the 5'UTR. Exp Cell Res 2020; 396:112229. [PMID: 32818479 DOI: 10.1016/j.yexcr.2020.112229] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/28/2020] [Accepted: 08/07/2020] [Indexed: 01/06/2023]
Abstract
The 5' untranslated region (5'UTR) is critical in determining post-transcriptional control, which is partly mediated by short upstream open reading frames (uORFs) present in half of mammalian transcripts. uORFs are generally considered to provide functionally important repression of the main-ORF by engaging initiating ribosomes, but under specific environmental conditions such as cellular stress, uORFs can become essential to activate the translation of the main coding sequence. In addition, a growing number of uORF-encoded bioactive microproteins have been described, which have the potential to significantly increase cellular protein diversity. Here we review the diverse cellular contexts in which uORFs play a critical role and discuss the molecular mechanisms underlying their function and regulation. The progress over the last decades in dissecting uORF function suggests that the 5'UTR remains an exciting frontier towards understanding how the cellular proteome is shaped in health and disease.
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Affiliation(s)
- Peter F Renz
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
| | - Fabiola Valdivia-Francia
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland; Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ ETH Zurich, Switzerland
| | - Ataman Sendoel
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland.
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Lin Y, Chen H, Wang X, Xiang J, Wang H, Peng J. Mining the role of RECQL5 in gastric cancer and seeking potential regulatory network by bioinformatics analysis. Exp Mol Pathol 2020; 115:104477. [DOI: 10.1016/j.yexmp.2020.104477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 12/23/2022]
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6
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Lomakin IB, De S, Wang J, Borkar AN, Steitz TA. Crystal structure of the C-terminal domain of DENR. Comput Struct Biotechnol J 2020; 18:696-704. [PMID: 32257053 PMCID: PMC7114459 DOI: 10.1016/j.csbj.2020.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 02/04/2023] Open
Abstract
The density regulated protein (DENR) forms a stable heterodimer with malignant T-cell-amplified sequence 1 (MCT-1). DENR-MCT-1 heterodimer then participates in regulation of non-canonical translation initiation and ribosomal recycling. The N-terminal domain of DENR interacts with MCT-1 and carries a classical tetrahedral zinc ion-binding site, which is crucial for the dimerization. DENR-MCT-1 binds the small (40S) ribosomal subunit through interactions between MCT-1 and helix h24 of the 18S rRNA, and through interactions between the C-terminal domain of DENR and helix h44 of the 18S rRNA. This later interaction occurs in the vicinity of the P site that is also the binding site for canonical translation initiation factor eIF1, which plays the key role in initiation codon selection and scanning. Sequence homology modeling and a low-resolution crystal structure of the DENR-MCT-1 complex with the human 40S subunit suggests that the C-terminal domain of DENR and eIF1 adopt a similar fold. Here we present the crystal structure of the C-terminal domain of DENR determined at 1.74 Å resolution, which confirms its resemblance to eIF1 and advances our understanding of the mechanism by which DENR-MCT-1 regulates non-canonical translation initiation and ribosomal recycling.
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Affiliation(s)
- Ivan B. Lomakin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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Crystal structure of the DENR-MCT-1 complex revealed zinc-binding site essential for heterodimer formation. Proc Natl Acad Sci U S A 2018; 116:528-533. [PMID: 30584092 DOI: 10.1073/pnas.1809688116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein support noncanonical translation initiation, promote translation reinitiation on a specific set of mRNAs with short upstream reading frames, and regulate ribosome recycling. DENR and MCT-1 form a heterodimer, which binds to the ribosome. We determined the crystal structure of the heterodimer formed by human MCT-1 and the N-terminal domain of DENR at 2.0-Å resolution. The structure of the heterodimer reveals atomic details of the mechanism of DENR and MCT-1 interaction. Four conserved cysteine residues of DENR (C34, C37, C44, C53) form a classical tetrahedral zinc ion-binding site, which preserves the structure of the DENR's MCT-1-binding interface that is essential for the dimerization. Substitution of all four cysteines by alanine abolished a heterodimer formation. Our findings elucidate further the mechanism of regulation of DENR-MCT-1 activities in unconventional translation initiation, reinitiation, and recycling.
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8
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Hellen CUT. Translation Termination and Ribosome Recycling in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a032656. [PMID: 29735640 DOI: 10.1101/cshperspect.a032656] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Termination of mRNA translation occurs when a stop codon enters the A site of the ribosome, and in eukaryotes is mediated by release factors eRF1 and eRF3, which form a ternary eRF1/eRF3-guanosine triphosphate (GTP) complex. eRF1 recognizes the stop codon, and after hydrolysis of GTP by eRF3, mediates release of the nascent peptide. The post-termination complex is then disassembled, enabling its constituents to participate in further rounds of translation. Ribosome recycling involves splitting of the 80S ribosome by the ATP-binding cassette protein ABCE1 to release the 60S subunit. Subsequent dissociation of deacylated transfer RNA (tRNA) and messenger RNA (mRNA) from the 40S subunit may be mediated by initiation factors (priming the 40S subunit for initiation), by ligatin (eIF2D) or by density-regulated protein (DENR) and multiple copies in T-cell lymphoma-1 (MCT1). These events may be subverted by suppression of termination (yielding carboxy-terminally extended read-through polypeptides) or by interruption of recycling, leading to reinitiation of translation near the stop codon.
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Affiliation(s)
- Christopher U T Hellen
- Department of Cell Biology, State University of New York, Downstate Medical Center, New York, New York 11203
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eIF1 Loop 2 interactions with Met-tRNA i control the accuracy of start codon selection by the scanning preinitiation complex. Proc Natl Acad Sci U S A 2018; 115:E4159-E4168. [PMID: 29666249 DOI: 10.1073/pnas.1800938115] [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] [Indexed: 02/05/2023] Open
Abstract
The eukaryotic 43S preinitiation complex (PIC), bearing initiator methionyl transfer RNA (Met-tRNAi) in a ternary complex (TC) with eukaryotic initiation factor 2 (eIF2)-GTP, scans the mRNA leader for an AUG codon in favorable context. AUG recognition evokes rearrangement from an open PIC conformation with TC in a "POUT" state to a closed conformation with TC more tightly bound in a "PIN" state. eIF1 binds to the 40S subunit and exerts a dual role of enhancing TC binding to the open PIC conformation while antagonizing the PIN state, necessitating eIF1 dissociation for start codon selection. Structures of reconstituted PICs reveal juxtaposition of eIF1 Loop 2 with the Met-tRNAi D loop in the PIN state and predict a distortion of Loop 2 from its conformation in the open complex to avoid a clash with Met-tRNAi We show that Ala substitutions in Loop 2 increase initiation at both near-cognate UUG codons and AUG codons in poor context. Consistently, the D71A-M74A double substitution stabilizes TC binding to 48S PICs reconstituted with mRNA harboring a UUG start codon, without affecting eIF1 affinity for 40S subunits. Relatively stronger effects were conferred by arginine substitutions; and no Loop 2 substitutions perturbed the rate of TC loading on scanning 40S subunits in vivo. Thus, Loop 2-D loop interactions specifically impede Met-tRNAi accommodation in the PIN state without influencing the POUT mode of TC binding; and Arg substitutions convert the Loop 2-tRNAi clash to an electrostatic attraction that stabilizes PIN and enhances selection of poor start codons in vivo.
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Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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