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Hernández G, Vazquez-Pianzola P. eIF4E as a molecular wildcard in metazoans RNA metabolism. Biol Rev Camb Philos Soc 2023; 98:2284-2306. [PMID: 37553111 DOI: 10.1111/brv.13005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/01/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023]
Abstract
The evolutionary origin of eukaryotes spurred the transition from prokaryotic-like translation to a more sophisticated, eukaryotic translation. During this process, successive gene duplication of a single, primordial eIF4E gene encoding the mRNA cap-binding protein eukaryotic translation initiation factor 4E (eIF4E) gave rise to a plethora of paralog genes across eukaryotes that underwent further functional diversification in RNA metabolism. The ability to take different roles is due to eIF4E promiscuity in binding many partner proteins, rendering eIF4E a highly versatile and multifunctional player that functions as a molecular wildcard. Thus, in metazoans, eIF4E paralogs are involved in various processes, including messenger RNA (mRNA) processing, export, translation, storage, and decay. Moreover, some paralogs display differential expression in tissues and developmental stages and show variable biochemical properties. In this review, we discuss recent advances shedding light on the functional diversification of eIF4E in metazoans. We emphasise humans and two phylogenetically distant species which have become paradigms for studies on development, namely the fruit fly Drosophila melanogaster and the roundworm Caenorhabditis elegans.
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Affiliation(s)
- Greco Hernández
- mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (Instituto Nacional de Cancerología, INCan), 22 San Fernando Ave., Tlalpan, Mexico City, 14080, Mexico
| | - Paula Vazquez-Pianzola
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Berne, 3012, Switzerland
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2
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A Single Mutation in the Cryptic AUG (cAUG) Affects In Vitro Translation and Replication Efficiencies and In Vivo Virulence of Coxsackievirus B3 (CVB3). Curr Microbiol 2022; 79:288. [PMID: 35972696 DOI: 10.1007/s00284-022-02986-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/25/2022] [Indexed: 11/03/2022]
Abstract
The 5'UTR of the genomic RNA of CVB3, unusually long and rich on highly structured secondary structure, contains a conserved cis acting RNA element named the cryptic AUG (cAUG), where the cellular 48S complex is formed. In this study, we investigate the role of this cAUG in CVB3 translation, replication, and virulence. Mutant viral sub-genomic replicon RNA was constructed by site-directed mutagenesis. We characterize in vitro translation and replication efficiencies and in vivo virulence of a cAUG mutant in comparison with wild-type strain. UV-cross-linking assay and Real-Time PCR were used, respectively, to detect binding host proteins and to quantify viral production. Secondary structures of domain containing the cAUG site were studied and compared. The results suggest that introduced mutation in the CVB3 5'UTR affects in vitro and ex vivo viral translation which cannot be rescued by compensatory mutations. A reduced interaction of the La and PCBP2 translation initiation factors with cAUG residue of mutant was revealed. Decreasing production of viral mutant RNA was also demonstrated. Furthermore, secondary structure prediction reveals changes in the ribosome binding sites of the cAUG moiety of mutant sense strand RNA and no alterations in the structure of wild type, suggesting that cAUG mutation specifically affects the secondary structure of the sense RNA strand. Taken together, AUG integrity influences the efficiency of ribosome recruitment through IRES element and the capacity of replication.
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Meyberg R, Perroud PF, Haas FB, Schneider L, Heimerl T, Renzaglia KS, Rensing SA. Characterisation of evolutionarily conserved key players affecting eukaryotic flagellar motility and fertility using a moss model. THE NEW PHYTOLOGIST 2020; 227:440-454. [PMID: 32064607 PMCID: PMC8224819 DOI: 10.1111/nph.16486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/07/2020] [Indexed: 05/18/2023]
Abstract
Defects in flagella/cilia are often associated with infertility and disease. Motile male gametes (sperm cells) are an ancestral eukaryotic trait that has been lost in several lineages like flowering plants. Here, we made use of a phenotypic male fertility difference between two moss (Physcomitrella patens) ecotypes to explore spermatozoid function. We compare genetic and epigenetic variation as well as expression profiles between the Gransden and Reute ecotype to identify a set of candidate genes associated with moss male infertility. We generated a loss-of-function mutant of a coiled-coil domain containing 39 (ccdc39) gene that is part of the flagellar hydin network. Defects in mammal and algal homologues of this gene coincide with a loss of fertility, demonstrating the evolutionary conservation of flagellar function related to male fertility across kingdoms. The Ppccdc39 mutant resembles the Gransden phenotype in terms of male fertility. Potentially, several somatic (epi-)mutations occurred during prolonged vegetative propagation of Gransden, causing regulatory differences of for example the homeodomain transcription factor BELL1. Probably these somatic changes are causative for the observed male fertility defect. We propose that moss spermatozoids might be employed as an easily accessible system to study male infertility of humans and animals in terms of flagellar structure and movement.
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Affiliation(s)
- Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Fabian B. Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
| | - Karen S. Renzaglia
- Department of Plant Biology, Southern Illinois University, Mail Code 6509, 1125 Lincoln Drive, Carbondale, IL 62901, USA
| | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Karl-von-Frisch Str. 8, 35043 Marburg, Germany
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Cho H, Cho HS, Hwang I. Emerging roles of RNA-binding proteins in plant development. CURRENT OPINION IN PLANT BIOLOGY 2019; 51:51-57. [PMID: 31071564 DOI: 10.1016/j.pbi.2019.03.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/27/2019] [Accepted: 03/30/2019] [Indexed: 05/22/2023]
Abstract
RNA-binding proteins (RBPs) influence the fate of target RNAs via direct interactions. During transcription, RBPs and interacting partners are recruited to and modify transcripts, after which they may also participate in critical steps to generate functional RNA. RBP-RNA interactions govern post-transcriptional processing of RNA, consequently regulating gene expression in a spatio-temporal manner. In plants, an increasing number of proteins have been classified as RBPs, many of which have been shown to function as key players in diverse developmental processes. However, a comprehensive understanding of how RBPs function, which RNAs are targeted, and where RBP-RNA interactions occur within plant cells is lacking. Here, we discuss recent findings in the field and newly defined roles for RBPs in plant growth and development. We also describe the mechanistic effects of RBPs on target RNA metabolism and translation.
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Affiliation(s)
- Hyunwoo Cho
- Department of Industrial Plant Science and Technology, College of Agricultural, Life and Environmental Sciences, Chungbuk National University, Cheongju 2864, Republic of Korea
| | - Hyun Seob Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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Keiper BD. Cap-Independent mRNA Translation in Germ Cells. Int J Mol Sci 2019; 20:ijms20010173. [PMID: 30621249 PMCID: PMC6337596 DOI: 10.3390/ijms20010173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 02/07/2023] Open
Abstract
Cellular mRNAs in plants and animals have a 5'-cap structure that is accepted as the recognition point to initiate translation by ribosomes. Consequently, it was long assumed that the translation initiation apparatus was built solely for a cap-dependent (CD) mechanism. Exceptions that emerged invoke structural damage (proteolytic cleavage) to eukaryotic initiation factor 4 (eIF4) factors that disable cap recognition. The residual eIF4 complex is thought to be crippled, but capable of cap-independent (CI) translation to recruit viral or death-associated mRNAs begrudgingly when cells are in great distress. However, situations where CI translation coexists with CD translation are now known. In such cases, CI translation is still a minor mechanism in the major background of CD synthesis. In this review, I propose that germ cells do not fit this mold. Using observations from various animal models of oogenesis and spermatogenesis, I suggest that CI translation is a robust partner to CD translation to carry out the translational control that is so prevalent in germ cell development. Evidence suggests that CI translation provides surveillance of germ cell homeostasis, while CD translation governs the regulated protein synthesis that ushers these meiotic cells through the remarkable steps in sperm/oocyte differentiation.
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Affiliation(s)
- Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA.
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6
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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Gritsenko AA, Weingarten-Gabbay S, Elias-Kirma S, Nir R, de Ridder D, Segal E. Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity. PLoS Comput Biol 2017; 13:e1005734. [PMID: 28922394 PMCID: PMC5630158 DOI: 10.1371/journal.pcbi.1005734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/06/2017] [Accepted: 08/22/2017] [Indexed: 01/25/2023] Open
Abstract
Translation of mRNAs through Internal Ribosome Entry Sites (IRESs) has emerged as a prominent mechanism of cellular and viral initiation. It supports cap-independent translation of select cellular genes under normal conditions, and in conditions when cap-dependent translation is inhibited. IRES structure and sequence are believed to be involved in this process. However due to the small number of IRESs known, there have been no systematic investigations of the determinants of IRES activity. With the recent discovery of thousands of novel IRESs in human and viruses, the next challenge is to decipher the sequence determinants of IRES activity. We present the first in-depth computational analysis of a large body of IRESs, exploring RNA sequence features predictive of IRES activity. We identified predictive k-mer features resembling IRES trans-acting factor (ITAF) binding motifs across human and viral IRESs, and found that their effect on expression depends on their sequence, number and position. Our results also suggest that the architecture of retroviral IRESs differs from that of other viruses, presumably due to their exposure to the nuclear environment. Finally, we measured IRES activity of synthetically designed sequences to confirm our prediction of increasing activity as a function of the number of short IRES elements.
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Affiliation(s)
- Alexey A. Gritsenko
- The Delft Bioinformatics Laboratory, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
- Platform Green Synthetic Biology, Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Shira Weingarten-Gabbay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Elias-Kirma
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ronit Nir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dick de Ridder
- The Delft Bioinformatics Laboratory, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
- Platform Green Synthetic Biology, Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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8
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Zhang D, Chen D, Cao L, Li G, Cheng H. The Effect of Codon Mismatch on the Protein Translation System. PLoS One 2016; 11:e0148302. [PMID: 26840415 PMCID: PMC4739699 DOI: 10.1371/journal.pone.0148302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/15/2016] [Indexed: 11/18/2022] Open
Abstract
Incorrect protein translation, caused by codon mismatch, is an important problem of living cells. In this work, a computational model was introduced to quantify the effects of codon mismatch and the model was used to study the protein translation of Saccharomyces cerevisiae. According to simulation results, the probability of codon mismatch will increase when the supply of amino acids is unbalanced, and the longer is the codon sequence, the larger is the probability for incorrect translation to occur, making the synthesis of long peptide chain difficult. By comparing to simulation results without codon mismatch effects taken into account, the fraction of mRNAs with bound ribosome decrease faster along the mRNAs, making the 5’ ramp phenomenon more obvious. It was also found in our work that the premature mechanism resulted from codon mismatch can reduce the proportion of incorrect translation when the amino acid supply is extremely unbalanced, which is one possible source of high fidelity protein synthesis after peptidyl transfer.
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Affiliation(s)
- Dinglin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Danfeng Chen
- Dalian City Fisherles Technical Extension Station, Dalian, Liaoning, 116025, China
| | - Liaoran Cao
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
- * E-mail: (GHL); (HC)
| | - Hong Cheng
- Shanghai Key Laboratory of Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- * E-mail: (GHL); (HC)
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Souii A, Ben M'hadheb-Gharbi M, Gharbi J. Role of RNA structure motifs in IRES-dependent translation initiation of the coxsackievirus B3: new insights for developing live-attenuated strains for vaccines and gene therapy. Mol Biotechnol 2014; 55:179-202. [PMID: 23881360 DOI: 10.1007/s12033-013-9674-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Internal ribosome entry site (IRES) elements are highly structured RNA sequences that function to recruit ribosomes for the initiation of translation. In contrast to the canonical cap-binding, the mechanism of IRES-mediated translation initiation is still poorly understood. Translation initiation of the coxsackievirus B3 (CVB3), a causative agent of viral myocarditis, has been shown to be mediated by a highly ordered structure of the 5' untranslated region (5'UTR), which harbors an IRES. Taking into account that efficient initiation of mRNA translation depends on temporally and spatially orchestrated sequence of RNA-protein and RNA-RNA interactions, and that, at present, little is known about these interactions, we aimed to describe recent advances in our understanding of molecular structures and biochemical functions of the translation initiation process. Thus, this review will explore the IRES elements as important RNA structures and the significance of these structures in providing an alternative mechanism of translation initiation of the CVB3 RNA. Since translation initiation is the first intracellular step during the CVB3 infection cycle, the IRES region provides an ideal target for antiviral therapies. Interestingly, the 5' and 3'UTRs represent promising candidates for the study of CVB3 cardiovirulence and provide new insights for developing live-attenuated vaccines.
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Affiliation(s)
- Amira Souii
- Institut Supérieur de Biotechnologie de Monastir-Université de Monastir, Avenue Tahar Hadded, BP 74, 5000, Monastir, Tunisia
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In vitro molecular characterization of RNA-proteins interactions during initiation of translation of a wild-type and a mutant Coxsackievirus B3 RNAs. Mol Biotechnol 2013; 54:515-27. [PMID: 22923320 DOI: 10.1007/s12033-012-9592-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Translation initiation of Coxsackievirus B3 (CVB3) RNA is directed by an internal ribosome entry site (IRES) within the 5' untranslated region. Host cell factors involved in this process include some canonical translation factors and additional RNA-binding proteins. We have, previously, described that the Sabin3-like mutation (U475 → C) introduced in CVB3 genome led to a defective mutant with a serious reduction in translation efficiency. With the aim to identify proteins interacting with CVB3 wild-type and Sabin3-like IRESes and to study interactions between HeLa cell or BHK-21 protein extracts and CVB3 RNAs, UV-cross-linking assays were performed. We have observed a number of proteins that specifically interact with both RNAs. In particular, molecular weights of five of these proteins resemble to those of the eukaryotic translation initiation factors 4G, 3b, 4B, and PTB. According to cross-linking patterns obtained, we have demonstrated a better affinity of CVB3 RNA binding to BHK-21 proteins and a reduced interaction of the mutant RNA with almost cellular polypeptides compared to the wild-type IRES. On the basis of phylogeny of some initiation factors and on the knowledge of the initiation of translation process, we focused on the interaction of both IRESes with eIF3, p100 (eIF4G), and 40S ribosomal subunit by filter-binding assays. We have demonstrated a better affinity of binding to the wild-type CVB3 IRES. Thus, the reduction efficiency of the mutant RNA to bind to cellular proteins involved in the translation initiation could be the reason behind inefficient IRES function.
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11
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Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists. Comp Funct Genomics 2012; 2012:134839. [PMID: 22778692 PMCID: PMC3388326 DOI: 10.1155/2012/134839] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 04/09/2012] [Indexed: 01/01/2023] Open
Abstract
The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasite Babesia bovis to 112,000-220,050 Mb in the dinoflagellate Prorocentrum micans. Protists possess numerous cellular, molecular and biochemical traits not observed in “text-book” model organisms. These features challenge some of the concepts and assumptions about the regulation of gene expression in eukaryotes. Like multicellular eukaryotes, many protists encode multiple eIF4Es, but few functional studies have been undertaken except in parasitic species. An earlier phylogenetic analysis of protist eIF4Es indicated that they cannot be grouped within the three classes that describe eIF4E family members from multicellular organisms. Many more protist sequences are now available from which three clades can be recognized that are distinct from the plant/fungi/metazoan classes. Understanding of the protist eIF4Es will be facilitated as more sequences become available particularly for the under-represented opisthokonts and amoebozoa. Similarly, a better understanding of eIF4Es within each clade will develop as more functional studies of protist eIF4Es are completed.
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Hernández G, Proud CG, Preiss T, Parsyan A. On the Diversification of the Translation Apparatus across Eukaryotes. Comp Funct Genomics 2012; 2012:256848. [PMID: 22666084 PMCID: PMC3359775 DOI: 10.1155/2012/256848] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 03/07/2012] [Indexed: 11/21/2022] Open
Abstract
Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.
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Affiliation(s)
- Greco Hernández
- Division of Basic Research, National Institute for Cancer (INCan), Avenida San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080 Mexico City, Mexico
| | - Christopher G. Proud
- Centre for Biological Sciences, University of Southampton, Life Sciences Building (B85), Southampton SO17 1BJ, UK
| | - Thomas Preiss
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Building 131, Garran Road, Acton, Canberra, ACT 0200, Australia
| | - Armen Parsyan
- Goodman Cancer Centre and Department of Biochemistry, Faculty of Medicine, McGill University, 1160 Pine Avenue West, Montreal, QC, Canada H3A 1A3
- Division of General Surgery, Department of Surgery, Faculty of Medicine, McGill University Health Centre, Royal Victoria Hospital, 687 Pine Avenue West, Montreal, QC, Canada H3A 1A1
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Shay KP, Michels AJ, Li W, Kong ANT, Hagen TM. Cap-independent Nrf2 translation is part of a lipoic acid-stimulated detoxification stress response. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1102-9. [PMID: 22521877 DOI: 10.1016/j.bbamcr.2012.04.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 04/03/2012] [Accepted: 04/04/2012] [Indexed: 10/28/2022]
Abstract
Little is known about either the basal or stimulated homeostatic mechanisms regulating nuclear tenure of Nf-e2-related factor 2 (Nrf2), a transcription factor that mediates expression of over 200 detoxification genes. Our data show that stress-induced nuclear Nrf2 accumulation is largely from de novo protein synthesis, rather than translocation from a pre-existing cytoplasmic pool. HepG2 cells were used to monitor nuclear Nrf2 24h following treatment with the dithiol micronutrient (R)-α-lipoic acid (LA; 50μM), or vehicle. LA caused a ≥2.5-fold increase in nuclear Nrf2 within 1h. However, pretreating cells with cycloheximide (50μg/ml) inhibited LA-induced Nrf2 nuclear accumulation by 94%. Providing cells with the mTOR inhibitor, rapamycin, decreased basal Nrf2 levels by 84% after 4h, but LA overcame this inhibition. LA-mediated de novo protein translation was confirmed using HepG2 cells transfected with a bicistronic construct containing an internal ribosome entry sequence (IRES) for Nrf2, with significant (P<0.05) increase in IRES use under LA treatment. These results suggest that a dithiol stimulus mediates Nrf2 nuclear tenure via cap-independent protein translation. Thus, translational control of Nrf2 synthesis, rather than reliance solely on pre-existing protein, may mediate the rapid burst of Nrf2 nuclear accumulation following stress stimuli.
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Affiliation(s)
- Kate Petersen Shay
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA
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14
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Li D, Wang M. Construction of a bicistronic vector for the co-expression of two genes in Caenorhabditis elegans using a newly identified IRES. Biotechniques 2012; 52:173-6. [PMID: 22401550 DOI: 10.2144/000113821] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 12/21/2011] [Indexed: 11/23/2022] Open
Abstract
The nematode Caenorhabditis elegans is an important model animal for biological research. Currently, transgenic C. elegans strains are mainly generated by injecting DNA encoding a gene of interest, in combination with a reporter gene, into the gonad. With this approach, the interpretation of negative results, such as the failure to observe reporter expression, is frequently required. Single, selectable vectors are urgently required. Internal ribosome entry site (IRES) elements are known to bind the eukaryotic ribosomal translation initiation complex and independently promote translation initiation. Bioinformatic analysis predicted an IRES motif upstream of the start codon of the C. elegans Hsp-3 gene. While this sequence has a Y-shaped double-hairpin secondary structure characteristic of IRES elements, it was unclear if it could function as an IRES. In the present study, this predicted Hsp-3 IRES was incorporated into a bicistronic vector driven by the myo-3 promoter, which allowed co-expression of RFP and GFP genes in the muscle tissue of C. elegans and thereby demonstrated that this IRES element is functional. This vector provides a novel, powerful tool for C. elegans research.
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Affiliation(s)
- Dirui Li
- National Animal Protozoa Laboratory, Key Laboratory of Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agriculture University, Beijing, China
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15
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Alternative Mechanisms to Initiate Translation in Eukaryotic mRNAs. Comp Funct Genomics 2012; 2012:391546. [PMID: 22536116 PMCID: PMC3321441 DOI: 10.1155/2012/391546] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 01/20/2012] [Indexed: 12/13/2022] Open
Abstract
The composition of the cellular proteome is under the control of multiple processes, one of the most important being translation initiation. The majority of eukaryotic cellular mRNAs initiates translation by the cap-dependent or scanning mode of translation initiation, a mechanism that depends on the recognition of the m(7)G(5')ppp(5')N, known as the cap. However, mRNAs encoding proteins required for cell survival under stress bypass conditions inhibitory to cap-dependent translation; these mRNAs often harbor internal ribosome entry site (IRES) elements in their 5'UTRs that mediate internal initiation of translation. This mechanism is also exploited by mRNAs expressed from the genome of viruses infecting eukaryotic cells. In this paper we discuss recent advances in understanding alternative ways to initiate translation across eukaryotic organisms.
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Ribosome binding to a 5' translational enhancer is altered in the presence of the 3' untranslated region in cap-independent translation of turnip crinkle virus. J Virol 2011; 85:4638-53. [PMID: 21389125 DOI: 10.1128/jvi.00005-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plus-strand RNA viruses without 5' caps require noncanonical mechanisms for ribosome recruitment. A translational enhancer in the 3' untranslated region (UTR) of Turnip crinkle virus (TCV) contains an internal T-shaped structure (TSS) that binds to 60S ribosomal subunits. We now report that the 63-nucleotide (nt) 5' UTR of TCV contains a 19-nt pyrimidine-rich element near the initiation codon that supports translation of an internal open reading frame (ORF) independent of upstream 5' UTR sequences. Addition of 80S ribosomes to the 5' UTR reduced the flexibility of the polypyrimidine residues and generated a toeprint consistent with binding to this region. Binding of salt-washed 40S ribosomal subunits was reduced 6-fold when the pyrimidine-rich sequence was mutated. 40S subunit binding generated the same toeprint as 80S ribosomes but also additional ones near the 5' end. Generation of out-of-frame AUGs upstream of the polypyrimidine region reduced translation, which suggests that 5'-terminal entry of 40S subunits is followed by scanning and that the polypyrimidine region is needed for an alternative function that requires ribosome binding. No evidence for RNA-RNA interactions between 5' and 3' sequences was found, suggesting that TCV utilizes an alternative means for circularizing its genome. Combining 5' and 3' UTR fragments in vitro had no discernible effect on the structures of the RNAs. In contrast, when 80S ribosomes were added to both fragments, structural changes were found in the 5' UTR polypyrimidine tract that were not evident when ribosomes interacted with the individual fragments. This suggests that ribosomes can promote an interaction between the 5' and 3' UTRs of TCV.
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17
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Malys N, McCarthy JEG. Translation initiation: variations in the mechanism can be anticipated. Cell Mol Life Sci 2011; 68:991-1003. [PMID: 21076851 PMCID: PMC11115079 DOI: 10.1007/s00018-010-0588-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 10/25/2010] [Accepted: 10/28/2010] [Indexed: 01/05/2023]
Abstract
Translation initiation is a critical step in protein synthesis. Previously, two major mechanisms of initiation were considered as essential: prokaryotic, based on SD interaction; and eukaryotic, requiring cap structure and ribosomal scanning. Although discovered decades ago, cap-independent translation has recently been acknowledged as a widely spread mechanism in viruses, which may take place in some cellular mRNA translations. Moreover, it has become evident that translation can be initiated on the leaderless mRNA in all three domains of life. New findings demonstrate that other distinguishable types of initiation exist, including SD-independent in Bacteria and Archaea, and various modifications of 5' end-dependent and internal initiation mechanisms in Eukarya. Since translation initiation has developed through the loss, acquisition, and modification of functional elements, all of which have been elevated by competition with viral translation in a large number of organisms of different complexity, more variation in initiation mechanisms can be anticipated.
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Affiliation(s)
- Naglis Malys
- Manchester Centre for Integrative Systems Biology, Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, The University of Manchester, UK.
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18
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Abstract
The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for l-amino acids, but did not completely exclude d-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.
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Affiliation(s)
- George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA.
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19
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Mechanisms of the initiation of protein synthesis: in reading frame binding of ribosomes to mRNA. Mol Biol Rep 2010; 38:847-55. [PMID: 20467902 DOI: 10.1007/s11033-010-0176-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 04/12/2010] [Indexed: 12/21/2022]
Abstract
The various mechanisms proposed to describe the initiation of protein synthesis are reviewed with a focus on their initiation signals. A characteristic feature of the various mechanisms is that each one of them postulates a distinct initiation signal. The signals of the Shine-Dalgarno (SD), the scanning and the internal ribosome entry site (IRES) mechanisms are all located exclusively in the 5' leader sequence, whereas, the signal of the cumulative specificity (CS) mechanism includes the entire initiation site (IS). Computer analysis of known E. coli IS sequences showed signal characteristics in the entire model IS consisting of 47 bases, in segments of the 5' leader and of the protein-coding regions. The proposal that eukaryotic translation actually occurs in two steps is scrutinized. In a first step, initiation factors (eIF4F) interact with the cap of the mRNA, thereby enhancing the accessibility of the IS. In the second step, initiation is by the conserved prokaryotic mechanism in which the ribosomes bind directly to the mRNA without ribosomal scanning. This binding occurs by the proposed process of in reading frame binding of ribosomes to mRNA, which is consistent with the CS mechanism. The basic CS mechanism is able to account for the initiation of translation of leaderless mRNAs, as well as for that of canonical mRNAs. The SD, the scanning and the IRES mechanisms, on the other hand, are inconsistent with the initiation of translation of leaderless mRNAs. Based on these and other observations, it is deemed that the CS mechanism is the universal initiation mechanism.
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20
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Hernández G, Altmann M, Lasko P. Origins and evolution of the mechanisms regulating translation initiation in eukaryotes. Trends Biochem Sci 2010; 35:63-73. [DOI: 10.1016/j.tibs.2009.10.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 10/27/2009] [Accepted: 10/28/2009] [Indexed: 02/08/2023]
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21
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The 5' leader of the mRNA encoding the marek's disease virus serotype 1 pp14 protein contains an intronic internal ribosome entry site with allosteric properties. J Virol 2009; 83:12769-78. [PMID: 19793814 DOI: 10.1128/jvi.01010-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We demonstrate the presence of a functional internal ribosome entry site (IRES) within the 5' leader (designated 5L) from a variant of bicistronic mRNAs that encode the pp14 and RLORF9 proteins from Marek's disease virus (MDV) serotype 1. Transcribed as a 1.8-kb family of immediate-early genes, the mature bicistronic mRNAs have variable 5' leader sequences due to alternative splicing or promoter usage. Consequently, the presence or absence of the 5L IRES in the mRNA dictates the mode of pp14 translation and leads to the production of two pp14 isoforms that differ in their N-terminal sequences. Real-time reverse transcription-quantitative PCR indicates that the mRNA variants with the 5L IRES is two to three times more abundant in MDV-infected and transformed cells than the mRNA variants lacking the 5L IRES. A common feature to all members of the 1.8-kb family of transcripts is the presence of an intercistronic IRES that we have previously shown to control the translation of the second open reading frame (i.e., RLORF9). Investigation of the two IRESs residing in the same bicistronic reporter mRNA revealed functional synergism for translation efficiency. In analogy with allosteric models in proteins, we propose IRES allostery to describe such a novel phenomenon. The functional implications of our findings are discussed in relation to host-virus interactions and translational control.
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Deniz N, Lenarcic EM, Landry DM, Thompson SR. Translation initiation factors are not required for Dicistroviridae IRES function in vivo. RNA (NEW YORK, N.Y.) 2009; 15:932-46. [PMID: 19299549 PMCID: PMC2673076 DOI: 10.1261/rna.1315109] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 01/27/2009] [Indexed: 05/22/2023]
Abstract
The cricket paralysis virus (CrPV) intergenic region (IGR) internal ribosome entry site (IRES) uses an unusual mechanism of initiating translation, whereby the IRES occupies the P-site of the ribosome and the initiating tRNA enters the A-site. In vitro experiments have demonstrated that the CrPV IGR IRES is able to bind purified ribosomes and form 80S complexes capable of synthesizing small peptides in the absence of any translation initiation factors. These results suggest that initiation by this IRES is factor-independent. To determine whether the IGR IRES functions in the absence of initiation factors in vivo, we assayed IGR IRES activity in various yeast strains harboring mutations in canonical translation initiation factors. We used a dicistronic reporter assay in yeast to determine whether the CrPV IGR IRES is able to promote translation sufficient to support growth in the presence of various deletions or mutations in translation initiation factors. Using this assay, we have previously shown that the CrPV IGR IRES functions efficiently in yeast when ternary complexes (eIF2*GTP*initiator tRNA(met)) are reduced. Here, we demonstrate that the CrPV IGR IRES activity does not require the eukaryotic initiation factors eIF4G1 or eIF5B, and it is enhanced when eIF2B, the eIF3b subunit of eIF3, or eIF4E are impaired. Taken together, these data support a model in which the CrPV IGR IRES is capable of initiating protein synthesis in the absence of any initiation factors in vivo, and suggests that the CrPV IGR IRES initiates translation by directly recruiting the ribosomal subunits in vivo.
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Affiliation(s)
- Nilsa Deniz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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23
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Chen WS, Chang YC, Chen YJ, Chen YJ, Teng CY, Wang CH, Wu TY. Development of a prokaryotic-like polycistronic baculovirus expression vector by the linkage of two internal ribosome entry sites. J Virol Methods 2009; 159:152-9. [PMID: 19490969 DOI: 10.1016/j.jviromet.2009.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2008] [Revised: 03/09/2009] [Accepted: 03/16/2009] [Indexed: 10/21/2022]
Abstract
Recombinant baculoviruses are suitable for the high-level production of large multi-protein complexes. A tri-cistronic expression vector was constructed by the inclusion of two internal ribosome entry sites (IRESs). In this novel polycistronic vector, one single polyhedrin promoter controlled the transcription of a tri-cistronic transcript. Also, the first cistron was translated through a cap-dependent mechanism, while the second and third cistrons were translated by the IRESs derived from the 5' UTR of Rhopalosiphum padi virus (RhPV) and Perina nuda virus (PnV), respectively. The ratio of tri-cistronic gene expression levels produced by the three translational initiation modules is about 2:1:1 (cap:PnV IRES:RhPV IRES). This study indicates that polycistronic genes can be co-expressed at the translational level as in prokaryotic expression system by baculovirus biotechnology.
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Affiliation(s)
- Wen-Shuo Chen
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
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24
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Identification of an intercistronic internal ribosome entry site in a Marek's disease virus immediate-early gene. J Virol 2009; 83:5846-53. [PMID: 19297480 DOI: 10.1128/jvi.02602-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In this study, we have identified an internal ribosome entry site (IRES) from the highly infectious herpesvirus Marek's disease virus (MDV). The IRES was mapped to the intercistronic region (ICR) of a bicistronic mRNA that we cloned from the MDV-transformed CD4(+) T-cell line MSB-1. The transcript is a member of a family of mRNAs expressed as immediate-early genes with two open reading frames (ORF). The first ORF encodes a 14-kDa polypeptide with two N-terminal splice variants, whereas the second ORF is contained entirely within a single exon and encodes a 12-kDa protein also known as RLORF9. We have shown that the ICR that separates the two ORFs functions as an IRES that controls the translation of RLORF9 when cap-dependent translation is inhibited. Deletion analysis revealed that there are two potential IRES elements within the ICR. Reverse genetic experiments with the oncogenic strain of MDV type 1 indicated that deletion of IRES-controlled RLORF9 does not significantly affect viral replication or MDV-induced mortality.
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25
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Hernández G. On the origin of the cap-dependent initiation of translation in eukaryotes. Trends Biochem Sci 2009; 34:166-75. [PMID: 19299142 DOI: 10.1016/j.tibs.2009.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 02/04/2009] [Accepted: 02/04/2009] [Indexed: 01/13/2023]
Abstract
The Shine-Dalgarno sequence of prokaryotic mRNAs, which helps to bind and position the ribosome at the start site for protein synthesis, is absent from eukaryotic mRNAs. Instead, for most, a structure at the 5' end and a much larger number of protein initiation factors are needed for both binding of the ribosome and for successful start-site selection, that is, a 'cap-dependent' initiation mechanism. Although the mechanics of this process are well studied, what is not clear is how it evolved. By analyzing recent progress in different fields, I suggest that it was the need to adjust to the arrival of the nuclear membrane and the subsequent requirement to export intron-less mRNAs to the cytoplasm that spurred the shift to the more complex translation initiation mechanism in eukaryotes.
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Affiliation(s)
- Greco Hernández
- Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC. H3A 1B1, Canada.
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26
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Xia X, Holcik M. Strong eukaryotic IRESs have weak secondary structure. PLoS One 2009; 4:e4136. [PMID: 19125192 PMCID: PMC2607549 DOI: 10.1371/journal.pone.0004136] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 12/03/2008] [Indexed: 12/13/2022] Open
Abstract
Background The objective of this work was to investigate the hypothesis that eukaryotic Internal Ribosome Entry Sites (IRES) lack secondary structure and to examine the generality of the hypothesis. Methodology/Principal Findings IRESs of the yeast and the fruit fly are located in the 5′UTR immediately upstream of the initiation codon. The minimum folding energy (MFE) of 60 nt RNA segments immediately upstream of the initiation codons was calculated as a proxy of secondary structure stability. MFE of the reverse complements of these 60 nt segments was also calculated. The relationship between MFE and empirically determined IRES activity was investigated to test the hypothesis that strong IRES activity is associated with weak secondary structure. We show that IRES activity in the yeast and the fruit fly correlates strongly with the structural stability, with highest IRES activity found in RNA segments that exhibit the weakest secondary structure. Conclusions We found that a subset of eukaryotic IRESs exhibits very low secondary structure in the 5′-UTR sequences immediately upstream of the initiation codon. The consistency in results between the yeast and the fruit fly suggests a possible shared mechanism of cap-independent translation initiation that relies on an unstructured RNA segment.
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Affiliation(s)
- Xuhua Xia
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Martin Holcik
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Ottawa, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- * E-mail:
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Fernández-Miragall O, López de Quinto S, Martínez-Salas E. Relevance of RNA structure for the activity of picornavirus IRES elements. Virus Res 2008; 139:172-82. [PMID: 18692097 DOI: 10.1016/j.virusres.2008.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 07/02/2008] [Accepted: 07/04/2008] [Indexed: 02/02/2023]
Abstract
The RNA of all members of the Picornaviridae family initiates translation internally, via an internal ribosome entry site (IRES) element present in their 5' untranslated region. IRES elements consist of cis-acting RNA structures that often operate in association with specific RNA-binding proteins to recruit the translational machinery. This specialized mechanism of translation initiation is shared with other viral RNAs, and represents an alternative to the general cap-dependent initiation mechanism. In this review we discuss recent evidences concerning the relationship between RNA structure and IRES function in the genome of picornaviruses. The biological implications of conserved RNA structural elements for the mechanism of internal translation initiation driven by representative members of enterovirus and rhinovirus (type I IRES) and cardiovirus and aphthovirus (type II IRES) will be discussed.
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Affiliation(s)
- Olga Fernández-Miragall
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco 28049, Madrid, Spain
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28
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Kieft JS. Viral IRES RNA structures and ribosome interactions. Trends Biochem Sci 2008; 33:274-83. [PMID: 18468443 DOI: 10.1016/j.tibs.2008.04.007] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 04/14/2008] [Accepted: 04/15/2008] [Indexed: 02/05/2023]
Abstract
In eukaryotes, protein synthesis initiates primarily by a mechanism that requires a modified nucleotide 'cap' on the mRNA and also proteins that recruit and position the ribosome. Many pathogenic viruses use an alternative, cap-independent mechanism that substitutes RNA structure for the cap and many proteins. The RNAs driving this process are called internal ribosome-entry sites (IRESs) and some are able to bind the ribosome directly using a specific 3D RNA structure. Recent structures of IRES RNAs and IRES-ribosome complexes are revealing the structural basis of viral IRES' 'hijacking' of the protein-making machinery. It now seems that there are fundamental differences in the 3D structures used by different IRESs, although there are some common features in how they interact with ribosomes.
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Affiliation(s)
- Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Mail stop 8101, PO Box 6511, Aurora, CO 80045, USA.
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