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Yeckes AR, Victor AR, Zhu Z, Narayanan M, Srinivasan B, Bruce B, Kaye J. The Tox Gene Encodes Two Proteins with Distinct and Shared Roles in Gene Regulation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1889-1898. [PMID: 37115203 PMCID: PMC10247481 DOI: 10.4049/jimmunol.2200659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/06/2023] [Indexed: 04/29/2023]
Abstract
Here we report that the murine Tox gene encodes two proteins from a single mRNA, and we investigate the mechanism of production and function of these proteoforms. The annotated thymocyte selection-associated HMG-box protein (TOX) coding sequence is predicted to produce a 526-aa protein (TOXFL). However, Western blots reveal two bands. We found that the lower band consists of an N-terminally truncated variant of TOX (TOXΔN), whereas the slower-migrating band is TOXFL. The TOXΔN proteoform is alternatively translated via leaky ribosomal scanning from an evolutionarily conserved translation initiation site downstream of the annotated translation initiation site. When expressed exogenously from a cDNA in murine CD8 T cells or HEK cells, or endogenously from the murine Tox locus, both forms are translated, although the ratio of TOXFL/TOXΔN significantly varies with cellular context. This includes regulation of proteoform production during development of murine CD4 T cells in the thymus, where the positive selection of CD4+CD8+ cells and subsequent differentiation to CD4+CD8lo transitional and CD4SP cell subsets is associated with both an increase in total TOX protein and increased TOXΔN production relative to TOXFL. Finally, we found that sole expression of TOXFL had a greater effect on gene regulation during chronic stimulation of murine CD8 T cells in culture mimicking exhaustion than did TOXΔN, including uniquely regulated cell cycle and other genes.
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Affiliation(s)
- Alyson R. Yeckes
- Research Division of Immunology, Department of Biomedical Sciences, Los Angeles, CA 90048
| | - Aaron R. Victor
- Research Division of Immunology, Department of Biomedical Sciences, Los Angeles, CA 90048
- Department of Pathology and Laboratory Medicine, Los Angeles, CA 90048
| | - Zheng Zhu
- Research Division of Immunology, Department of Biomedical Sciences, Los Angeles, CA 90048
| | - Meena Narayanan
- Research Division of Immunology, Department of Biomedical Sciences, Los Angeles, CA 90048
| | - Bharani Srinivasan
- Research Division of Immunology, Department of Biomedical Sciences, Los Angeles, CA 90048
| | - Bethany Bruce
- Research Division of Immunology, Department of Biomedical Sciences, Los Angeles, CA 90048
| | - Jonathan Kaye
- Research Division of Immunology, Department of Biomedical Sciences, Los Angeles, CA 90048
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
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The Role of the Universally Conserved ATPase YchF/Ola1 in Translation Regulation during Cellular Stress. Microorganisms 2021; 10:microorganisms10010014. [PMID: 35056463 PMCID: PMC8779481 DOI: 10.3390/microorganisms10010014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022] Open
Abstract
The ability to respond to metabolic or environmental changes is an essential feature in all cells and involves both transcriptional and translational regulators that adjust the metabolic activity to fluctuating conditions. While transcriptional regulation has been studied in detail, the important role of the ribosome as an additional player in regulating gene expression is only beginning to emerge. Ribosome-interacting proteins are central to this translational regulation and include universally conserved ribosome interacting proteins, such as the ATPase YchF (Ola1 in eukaryotes). In both eukaryotes and bacteria, the cellular concentrations of YchF/Ola1 determine the ability to cope with different stress conditions and are linked to several pathologies in humans. The available data indicate that YchF/Ola1 regulates the stress response via controlling non-canonical translation initiation and via protein degradation. Although the molecular mechanisms appear to be different between bacteria and eukaryotes, increased non-canonical translation initiation is a common consequence of YchF/Ola1 regulated translational control in E. coli and H. sapiens. In this review, we summarize recent insights into the role of the universally conserved ATPase YchF/Ola1 in adapting translation to unfavourable conditions.
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Sriram A, Bohlen J, Teleman AA. Translation acrobatics: how cancer cells exploit alternate modes of translational initiation. EMBO Rep 2018; 19:embr.201845947. [PMID: 30224410 DOI: 10.15252/embr.201845947] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/09/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Recent work has brought to light many different mechanisms of translation initiation that function in cells in parallel to canonical cap-dependent initiation. This has important implications for cancer. Canonical cap-dependent translation initiation is inhibited by many stresses such as hypoxia, nutrient limitation, proteotoxic stress, or genotoxic stress. Since cancer cells are often exposed to these stresses, they rely on alternate modes of translation initiation for protein synthesis and cell growth. Cancer mutations are now being identified in components of the translation machinery and in cis-regulatory elements of mRNAs, which both control translation of cancer-relevant genes. In this review, we provide an overview on the various modes of non-canonical translation initiation, such as leaky scanning, translation re-initiation, ribosome shunting, IRES-dependent translation, and m6A-dependent translation, and then discuss the influence of stress on these different modes of translation. Finally, we present examples of how these modes of translation are dysregulated in cancer cells, allowing them to grow, to proliferate, and to survive, thereby highlighting the importance of translational control in cancer.
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Affiliation(s)
- Ashwin Sriram
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Jonathan Bohlen
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany .,Heidelberg University, Heidelberg, Germany
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Ross MJ, Bradford SS, Cowan JA. Catalytic metallodrugs based on the LaR2C peptide target HCV SLIV IRES RNA. Dalton Trans 2015; 44:20972-82. [PMID: 26583601 PMCID: PMC4691540 DOI: 10.1039/c5dt02837j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Prior work has demonstrated the potential effectiveness of a new class of metallopeptides as catalytic metallodrugs that target HCV IRES SLIIb RNA (Cu-GGHYrFK, 1). Herein new catalytic metallodrugs (GGHKYKETDLLILFKDDYFAKKNEERK, 2; and GGHKYKETDL, 3) are described based on the LaR2C peptide that has been shown to bind to the SLIV HCV IRES domain. In vitro fluorescence assays yielded KD values ∼10 μM for both peptides and reaction of the copper derivatives with SLIV RNA demonstrated initial rates comparable across different assays as well as displaying pseudo-Michaelis-Menten behavior. The sites of reaction and cleavage mechanisms were determined by MALDI-TOF mass spectrometry. The primary site of copper-promoted SLIV cleavage is shown to occur in the vicinity of the 5'-G17C18A19C20-3' sequence that corresponds to a known binding site of the RM2 motif of the human La protein and has previously been reported to be important for viral translation. This domain also flanks the internal start codon (AUG). Both copper complexes also showed efficacy in an HCV replicon assay (IC50 = 0.75 μM for 2-Cu, and 2.17 μM for 3-Cu) and show potential for treatment of hepatitis C, complementing other marketed drugs by acting on a distinct therapeutic target by a novel mechanism of action.
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Affiliation(s)
- Martin James Ross
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Seth S. Bradford
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - J. A. Cowan
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
- MetalloPharm, 1790 Riverstone Dr., Delaware, OH 43015
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Joseph AP, Bhat P, Das S, Srinivasan N. Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA. RNA Biol 2015; 11:891-905. [PMID: 25268799 DOI: 10.4161/rna.29545] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In this study, we combine available high resolution structural information on eukaryotic ribosomes with low resolution cryo-EM data on the Hepatitis C Viral RNA (IRES) human ribosome complex. Aided further by the prediction of RNA-protein interactions and restrained docking studies, we gain insights on their interaction at the residue level. We identified the components involved at the major and minor contact regions, and propose that there are energetically favorable local interactions between 40S ribosomal proteins and IRES domains. Domain II of the IRES interacts with ribosomal proteins S5 and S25 while the pseudoknot and the downstream domain IV region bind to ribosomal proteins S26, S28 and S5. We also provide support using UV cross-linking studies to validate our proposition of interaction between the S5 and IRES domains II and IV. We found that domain IIIe makes contact with the ribosomal protein S3a (S1e). Our model also suggests that the ribosomal protein S27 interacts with domain IIIc while S7 has a weak contact with a single base RNA bulge between junction IIIabc and IIId. The interacting residues are highly conserved among mammalian homologs while IRES RNA bases involved in contact do not show strict conservation. IRES RNA binding sites for S25 and S3a show the best conservation among related viral IRESs. The new contacts identified between ribosomal proteins and RNA are consistent with previous independent studies on RNA-binding properties of ribosomal proteins reported in literature, though information at the residue level is not available in previous studies.
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Affiliation(s)
- Agnel Praveen Joseph
- Molecular Biophysics Unit. Indian Institute of Science, Bangalore, India; Present address: Science and Technology Facilities Council, RAL, Harwell, Didcot, UK
| | - Prasanna Bhat
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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Liu WJ, Yang YT, Zhao MQ, Dong XY, Gou HC, Pei JJ, Chen JD. PKR activation enhances replication of classical swine fever virus in PK-15 cells. Virus Res 2015; 204:47-57. [PMID: 25899421 PMCID: PMC7114430 DOI: 10.1016/j.virusres.2015.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/25/2015] [Accepted: 04/09/2015] [Indexed: 12/22/2022]
Abstract
CSFV infection triggers PKR and eIF2α protein phosphorylation. PKR overexpression stimulates viral replication. PKR depletion blocks eIF2α phosphorylation and suppresses viral replication. PKR depletion increases IFN-β, and enhances the antiviral effect of IFN.
Classical swine fever (CSF) is a highly contagious swine disease that is responsible for economic losses worldwide. Protein kinase R (PK)R is an important protein in the host viral response; however, the role of PKR in CSFV infection remains unknown. This issue was addressed in the present study using the PK-15 swine kidney cell line. We found that CSFV infection increased the phosphorylation of eukaryotic translation initiation factor (eIF)2α and its kinase PKR. However, the expression of viral proteins continued to increase. Furthermore, PKR overexpression enhanced CSFV replication, while PKR inhibition resulted in reduced CSFV replication and an increase in interferon (IFN) induction. In addition, PKR was responsible for eIF2α phosphorylation in CSFV-infected cells. These results suggest that the activation of PKR during CSFV infection is beneficial to the virus. The virus is able to commandeer the host cell's translation machinery for viral protein synthesis while evading innate immune defenses.
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Affiliation(s)
- Wen-Jun Liu
- College of Veterinary Medicine, South China Agricultural University, 483 Wu Shan Road, Tian He District, Guangzhou 510642, China
| | - You-Tian Yang
- College of Veterinary Medicine, South China Agricultural University, 483 Wu Shan Road, Tian He District, Guangzhou 510642, China
| | - Ming-Qiu Zhao
- College of Veterinary Medicine, South China Agricultural University, 483 Wu Shan Road, Tian He District, Guangzhou 510642, China
| | - Xiao-Ying Dong
- College of Veterinary Medicine, South China Agricultural University, 483 Wu Shan Road, Tian He District, Guangzhou 510642, China
| | - Hong-Chao Gou
- College of Veterinary Medicine, South China Agricultural University, 483 Wu Shan Road, Tian He District, Guangzhou 510642, China
| | - Jing-Jing Pei
- College of Veterinary Medicine, South China Agricultural University, 483 Wu Shan Road, Tian He District, Guangzhou 510642, China
| | - Jin-Ding Chen
- College of Veterinary Medicine, South China Agricultural University, 483 Wu Shan Road, Tian He District, Guangzhou 510642, China.
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7
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Jheng JR, Ho JY, Horng JT. ER stress, autophagy, and RNA viruses. Front Microbiol 2014; 5:388. [PMID: 25140166 PMCID: PMC4122171 DOI: 10.3389/fmicb.2014.00388] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/11/2014] [Indexed: 12/19/2022] Open
Abstract
Endoplasmic reticulum (ER) stress is a general term for representing the pathway by which various stimuli affect ER functions. ER stress induces the evolutionarily conserved signaling pathways, called the unfolded protein response (UPR), which compromises the stimulus and then determines whether the cell survives or dies. In recent years, ongoing research has suggested that these pathways may be linked to the autophagic response, which plays a key role in the cell's response to various stressors. Autophagy performs a self-digestion function, and its activation protects cells against certain pathogens. However, the link between the UPR and autophagy may be more complicated. These two systems may act dependently, or the induction of one system may interfere with the other. Experimental studies have found that different viruses modulate these mechanisms to allow them to escape the host immune response or, worse, to exploit the host's defense to their advantage; thus, this topic is a critical area in antiviral research. In this review, we summarize the current knowledge about how RNA viruses, including influenza virus, poliovirus, coxsackievirus, enterovirus 71, Japanese encephalitis virus, hepatitis C virus, and dengue virus, regulate these processes. We also discuss recent discoveries and how these will produce novel strategies for antiviral treatment.
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Affiliation(s)
- Jia-Rong Jheng
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University Kweishan, Taiwan
| | - Jin-Yuan Ho
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University Kweishan, Taiwan
| | - Jim-Tong Horng
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University Kweishan, Taiwan ; Research Center for Emerging Viral Infections, Chang Gung University Kweishan, Taiwan ; Department of Medical Research, Chang Gung Memorial Hospital Kweishan, Taiwan
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8
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The DNA virus white spot syndrome virus uses an internal ribosome entry site for translation of the highly expressed nonstructural protein ICP35. J Virol 2013; 87:13263-78. [PMID: 24089551 DOI: 10.1128/jvi.01732-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although shrimp white spot syndrome virus (WSSV) is a large double-stranded DNA virus (∼300 kbp), it expresses many polycistronic mRNAs that are likely to use internal ribosome entry site (IRES) elements for translation. A polycistronic mRNA encodes the gene of the highly expressed nonstructural protein ICP35, and here we use a dual-luciferase assay to demonstrate that this protein is translated cap independently by an IRES element located in the 5' untranslated region of icp35. A deletion analysis of this region showed that IRES activity was due to stem-loops VII and VIII. A promoterless assay, a reverse transcription-PCR together with quantitative real-time PCR analysis, and a stable stem-loop insertion upstream of the Renilla luciferase open reading frame were used, respectively, to rule out the possibility that cryptic promoter activity, abnormal splicing, or read-through was contributing to the IRES activity. In addition, a Northern blot analysis was used to confirm that only a single bicistronic mRNA was expressed. The importance of ICP35 to viral replication was demonstrated in a double-stranded RNA (dsRNA) interference knockdown experiment in which the mortality of the icp35 dsRNA group was significantly reduced. Tunicamycin was used to show that the α subunit of eukaryotic initiation factor 2 is required for icp35 IRES activity. We also found that the intercalating drug quinacrine significantly inhibited icp35 IRES activity in vitro and reduced the mortality rate and viral copy number in WSSV-challenged shrimp. Lastly, in Sf9 insect cells, we found that knockdown of the gene for the Spodoptera frugiperda 40S ribosomal protein RPS10 decreased icp35 IRES-regulated firefly luciferase activity but had no effect on cap-dependent translation.
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9
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Yin JY, Dong ZZ, Liu RY, Chen J, Liu ZQ, Zhang JT. Translational regulation of RPA2 via internal ribosomal entry site and by eIF3a. Carcinogenesis 2013; 34:1224-31. [PMID: 23393223 DOI: 10.1093/carcin/bgt052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RPA2 is a subunit of a trimeric replication protein A (RPA) complex important for DNA repair and replication. Although it is known that RPA activity is regulated by post-translational modification, whether RPA expression is regulated and the mechanism therein is currently unknown. eIF3a, the largest subunit of eIF3, is an important player in translational control and has been suggested to regulate translation of a subset of messenger RNAs important for tumorigenesis, metastasis, cell cycle progression, drug response and DNA repair. In the present study, we show that RPA2 expression is regulated at translational level via internal ribosome entry site (IRES)-mediated initiation in response to DNA damage. We also found that eIF3a suppresses RPA2 synthesis and inhibits its cellular IRES activity by directly binding to the IRES element of RPA2 located at -50 to -150 bases upstream of the translation start site. Taken together, we conclude that RPA2 expression is translationally regulated via IRES and by eIF3a and that this regulation is partly accountable for cellular response to DNA damage and survival.
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Affiliation(s)
- Ji-Ye Yin
- Department of Pharmacology/Toxicology, IU Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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10
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Hodges EN, Connor JH. Translational control by negative-strand RNA viruses: methods for the study of a crucial virus/host interaction. Methods 2012; 59:180-7. [PMID: 23009810 DOI: 10.1016/j.ymeth.2012.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 07/02/2012] [Accepted: 09/13/2012] [Indexed: 01/06/2023] Open
Abstract
Protein synthesis is a vital step in the successful replication of negative-strand RNA viruses. Protein synthesis is also a critical step in the development of a successful antiviral response from the host. This makes understanding the interplay between host and viral translation an important aspect of defining the virus/host interaction. For the negative-strand RNA viruses there are disparate mechanism of how viruses interact with the host protein synthesis apparatus, ranging from the complete takeover of all protein synthesis to the subtle insertion of viral mRNAs into an otherwise unchanged protein synthesis pattern. In this article, we discuss different ways to investigate protein synthesis in virus-infected cells, ranging from the use of metabolic labeling for the study of general translation changes to using fluorescence-coupled labeling techniques that allow the pinpointing of any subcellular localization of protein synthesis during virus replication. We also discuss methods for analyzing the translation initiation factors that are frequently modified in virus-infected cells.
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Affiliation(s)
- Erin N Hodges
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
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11
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Chandra PK, Kundu AK, Hazari S, Chandra S, Bao L, Ooms T, Morris GF, Wu T, Mandal TK, Dash S. Inhibition of hepatitis C virus replication by intracellular delivery of multiple siRNAs by nanosomes. Mol Ther 2012; 20:1724-36. [PMID: 22617108 PMCID: PMC3437587 DOI: 10.1038/mt.2012.107] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 04/23/2012] [Indexed: 02/07/2023] Open
Abstract
Sustained antiviral responses of chronic hepatitis C virus (HCV) infection have improved recently by the use of direct-acting antiviral agents along with interferon (IFN)-α and ribavirin. However, the emergence of drug-resistant variants is expected to be a major problem. We describe here a novel combinatorial small interfering RNA (siRNA) nanosome-based antiviral approach to clear HCV infection. Multiple siRNAs targeted to the highly conserved 5'-untranslated region (UTR) of the HCV genome were synthesized and encapsulated into lipid nanoparticles called nanosomes. We show that siRNA can be repeatedly delivered to 100% of cells in culture using nanosomes without toxicity. Six siRNAs dramatically reduced HCV replication in both the replicon and infectious cell culture model. Repeated treatments with two siRNAs were better than a single siRNA treatment in minimizing the development of an escape mutant, resulting in rapid inhibition of viral replication. Systemic administration of combinatorial siRNA-nanosomes is well tolerated in BALB/c mice without liver injury or histological toxicity. As a proof-of-principle, we showed that systemic injections of siRNA nanosomes significantly reduced HCV replication in a liver tumor-xenotransplant mouse model of HCV. Our results indicate that systemic delivery of combinatorial siRNA nanosomes can be used to minimize the development of escape mutants and inhibition of HCV infection.
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Affiliation(s)
- Partha K Chandra
- Department of Pathology and Laboratory Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
| | - Anup K Kundu
- Center for Nanomedicine and Drug Delivery, College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana, USA
| | - Sidhartha Hazari
- Department of Pathology and Laboratory Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
| | - Sruti Chandra
- Department of Pathology and Laboratory Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
| | - Lili Bao
- Department of Pathology and Laboratory Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
| | - Tara Ooms
- Department of Comparative Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
| | - Gilbert F Morris
- Department of Pathology and Laboratory Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
| | - Tong Wu
- Department of Pathology and Laboratory Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
| | - Tarun K Mandal
- Center for Nanomedicine and Drug Delivery, College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana, USA
| | - Srikanta Dash
- Department of Pathology and Laboratory Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
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Poly(A) binding protein abundance regulates eukaryotic translation initiation factor 4F assembly in human cytomegalovirus-infected cells. Proc Natl Acad Sci U S A 2012; 109:5627-32. [PMID: 22431630 DOI: 10.1073/pnas.1202829109] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
By commandeering cellular translation initiation factors, or destroying those dispensable for viral mRNA translation, viruses often suppress host protein synthesis. In contrast, cellular protein synthesis proceeds in human cytomegalovirus (HCMV)-infected cells, forcing viral and cellular mRNAs to compete for limiting translation initiation factors. Curiously, inactivating the host translational repressor 4E-BP1 in HCMV-infected cells stimulates synthesis of the cellular poly(A) binding protein (PABP), significantly increasing PABP abundance. Here, we establish that new PABP synthesis is translationally controlled by the HCMV-encoded UL38 mammalian target of rapamycin complex 1-activator. The 5' UTR within the mRNA encoding PABP contains a terminal oligopyrimidine (TOP) element found in mRNAs, the translation of which is stimulated in response to mitogenic, growth, and nutritional stimuli, and proteins encoded by TOP-containing mRNAs accumulated in HCMV-infected cells. Furthermore, UL38 expression was necessary and sufficient to regulate expression of a PABP TOP-containing reporter. Remarkably, preventing the rise in PABP abundance by RNAi impaired eIF4E binding to eIF4G, thereby reducing assembly of the multisubunit initiation factor eIF4F, viral protein production, and replication. This finding demonstrates that viruses can increase host translation initiation factor concentration to foster their replication and defines a unique mechanism whereby control of PABP abundance regulates eIF4F assembly.
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Plank TDM, Kieft JS. The structures of nonprotein-coding RNAs that drive internal ribosome entry site function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2012; 3:195-212. [PMID: 22215521 PMCID: PMC3973487 DOI: 10.1002/wrna.1105] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Internal ribosome entry sites (IRESs) are RNA sequences that can recruit the translation machinery independent of the 5' end of the messenger RNA. IRESs are found in both viral and cellular RNAs and are important for regulating gene expression. There is great diversity in the mechanisms used by IRESs to recruit the ribosome and this is reflected in a variety of RNA sequences that function as IRESs. The ability of an RNA sequence to function as an IRES is conferred by structures operating at multiple levels from primary sequence through higher-order three-dimensional structures within dynamic ribonucleoproteins (RNPs). When these diverse structures are compared, some trends are apparent, but overall it is not possible to find universal rules to describe IRES structure and mechanism. Clearly, many different sequences and structures have evolved to perform the function of recruiting, positioning, and activating a ribosome without using the canonical cap-dependent mechanism. However, as our understanding of the specific sequences, structures, and mechanisms behind IRES function improves, more common features may emerge to link these diverse RNAs.
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Affiliation(s)
- Terra-Dawn M. Plank
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
| | - Jeffrey S. Kieft
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, 80045, USA
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14
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Bradford S, Cowan JA. Catalytic metallodrugs targeting HCV IRES RNA. Chem Commun (Camb) 2012; 48:3118-20. [DOI: 10.1039/c2cc17377h] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Duck Hepatitis A virus possesses a distinct type IV internal ribosome entry site element of picornavirus. J Virol 2011; 86:1129-44. [PMID: 22090106 DOI: 10.1128/jvi.00306-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Sequence analysis of duck hepatitis virus type 1 (DHV-1) led to its classification as the only member of a new genus, Avihepatovirus, of the family Picornaviridae, and so was renamed duck hepatitis A virus (DHAV). The 5' untranslated region (5' UTR) plays an important role in translation initiation and RNA synthesis of the picornavirus. Here, we provide evidence that the 651-nucleotide (nt)-long 5' UTR of DHAV genome contains an internal ribosome entry site (IRES) element that functions efficiently in vitro and within BHK cells. Comparative sequence analysis showed that the 3' part of the DHAV 5' UTR is similar to the porcine teschovirus 1 (PTV-1) IRES in sequence and predicted secondary structure. Further mutational analyses of the predicted domain IIId, domain IIIe, and pseudoknot structure at the 3' end of the DHAV IRES support our predicted secondary structure. However, unlike the case for the PTV-1 IRES element, analysis of various deletion mutants demonstrated that the optimally functional DHAV IRES element with a size of approximately 420 nt is larger than that of PTV-1 and contains other peripheral domains (Id and Ie) that do not exist within the type IV IRES elements. The domain Ie, however, could be removed without significant loss of activity. Surprisingly, like the hepatitis A virus (HAV) IRES element, the activity of DHAV IRES could be eliminated by expression of enterovirus 2A protease. These findings indicate that the DHAV IRES shares common features with type IV picornavirus IRES elements, whereas it exhibits significant differences from type IV IRESs. Therefore, we propose that DHAV possesses a distinct type IV IRES element of picornavirus.
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Poly(C)-binding protein 2 interacts with sequences required for viral replication in the hepatitis C virus (HCV) 5' untranslated region and directs HCV RNA replication through circularizing the viral genome. J Virol 2011; 85:7954-64. [PMID: 21632751 DOI: 10.1128/jvi.00339-11] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sequences in the 5' untranslated region (5'UTR) of hepatitis C virus (HCV) RNA is important for modulating both translation and RNA replication. The translation of the HCV genome depends on an internal ribosome entry site (IRES) located within the 341-nucleotide 5'UTR, while RNA replication requires a smaller region. A question arises whether the replication and translation functions require different regions of the 5'UTR and different sets of RNA-binding proteins. Here, we showed that the 5'-most 157 nucleotides of HCV RNA is the minimum 5'UTR for RNA replication, and it partially overlaps with the IRES. Stem-loops 1 and 2 of the 5'UTR are essential for RNA replication, whereas stem-loop 1 is not required for translation. We also found that poly(C)-binding protein 2 (PCBP2) bound to the replication region of the 5'UTR and associated with detergent-resistant membrane fractions, which are the sites of the HCV replication complex. The knockdown of PCBP2 by short hairpin RNA decreased the amounts of HCV RNA and nonstructural proteins. Antibody-mediated blocking of PCBP2 reduced HCV RNA replication in vitro, indicating that PCBP2 is directly involved in HCV RNA replication. Furthermore, PCBP2 knockdown reduced IRES-dependent translation preferentially from a dual reporter plasmid, suggesting that PCBP2 also regulated IRES activity. These findings indicate that PCBP2 participates in both HCV RNA replication and translation. Moreover, PCBP2 interacts with HCV 5'- and 3'UTR RNA fragments to form an RNA-protein complex and induces the circularization of HCV RNA, as revealed by electron microscopy. This study thus demonstrates the mechanism of the participation of PCBP2 in HCV translation and replication and provides physical evidence for HCV RNA circularization through 5'- and 3'UTR interaction.
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López-Lastra M, Ramdohr P, Letelier A, Vallejos M, Vera-Otarola J, Valiente-Echeverría F. Translation initiation of viral mRNAs. Rev Med Virol 2010; 20:177-95. [PMID: 20440748 PMCID: PMC7169124 DOI: 10.1002/rmv.649] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Viruses depend on cells for their replication but have evolved mechanisms to achieve this in an efficient and, in some instances, a cell‐type‐specific manner. The expression of viral proteins is frequently subject to translational control. The dominant target of such control is the initiation step of protein synthesis. Indeed, during the early stages of infection, viral mRNAs must compete with their host counterparts for the protein synthetic machinery, especially for the limited pool of eukaryotic translation initiation factors (eIFs) that mediate the recruitment of ribosomes to both viral and cellular mRNAs. To circumvent this competition viruses use diverse strategies so that ribosomes can be recruited selectively to viral mRNAs. In this review we focus on the initiation of protein synthesis and outline some of the strategies used by viruses to ensure efficient translation initiation of their mRNAs. Copyright © 2010 John Wiley & Sons, Ltd.
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Affiliation(s)
- Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile.
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Stress-inducible alternative translation initiation of human cytomegalovirus latency protein pUL138. J Virol 2010; 84:9472-86. [PMID: 20592073 DOI: 10.1128/jvi.00855-10] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We have previously characterized a 21-kDa protein encoded by UL138 (pUL138) as a viral factor inherent to low-passage strains of human cytomegalovirus (HCMV) that is required for latent infection in vitro. pUL138 is encoded on 3.6-, 2.7-, and 1.4-kb 3' coterminal transcripts that are produced during productive and latent infections. pUL138 is encoded at the 3' end of each transcript and is preceded by an extensive 5' sequence (approximately 0.5 to 2.5 kb) containing several putative open reading frames (ORFs). We determined that three putative ORFs upstream of UL138 (UL133, UL135, and UL136) encode proteins. The UL138 transcripts are polycistronic, such that each transcript expresses pUL138 in addition to the most-5' ORF. The upstream coding sequences (CDS) present a significant challenge for the translation of pUL138 in mammalian cells. We hypothesized that sequences 5' of UL138 mediate translation initiation of pUL138 by alternative strategies. Accordingly, a 663-nucloetide (nt) sequence overlapping the UL136 CDS supported expression of a downstream cistron in a bicistronic reporter system. We did not detect cryptic promoter activity or RNA splicing events that could account for downstream cistron expression. These data are consistent with the sequence element functioning as an internal ribosome entry site (IRES). Interestingly, pUL138 expression from the 3.6- and 2.7-kb transcripts was induced by serum stress, which concomitantly inhibited normal cap-dependent translation. Our work suggests that an alternative and stress-inducible strategy of translation initiation ensures expression of pUL138 under a variety of cellular contexts. The UL138 polycistronic transcripts serve to coordinate the expression of multiple proteins, including a viral determinant of HCMV latency.
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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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20
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Filbin ME, Kieft JS. Toward a structural understanding of IRES RNA function. Curr Opin Struct Biol 2009; 19:267-76. [PMID: 19362464 DOI: 10.1016/j.sbi.2009.03.005] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 03/07/2009] [Indexed: 01/23/2023]
Abstract
Protein synthesis of an RNA template can start by two different known mechanisms: cap-dependent translation initiation and cap-independent translation initiation. The latter is driven by RNA sequences called internal ribosome entry sites (IRESs) that are found in both viral RNAs and cellular mRNAs. The diverse mechanisms used by IRESs are reflected in their structural diversity, and this structural diversity challenges us to develop a cohesive model linking IRES function to structure. With more direct structural information available for the viral IRESs, data suggest an inverse correlation between the degree to which an IRES RNA can form a stable structure on its own and the number of factors that it requires to function. Lessons learned from the viral IRESs may help understand the cellular IRESs, although more structural data are needed before any strong links can be made.
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Affiliation(s)
- Megan E Filbin
- 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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Abstract
Viruses are ubiquitous in the sea and appear to outnumber all other forms of marine life by at least an order of magnitude. Through selective infection, viruses influence nutrient cycling, community structure, and evolution in the ocean. Over the past 20 years we have learned a great deal about the diversity and ecology of the viruses that constitute the marine virioplankton, but until recently the emphasis has been on DNA viruses. Along with expanding knowledge about RNA viruses that infect important marine animals, recent isolations of RNA viruses that infect single-celled eukaryotes and molecular analyses of the RNA virioplankton have revealed that marine RNA viruses are novel, widespread, and genetically diverse. Discoveries in marine RNA virology are broadening our understanding of the biology, ecology, and evolution of viruses, and the epidemiology of viral diseases, but there is still much that we need to learn about the ecology and diversity of RNA viruses before we can fully appreciate their contributions to the dynamics of marine ecosystems. As a step toward making sense of how RNA viruses contribute to the extraordinary viral diversity in the sea, we summarize in this review what is currently known about RNA viruses that infect marine organisms.
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Affiliation(s)
- Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada.
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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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mRNA translation regulation by the Gly-Ala repeat of Epstein-Barr virus nuclear antigen 1. J Virol 2008; 83:1289-98. [PMID: 19019958 DOI: 10.1128/jvi.01369-08] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The glycine-alanine repeat (GAr) sequence of the Epstein-Barr virus-encoded EBNA-1 prevents presentation of antigenic peptides to major histocompatibility complex class I molecules. This has been attributed to its capacity to suppress mRNA translation in cis. However, the underlying mechanism of this function remains largely unknown. Here, we have further investigated the effect of the GAr as a regulator of mRNA translation. Introduction of silent mutations in each codon of a 30-amino-acid GAr sequence does not significantly affect the translation-inhibitory capacity, whereas minimal alterations in the amino acid composition have strong effects, which underscores the observation that the amino acid sequence and not the mRNA sequence mediates GAr-dependent translation suppression. The capacity of the GAr to repress translation is dose and position dependent and leads to a relative accumulation of preinitiation complexes on the mRNA. Taken together with the surprising observation that fusion of the 5' untranslated region (UTR) of the c-myc mRNA to the 5' UTR of GAr-carrying mRNAs specifically inactivates the effect of the GAr, these results indicate that the GAr targets components of the translation initiation process. We propose a model in which the nascent GAr peptide delays the assembly of the initiation complex on its own mRNA.
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Starck SR, Ow Y, Jiang V, Tokuyama M, Rivera M, Qi X, Roberts RW, Shastri N. A distinct translation initiation mechanism generates cryptic peptides for immune surveillance. PLoS One 2008; 3:e3460. [PMID: 18941630 PMCID: PMC2565129 DOI: 10.1371/journal.pone.0003460] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 09/29/2008] [Indexed: 12/04/2022] Open
Abstract
MHC class I molecules present a comprehensive mixture of peptides on the cell surface for immune surveillance. The peptides represent the intracellular protein milieu produced by translation of endogenous mRNAs. Unexpectedly, the peptides are encoded not only in conventional AUG initiated translational reading frames but also in alternative cryptic reading frames. Here, we analyzed how ribosomes recognize and use cryptic initiation codons in the mRNA. We find that translation initiation complexes assemble at non-AUG codons but differ from canonical AUG initiation in response to specific inhibitors acting within the peptidyl transferase and decoding centers of the ribosome. Thus, cryptic translation at non-AUG start codons can utilize a distinct initiation mechanism which could be differentially regulated to provide peptides for immune surveillance.
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Affiliation(s)
- Shelley R. Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Yongkai Ow
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Vivian Jiang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Maria Tokuyama
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Mark Rivera
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Xin Qi
- Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Richard W. Roberts
- Department of Chemistry, Chemical Engineering, and Biology, University of Southern California, Los Angeles, California, United States of America
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- * E-mail:
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Martínez-Salas E, Pacheco A, Serrano P, Fernandez N. New insights into internal ribosome entry site elements relevant for viral gene expression. J Gen Virol 2008; 89:611-626. [PMID: 18272751 DOI: 10.1099/vir.0.83426-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A distinctive feature of positive-strand RNA viruses is the presence of high-order structural elements at the untranslated regions (UTR) of the genome that are essential for viral RNA replication. The RNA of all members of the family Picornaviridae initiate translation internally, via an internal ribosome entry site (IRES) element present in the 5' UTR. IRES elements consist of cis-acting RNA structures that usually require specific RNA-binding proteins for translational machinery recruitment. This specialized mechanism of translation initiation is shared with other viral RNAs, e.g. from hepatitis C virus and pestivirus, and represents an alternative to the cap-dependent mechanism. In cells infected with many picornaviruses, proteolysis or changes in phosphorylation of key host factors induces shut off of cellular protein synthesis. This event occurs simultaneously with the synthesis of viral gene products since IRES activity is resistant to the modifications of the host factors. Viral gene expression and RNA replication in positive-strand viruses is further stimulated by viral RNA circularization, involving direct RNA-RNA contacts between the 5' and 3' ends as well as RNA-binding protein bridges. In this review, we discuss novel insights into the mechanisms that control picornavirus gene expression and compare them to those operating in other positive-strand RNA viruses.
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Affiliation(s)
- Encarnación Martínez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
| | - Almudena Pacheco
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
| | - Paula Serrano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
| | - Noemi Fernandez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
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26
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Fernández-Miragall O, Martínez-Salas E. In vivo footprint of a picornavirus internal ribosome entry site reveals differences in accessibility to specific RNA structural elements. J Gen Virol 2007; 88:3053-3062. [PMID: 17947530 DOI: 10.1099/vir.0.83218-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Internal ribosome entry site (IRES) elements were described in picornaviruses as an essential region of the viral RNA. Understanding of IRES function requires a detailed knowledge of each step involved in the internal initiation process, from RNA folding and IRES-protein interaction to ribosome recruitment. Thus, deciphering IRES accessibility to external agents due to RNA structural features, as well as RNA-protein protection within living cells, is of primary importance. In this study, two chemical reagents, dimethylsulfate (DMS) and aminomethylpsoralen, have been used to footprint the entire IRES of foot-and-mouth disease virus (FMDV) in living cells; these reagents enter the cell membrane and interact with nucleic acids in a structure-dependent manner. For FMDV, as in other picornaviruses, viral infection is dependent on the correct function of the IRES; therefore, the IRES region itself constitutes a useful target of antiviral drugs. Here, the in vivo footprint of a picornavirus IRES element in the context of a biologically active mRNA is shown for the first time. The accessibility of unpaired adenosine and cytosine nucleotides in the entire FMDV IRES was first obtained in vitro by DMS probing; subsequently, this information was used to interpret the footprint data obtained in vivo for the mRNA encompassing the IRES element in the intercistronic space. The results of DMS accessibility and UV-psoralen cross-linking studies in the competitive cellular environment provided evidence for differences in RNA structure from data obtained in vitro, and provided essential information to identify appropriate targets within the FMDV IRES aimed at combating this important pathogen.
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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
| | - Encarnación Martínez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Oem JK, Xiang Z, Zhou Y, Babiuk LA, Liu Q. Utilization of RNA polymerase I promoter and terminator sequences to develop a DNA transfection system for the study of hepatitis C virus internal ribosomal entry site-dependent translation. J Clin Virol 2007; 40:55-9. [PMID: 17632032 DOI: 10.1016/j.jcv.2007.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 05/22/2007] [Accepted: 06/04/2007] [Indexed: 02/05/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) causes severe liver diseases in a large population worldwide. HCV protein translation is controlled by an internal ribosomal entry site (IRES) within the 5'-untranslated region (UTR). HCV IRES-dependent translation is critical for HCV-associated pathogenesis. OBJECTIVE To develop a plasmid DNA transfection system by using RNA polymerase I promoter and terminator sequences for studying HCV IRES-dependent translation. STUDY DESIGN A gene cassette containing HCV 5'-UTR, Renilla luciferase reporter gene, and HCV 3'-UTR was inserted between RNA polymerase I promoter and terminator sequences. HCV IRES-directed translation was determined by luciferase assay after transfection. RESULTS Transfection of the RNA polymerase I-HCV IRES plasmid into human hepatoma Huh-7 and HepG2 cells resulted in luciferase gene expression. Deletion of the IIIf domain in HCV IRES dramatically reduced luciferase activity. CONCLUSION Our results indicated that the plasmid vector system-based on RNA polymerase I promoter and terminator sequences represents an effective approach for the study of HCV IRES-dependent translation.
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Affiliation(s)
- Jae-Ku Oem
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, 120 Veterinary Road, Saskatoon, Sask., Canada S7N 5E3
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Serrano P, Gomez J, Martínez-Salas E. Characterization of a cyanobacterial RNase P ribozyme recognition motif in the IRES of foot-and-mouth disease virus reveals a unique structural element. RNA (NEW YORK, N.Y.) 2007; 13:849-59. [PMID: 17449727 PMCID: PMC1869033 DOI: 10.1261/rna.506607] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Translation initiation driven by internal ribosome entry site (IRES) elements is dependent on the structural organization of the IRES region. Picornavirus IRES are organized in structural domains, in which the terminal stem-loops participate in functional RNA-protein interactions. However, the mechanistic role performed by the central domain during internal initiation has not been elucidated yet. Here we show that the foot-and-mouth-disease virus IRES contains a structural motif that serves in vitro as substrate for the Synechocystis sp. RNase P ribozyme, a structure-dependent endonuclease that participates in tRNA precursor processing. Recognition of the IRES substrate was dose dependent, required high magnesium concentration, and resulted in the formation of cleavage products with 5' phosphate and 3' hydroxyl ends. Mapping of the core recognition motif indicated that it overlapped with the apical region of the central domain. Two IRES constructs containing nucleotide substitutions in the apical region of the central domain that reorganized RNA structure displayed an altered pattern of cleavage by the cyanobacterial ribozyme generating new cleavage events in nearby residues. From these data it is inferred that the central domain of the IRES region has evolved a tRNA structural mimicry that renders it a substrate for RNase P ribozyme reaction. Recognition of this motif was affected in defective IRES mutants with a local RNA structure reorganization, suggesting that its structural preservation is required for IRES activity.
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Affiliation(s)
- Paula Serrano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
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Rodríguez Pulido M, Serrano P, Sáiz M, Martínez-Salas E. Foot-and-mouth disease virus infection induces proteolytic cleavage of PTB, eIF3a,b, and PABP RNA-binding proteins. Virology 2007; 364:466-74. [PMID: 17445855 DOI: 10.1016/j.virol.2007.03.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 03/07/2007] [Accepted: 03/08/2007] [Indexed: 11/25/2022]
Abstract
Foot-and-mouth disease virus (FMDV) infection induces major changes in the host cell including the shutoff of cellular protein synthesis. Here, protein extracts from FMDV-infected cells have been used to monitor changes in the profile of RNA-binding factors interacting with regulatory regions of the viral RNA. Relevant differences have been detected in the pattern of interaction with proteins prepared from either infected or uninfected cells with RNA probes encompassing the internal ribosome entry site (IRES), the 5' and 3'end regions. The binding patterns obtained for two divergent FMDV isolates showed differences depending on the viral isolate used. The identity of the host proteins giving a shifted binding pattern to RNA regulatory regions has been inferred by immunoblotting. Our results show that polypyrimidine tract-binding protein (PTB) and two subunits of translation initiation factor eIF3 interacting with the IRES undergo proteolytic processing during FMDV infection. In addition, poly(A)-binding protein (PABP), interacting with the 3'end of the viral RNA is partially processed. Proteolysis of eIF3a, eIF3b, PABP and PTB correlated with the extent of cytopathic effect induced by FMDV in infected cells.
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30
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Hsu YY, Liu YN, Wang W, Kao FJ, Kung SH. In vivo dynamics of enterovirus protease revealed by fluorescence resonance emission transfer (FRET) based on a novel FRET pair. Biochem Biophys Res Commun 2007; 353:939-45. [PMID: 17207462 DOI: 10.1016/j.bbrc.2006.12.145] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 12/13/2006] [Indexed: 10/23/2022]
Abstract
An in vivo protease assay suitable for analysis by fluorescence resonance energy transfer (FRET) was developed on the basis of a novel FRET pair. The specifically designed fusion substrate consists of green fluorescent protein 2 (GFP2)-peptide-red fluorescent protein 2 (DsRed2), with a cleavage motif for the enterovirus 2A protease (2Apro) embedded within the peptide region. FRET can be readily visualized in real-time from cells expressing the fusion substrate until a proteolytic cleavage by 2Apro from the input virus. The level of FRET decay is a function of the amount and infection duration of the inoculated virus as measured by a fluorometer assay. The FRET biosensor also responded well to other related enteroviruses but not to a phylogenetically distant virus. Western blot analysis confirmed the physical cleavage of the fusion substrate upon the infections. The study provides proof of principle for applying the FRET technology to diagnostics, screening procedures, and cell biological research.
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Affiliation(s)
- Yueh-Ying Hsu
- Faculty of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan, ROC
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31
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Lu J, Zhang J, Wang X, Jiang H, Liu C, Hu Y. In vitro and in vivo identification of structural and sequence elements in the 5' untranslated region of Ectropis obliqua picorna-like virus required for internal initiation. J Gen Virol 2006; 87:3667-3677. [PMID: 17098984 DOI: 10.1099/vir.0.82090-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ectropis obliqua picorna-like virus (EoPV) is a newly described insect virus that is classified as a putative member of the genus Iflavirus. The virus possesses a large, positive-sense RNA genome encoding a single polyprotein that shares physicochemical properties with those of members of the family Picornaviridae. The 5' untranslated region (5' UTR) plays an important role in picornavirus translation initiation, as it contains an internal ribosome entry site (IRES) that mediates cap-independent translation. To investigate translation in EoPV, an extensive range of mutations were engineered within the 5' UTR and the effects of these changes were examined in vitro and in vivo by using a bicistronic construct. Results showed that deletions within the first 63 nt had little impact on IRES activity, whilst core IRES function was contained within stem-loops C and D, as their removal abrogated IRES activity significantly. In contrast to these findings, removal of stem-loop G containing two cryptic AUGs caused a remarkable increase in IRES activity, which was further investigated by site-directed mutagenesis at these two positions. It was also confirmed that initiation of protein synthesis occurs at AUG6 (position 391-394) and not at the AUG immediately downstream of the polypyrimidine tract. Mutation of the polypyrimidine tract (CCTTTC) had a slight effect on EoPV IRES activity. Furthermore, mutations of the RAAA motif led to a decrease in IRES activity of approximately 40 % in vitro, but these results were not supported by in vivo experiments. In conclusion, this study reveals that the EoPV IRES element is unique, although it has features in common with the type II IRESs.
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Affiliation(s)
- Jie Lu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province 430072, China
| | - Jiamin Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province 430072, China
| | - Xiaochun Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province 430072, China
| | - Hong Jiang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province 430072, China
| | - Chuanfeng Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province 430072, China
| | - Yuanyang Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province 430072, China
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Bellecave P, Moradpour D. A picture says more than a thousand words: Structural insights into hepatitis C virus translation initiation. Hepatology 2006; 44:1687-90. [PMID: 17133497 DOI: 10.1002/hep.21450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Affiliation(s)
- Pantxika Bellecave
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
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33
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Abstract
Recruitment of the 40S ribosome to the 5' end of a eukaryotic mRNA requires assembly of translation initiation factors eIF4E, the cap-binding protein, together with eIF4A and eIF4G into a complex termed eIF4F. While the translational repressor 4E-BP1 regulates binding of eIF4E to eIF4G, the forces required to construct an eIF4F complex remain unidentified. Here, we establish that the herpes simplex virus-1 (HSV-1) ICP6 polypeptide associates with eIF4G to promote eIF4F complex assembly. Strikingly, release of eIF4E from the 4E-BP1 repressor is insufficient to drive complex formation, suggesting that ICP6 is an eIF4F-assembly chaperone. This is the first example of a translation initiation factor-associated protein that promotes active complex assembly and defines a new, controllable step in the initiation of translation. Homology of the N-terminal, eIF4G-binding segment of ICP6 with cellular chaperones suggest that factors capable of interacting with eIF4G and promoting eIF4F complex assembly may play important roles in a variety of processes where translation complexes need to be remodeled or assembled on populations of newly synthesized or derepressed mRNAs, including development, differentiation, and the response to a broad spectrum of environmental cues.
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Affiliation(s)
- Derek Walsh
- Department of Microbiology and New York University Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
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34
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Nagao I, Obokata J. In vitro selection of translational regulatory elements. Anal Biochem 2006; 354:1-7. [PMID: 16707091 DOI: 10.1016/j.ab.2006.03.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Revised: 03/23/2006] [Accepted: 03/28/2006] [Indexed: 11/17/2022]
Abstract
Untranslated regions (UTRs) of mRNAs carry various kinds of translational regulatory elements; however, our knowledge of them is still limited. We created an in vitro selection system that allows us to make a systematic enrichment of the sequences that alter translation efficiency (SESTRE) in any given mRNA and translation system. This method consists of the introduction of random nucleotide sequences into the UTRs of given mRNAs, followed by translation, size fractionation of the polyribosomes, and reverse transcription and PCR amplification (RT-PCR), with repeated cycles of these steps to enrich highly or poorly translatable mRNAs. With this experimental method, we examined how and where translational enhancer motifs emerge on mRNAs using the in vitro translation systems of wheat germ extract. The results indicate that the translational enhancers differentially emerge in response to the presence or absence of the 5' cap. Interestingly, the translational enhancers that activate cap-independent translation evolved more readily in the 3' UTR than in the 5' UTR in wheat germ extract. This SESTRE method should be a powerful tool with which to improve the translational efficiency of given mRNAs in given translation systems and to investigate the structure-function relationship of eukaryotic mRNAs underlying translational control.
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Affiliation(s)
- Issei Nagao
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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35
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Chard LS, Bordeleau ME, Pelletier J, Tanaka J, Belsham GJ. Hepatitis C virus-related internal ribosome entry sites are found in multiple genera of the family Picornaviridae. J Gen Virol 2006; 87:927-936. [PMID: 16528042 DOI: 10.1099/vir.0.81546-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The internal ribosome entry site (IRES) elements from porcine enterovirus 8 and simian virus 2, two members of a proposed new genus within the family Picornaviridae, were characterized. These IRES elements, in common with the porcine teschovirus 1 IRES, were found to be related functionally and structurally to the IRES element from Hepatitis C virus, a member of the family Flaviviridae. Partial secondary structure predictions were derived and functional assays demonstrated that these IRES elements continued to be active when eIF4G was cleaved and when the activity of eIF4A was blocked.
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Affiliation(s)
- Louisa S Chard
- BBSRC, Institute for Animal Health, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Marie-Eve Bordeleau
- Department of Biochemistry, McIntyre Medical Sciences Building, Montreal, QC H3G 1Y6, Canada
| | - Jerry Pelletier
- McGill Cancer Center, McIntyre Medical Sciences Building, Montreal, QC H3G 1Y6, Canada
- Department of Biochemistry, McIntyre Medical Sciences Building, Montreal, QC H3G 1Y6, Canada
| | - Junichi Tanaka
- Department of Chemistry, Biology and Marine Sciences, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Graham J Belsham
- BBSRC, Institute for Animal Health, Pirbright, Woking, Surrey GU24 0NF, UK
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36
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Chard LS, Kaku Y, Jones B, Nayak A, Belsham GJ. Functional analyses of RNA structures shared between the internal ribosome entry sites of hepatitis C virus and the picornavirus porcine teschovirus 1 Talfan. J Virol 2006; 80:1271-9. [PMID: 16415004 PMCID: PMC1346926 DOI: 10.1128/jvi.80.3.1271-1279.2006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The internal ribosome entry site (IRES) of porcine teschovirus 1 (PTV-1), a member of the Picornaviridae family, is quite distinct from other well-characterized picornavirus IRES elements, but it displays functional similarities to the IRES from hepatitis C virus (HCV), a member of the Flaviviridae family. In particular, a dominant negative mutant form of eIF4A does not inhibit the activity of the PTV-1 IRES. Furthermore, there is a high level (ca. 50%) of identity between the PTV-1 and HCV IRES sequences. A secondary-structure model of the whole PTV-1 IRES has been derived which includes a pseudoknot. Validation of specific features within the model has been achieved by mutagenesis and functional assays. The differences and similarities between the PTV-1 and HCV IRES elements should assist in defining the critical features of this type of IRES.
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Affiliation(s)
- Louisa S Chard
- BBSRC Institute for Animal Health, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
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37
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Park EH, Lee JM, Pelletier J. The Tie2 5' untranslated region is inhibitory to 5' end-mediated translation initiation. FEBS Lett 2006; 580:1309-19. [PMID: 16457819 DOI: 10.1016/j.febslet.2006.01.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 01/12/2006] [Indexed: 11/20/2022]
Abstract
Tie2 is an endothelium-specific receptor tyrosine kinase required for normal blood vessel maturation, remodeling, and stability. Tie2 expression is also upregulated in various cancers implicating a role in tumor angiogenesis. Its mRNA transcript contains an unusually long (372 nucleotides) 5' untranslated region (UTR) with five upstream open reading frames (uORFs) and an internal ribosome entry site (IRES) that allows this mRNA to be translated under hypoxic conditions. This sets up an alternative initiation pathway with the potential to clash with 5' end-mediated initiation from the same template. Herein, we define experimental conditions under which the Tie2 IRES is not active, allowing us to assess the contribution of the 5' UTR to cap-dependent translation on the Tie2 transcript. We find that the Tie2 5' UTR is inhibitory to translation initiation with ribosome flow decreasing following encounters with each uORF. No single uORF was found to harbor significant cis-acting inhibitory activity. Our results suggest that the uORFs within the Tie2 5' UTR serve to decrease the percent of ribosomes competent for reinitiation as these traverse the mRNA 5' UTR, thus minimizing interference with the IRES.
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Affiliation(s)
- Eun-Hee Park
- Department of Biochemistry, McIntyre Medical Sciences Building, Room 810, 3655 Promenade Sir William Osler, McGill University, Montreal, Que., Canada H3G 1Y6
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38
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39
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Caldarelli SA, Mehiri M, Di Giorgio A, Martin A, Hantz O, Zoulim F, Terreux R, Condom R, Patino N. A cyclic PNA-based compound targeting domain IV of HCV IRES RNA inhibits in vitro IRES-dependent translation. Bioorg Med Chem 2005; 13:5700-9. [PMID: 16061387 DOI: 10.1016/j.bmc.2005.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 06/03/2005] [Accepted: 06/03/2005] [Indexed: 11/28/2022]
Abstract
A cyclic molecule 1 constituted by a hepta-peptide nucleic acid sequence complementary to the apical loop of domain IV of hepatitis C virus (HCV) internal ribosome entry site (IRES) RNA has been prepared via a 'mixed' liquid-phase strategy, which relies on easily available protected PNA and poly(2-aminoethylglycinamide) building blocks. This compound 1 has been elaborated to mimic 'loop-loop' interactions. For comparison, its linear analog has also been investigated. Although preliminary biological assays have revealed the ability of 1 to inhibit in vitro the HCV IRES-dependent translation in a dose-dependent manner, the linear analog has shown a slightly higher activity.
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Affiliation(s)
- Sergio A Caldarelli
- Laboratoire de Chimie Bioorganique UMR-CNRS 6001, Université de Nice-Sophia Antipolis, Parc Valrose, 06108 Nice Cedex, France
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40
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Abstract
The ribosome is the macromolecular machinery in the host cell for which all viruses have to compete. Early in infection, the viral mRNAs have to compete with the host for both the ribosomes and for the limited pool of eukaryotic initiation factors that are needed to facilitate the recruitment of ribosomes to both viral and cellular mRNAs. To circumvent this competition, certain viruses have evolved to recruit ribosomes to IRESs (internal ribosome entry sites), highly specialized RNA elements that are located at the 5'-end of the viral genomes. Here, we discuss how divergent IRES elements can recruit ribosomes and start protein synthesis with only a minimal set of eukaryotic translation initiation factors, and how this mode of translation initiation aids viral gene amplification during early onset of innate immune responses.
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41
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Miyoshi H, Suehiro N, Tomoo K, Muto S, Takahashi T, Tsukamoto T, Ohmori T, Natsuaki T. Binding analyses for the interaction between plant virus genome-linked protein (VPg) and plant translational initiation factors. Biochimie 2005; 88:329-40. [PMID: 16300873 DOI: 10.1016/j.biochi.2005.09.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Accepted: 09/12/2005] [Indexed: 11/18/2022]
Abstract
The turnip mosaic virus (TuMV) genome-linked protein (VPg) and Arabidopsis thaliana translation initiation factors were expressed and purified in order to investigate their binding properties and kinetics. Affinity chromatography on m(7)GTP-sepharose showed that bound A. thaliana eIF(iso)4E was eluted with crude TuMV VPg. Further column studies with purified VPg and other A. thaliana eIF4E isoforms showed that VPg preferentially bound eIF(iso)4E. Structural data implicate Trp-46 and Trp-92 in eIF(iso)4E in cap recognition. When Trp-46 or Trp-92 were changed to Leu, eIF(iso)4E lost the ability to form a complex with both VPg and m(7)GTP-sepharose. This suggests that the VPg-binding site is located in or near the cap-recognition pocket on eIF(iso)4E. Affinity constants for the interactions with eIF(iso)4E of VPg and capped RNA oligomer were determined using surface plasmon resonance (SPR). The K(D) values showed that the binging affinity of VPg for eIF(iso)4E is stronger than that of capped RNA. This suggests that viral VPg can interfere with formation of a translational initiation complex on host plant cellular mRNA by sequestering eIF(iso)4E. Further experiments with affinity chromatography showed that VPg forms a ternary complex with eIF(iso)4E and eIF(iso)4G. Thus, VPg may participate in viral translational initiation by functioning as an alternative cap-like structure.
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Affiliation(s)
- Hiroshi Miyoshi
- Department of Microbiology, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki 216-8511, Japan.
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42
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Dhar D, Mapa K, Pudi R, Srinivasan P, Bodhinathan K, Das S. Human ribosomal protein L18a interacts with hepatitis C virus internal ribosome entry site. Arch Virol 2005; 151:509-24. [PMID: 16195786 DOI: 10.1007/s00705-005-0642-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Accepted: 08/15/2005] [Indexed: 02/05/2023]
Abstract
Translation initiation of hepatitis C virus RNA occurs via ribosome binding to an 'internal ribosome entry site (IRES)' located in the 5'untranslated region of the viral RNA. The principle interaction between the 40S ribosomal subunit and the HCV IRES has been shown to be largely factor independent, which is followed by the joining of the 60S ribosomal subunit to form functional 80S complex. However several additional cellular proteins have been reported to bind to HCV IRES and enhance the initiation of translation. In order to identify novel factors involved in the ribosome assembly during internal initiation of HCV RNA, northwestern screening of a HeLa cDNA expression library was performed, using HCV IRES RNA as probe. We demonstrate here, that human ribosomal protein L18a, a constituent of 60S subunit, interacts with HCV IRES RNA. This interaction was further confirmed by using a recombinant protein similar to L18a (sL18a), cloned from human blood. Interestingly, addition of increasing concentration of the purified recombinant sL18a protein, showed moderate stimulation of HCV IRES activity in the in vitro translation assay. These observations suggest that the human L18a might influence the HCV IRES mediated translation.
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Affiliation(s)
- D Dhar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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43
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Abstract
The human suffering exacted by the hepatitis C virus is enormous. Hundreds of thousands of people die each year from liver failure and cancer caused by this infection. There is no vaccine, and the available antiviral drugs are toxic, expensive and only partly effective. Progress has been hindered by the absence of cell culture and small-animal models of the infection. Nonetheless, recent advances have yielded several promising new antiviral drugs and enhanced the prospects of developing a vaccine. The recent development of a robust in vitro hepatitis C virus infection system will aid this search.
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44
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Florez PM, Sessions OM, Wagner EJ, Gromeier M, Garcia-Blanco MA. The polypyrimidine tract binding protein is required for efficient picornavirus gene expression and propagation. J Virol 2005; 79:6172-9. [PMID: 15858002 PMCID: PMC1091667 DOI: 10.1128/jvi.79.10.6172-6179.2005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Accepted: 01/12/2005] [Indexed: 02/05/2023] Open
Abstract
Mammalian host factors required for efficient viral gene expression and propagation have been often recalcitrant to genetic analysis. A case in point is the function of cellular factors that trans-activate internal ribosomal entry site (IRES)-driven translation, which is operative in many positive-stranded RNA viruses, including all picornaviruses. These IRES trans-acting factors have been elegantly studied in vitro, but their in vivo importance for viral gene expression and propagation has not been widely confirmed experimentally. Here we use RNA interference to deplete mammalian cells of one such factor, the polypyrimidine tract binding protein, and test its requirement in picornavirus gene expression and propagation. Depletion of the polypyrimidine tract binding protein resulted in a marked delay of particle propagation and significantly decreased synthesis and accumulation of viral proteins of poliovirus and encephalomyocarditis virus. These effects could be partially restored by expression of an RNA interference-resistant exogenous polypyrimidine tract binding protein. These data indicate a critical role for the polypyrimidine tract binding protein in picornavirus gene expression and strongly suggest a requirement for efficient IRES-dependent translation.
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Affiliation(s)
- Paola M Florez
- Duke University Medical Center, Box 3020 (451 Jones), Research Drive, Durham, NC 27710, USA
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45
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Domitrovich AM, Diebel KW, Ali N, Sarker S, Siddiqui A. Role of La autoantigen and polypyrimidine tract-binding protein in HCV replication. Virology 2005; 335:72-86. [PMID: 15823607 DOI: 10.1016/j.virol.2005.02.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Revised: 11/29/2004] [Accepted: 02/13/2005] [Indexed: 02/05/2023]
Abstract
To determine if the cellular factors La autoantigen (La) and polypyrimidine tract-binding protein (PTB) are required for hepatitis C virus (HCV) replication, we used siRNAs to silence these factors and then monitored their effect on HCV replication using quantitative RT-PCR. In addition, we determined the influence of PTB on the activity of the 3' noncoding region (NCR) of HCV and investigated its interaction with the components of the HCV replicase complex. We found that La is essential for efficient HCV replication while PTB appears to partially repress replication. PTB does, however, block the binding of HCV RNA-dependent RNA polymerase (RdRp, NS5B) to the 3'NCR. Indirect immunofluorescence microscopy showed co-localization of cytoplasmic PTB with the HCV RdRp in hepatoma cells (Huh-7) expressing HCV proteins, while in vitro translation of viral proteins from the HCV replicon revealed the interaction of PTB isoforms with NS5B polymerase and NS3.
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Affiliation(s)
- Angela M Domitrovich
- Program in Molecular Biology, Department of Microbiology, B172, University of Colorado Health Sciences Center, 4200 E. 9th Avenue, Denver, CO 80262, USA
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46
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Baril M, Brakier-Gingras L. Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein. Nucleic Acids Res 2005; 33:1474-86. [PMID: 15755749 PMCID: PMC1062877 DOI: 10.1093/nar/gki292] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The hepatitis C virus (HCV) genome contains an internal ribosome entry site (IRES) followed by a large open reading frame coding for a polyprotein that is cleaved into 10 proteins. An additional HCV protein, the F protein, was recently suggested to result from a +1 frameshift by a minority of ribosomes that initiated translation at the HCV AUG initiator codon of the polyprotein. In the present study, we reassessed the mechanism accounting for the synthesis of the F protein by measuring the expression in cultured cells of a luciferase reporter gene with an insertion encompassing the IRES plus the beginning of the HCV-coding region preceding the luciferase-coding sequence. The insertion was such that luciferase expression was either in the +1 reading frame relative to the HCV AUG initiator codon, mimicking the expression of the F protein, or in-frame with this AUG, mimicking the expression of the polyprotein. Introduction of a stop codon at various positions in-frame with the AUG initiator codon and substitution of this AUG with UAC inhibited luciferase expression in the 0 reading frame but not in the +1 reading frame, ruling out that the synthesis of the F protein results from a +1 frameshift. Introduction of a stop codon at various positions in the +1 reading frame identified the codon overlapping codon 26 of the polyprotein in the +1 reading frame as the translation start site for the F protein. This codon 26(+1) is either GUG or GCG in the viral variants. Expression of the F protein strongly increased when codon 26(+1) was replaced with AUG, or when its context was mutated into an optimal Kozak context, but was severely decreased in the presence of low concentrations of edeine. These observations are consistent with a Met-tRNAi-dependent initiation of translation at a non-AUG codon for the synthesis of the F protein.
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Affiliation(s)
| | - Léa Brakier-Gingras
- To whom correspondence should be addressed. Tel: +1 514 343 6316; Fax: +1 514 343 2210;
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47
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Costantino D, Kieft JS. A preformed compact ribosome-binding domain in the cricket paralysis-like virus IRES RNAs. RNA (NEW YORK, N.Y.) 2005; 11:332-43. [PMID: 15701733 PMCID: PMC1370722 DOI: 10.1261/rna.7184705] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The internal ribosome site RNA of the cricket paralysis-like viruses (CrPV-like) binds directly to the ribosome, assembling the translation machinery without initiation factors. This mechanism does not require initiator tRNA, and translation starts from a non-AUG codon. A wealth of biochemical data has yielded a working model for this process, but the three-dimensional structure and biophysical characteristics of the unbound CrPV-like IRES RNAs are largely unexplored. Here, we demonstrate that the CrPV-like IRESes prefold into a two-part structure in the presence of magnesium ions. The largest part is a prefolded compact RNA domain that shares folding and structural characteristics with other compactly folded RNAs such as group I intron RNAs and RNase P RNA. Chemical probing reveals that the CrPV-like IRES' compact domain contains RNA helices that are packed tightly enough to exclude solvent, and analytical ultracentrifugation indicates a large change in the shape of the IRES upon folding. Formation of this compact domain is necessary for binding of the 40S subunit, and the structural organization of the unbound IRES RNA is consistent with the hypothesis that the IRES is functionally and structurally preorganized before ribosome binding.
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Affiliation(s)
- David Costantino
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Mail stop 8101, P.O. Box 6511, Aurora, CO 80045, USA
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48
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Matsuda D, Bauer L, Tinnesand K, Dreher TW. Expression of the two nested overlapping reading frames of turnip yellow mosaic virus RNA is enhanced by a 5' cap and by 5' and 3' viral sequences. J Virol 2004; 78:9325-35. [PMID: 15308727 PMCID: PMC506944 DOI: 10.1128/jvi.78.17.9325-9335.2004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The translation efficiency of an mRNA molecule is typically determined by its 5'- and/or 3'-untranslated regions (UTRs). Previously, we have found that the 3'-UTR of Turnip yellow mosaic virus (TYMV) RNA enhances translation synergistically with a 5' cap. Here, we use a luciferase reporter system in cowpea protoplasts to show that the 5' 217 nucleotides from TYMV genomic RNA enhance expression relative to a vector-derived 17-nucleotide 5'-UTR. Maximum expression was observed from RNAs with a cap and both 5' and 3' TYMV sequences. In paired reporter constructs, the 5' 217 nucleotides harboring the UTR and the first 43 or 41 codons of the two overlapping TYMV open reading frames (ORFs), ORF-69 and ORF-206, respectively, were fused in frame with the luciferase gene. This allowed expression from the initiation codon of each ORF (AUG69 and AUG206) to be monitored separately but from the normal sequence environment. Expression from both AUG codons was heavily dependent on a 5' cap, with a threefold-higher expression occurring from AUG69 than from AUG206 in the presence of the genomic 3'-UTR. Changes that interrupted the cap/3'-UTR synergy (i.e., removal of the cap or TYMV 3'-UTR) resulted in a higher proportion of initiation from AUG206. Mutation of the 3'-UTR to prevent aminoacylation, as well as deletion of 75% of the 5'-UTR, likewise resulted in a lower ratio of expression from AUG69 relative to AUG206. Mutation of each AUG initiation codon increased initiation from the other. Taken together, these results do not fully conform to the expectations of standard leaky ribosomal scanning and leave open the precise mechanism of ribosome commitment to AUG69 and AUG206. However, our observations do not support a recent proposal based on in vitro studies in which the 3'-UTR is proposed to direct cap-independent initiation specifically at AUG206 and not at AUG69 (S. Barends et al., Cell 112:123-129, 2003).
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Affiliation(s)
- Daiki Matsuda
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
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49
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Phelan M, Banks RJ, Conn G, Ramesh V. NMR studies of the structure and Mg2+ binding properties of a conserved RNA motif of EMCV picornavirus IRES element. Nucleic Acids Res 2004; 32:4715-24. [PMID: 15353559 PMCID: PMC519103 DOI: 10.1093/nar/gkh805] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2004] [Revised: 08/17/2004] [Accepted: 08/17/2004] [Indexed: 11/13/2022] Open
Abstract
The structure and Mg(2+) binding properties of a conserved 75mer RNA motif of the internal ribosome entry site (IRES) element of encephalomyocarditis virus picornavirus have been investigated by (1)H-NMR and UV melting experiments. The assignment of the imino proton resonances with characteristic chemical shift dispersion for canonical and non-canonical base pairs confirmed the predicted secondary structure of the 75mer and its fragments. Addition of Mg(2+) resulted in a dramatic increase in apparent melting temperature, with the 75mer RNA registering the biggest increase, from 63 to 80 degrees C, thus providing evidence for enhanced stability arising from Mg(2+) binding. Similarly, addition of Mg(2+) induced selective changes to the chemical shifts of the imino protons of a GCGA tetraloop in the 75mer, that is essential for IRES activity, thereby highlighting a possible structural role for Mg(2+) in the folding of the 75mer. Significantly, the same protons show retarded exchange to water solvent, even at elevated temperature, which suggest that Mg(2+) induces a conformational rearrangement of the 75mer. Thus, we propose that Mg(2+) serves two important roles: (i) enhancing thermodynamic stability of the 75mer RNA (and its submotifs) via non-specific interactions with the phosphate backbone and (ii) promoting the folding of the 75mer RNA by binding to the GCGA tetraloop.
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Affiliation(s)
- Marie Phelan
- Department of Chemistry, University of Manchester Institute of Science and Technology, PO Box 88, Manchester M60 1QD, UK
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50
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Merrick WC. Cap-dependent and cap-independent translation in eukaryotic systems. Gene 2004; 332:1-11. [PMID: 15145049 DOI: 10.1016/j.gene.2004.02.051] [Citation(s) in RCA: 194] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Revised: 02/04/2004] [Accepted: 02/27/2004] [Indexed: 12/21/2022]
Abstract
Unlike bacterial protein synthesis, eukaryotic protein synthesis has several mechanisms to initiate translation including cap-dependent initiation, re-initiation and internal initiation. While there is extensive biochemical characterization of the multiple steps in cap-dependent initiation, most of the information on the other two mechanisms is derived from studies on the nucleic acid sequences that influence their efficiency. However, even in the best of circumstances, both re-initiation and internal initiation are only 25% as efficient as cap-dependent initiation and more commonly, are only 1-10% as efficient. This general lack of efficiency leaves open possibilities for mis-interpretation/artifacts in vivo (cryptic promoters, alternate splicing) or in vitro (nuclease degradation). Two examples are cited from the author's laboratory as background for the development of a general set of guidelines to minimize errors and validate authenticity for internal initiation.
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Affiliation(s)
- William C Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935, USA.
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