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Ma Y, Zheng S, Wang X, Zhu L, Wang J, Pan S, Zhang Y, Liu Z. AGEs induce high expression of Dll4 via endoplasmic reticulum stress PERK signaling-mediated internal ribosomal entry site mechanism in macrophages. Heliyon 2023; 9:e21170. [PMID: 37886757 PMCID: PMC10597754 DOI: 10.1016/j.heliyon.2023.e21170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Background and aim Advanced glycation end products (AGEs)- exposed macrophages was characterized by Delta-like ligand 4 (Dll4) high expressed and has been shown to participate in diabetes-related atherosclerosis. This study was aimed to investigate the translational regulatory mechanism of Dll4 high expression in macrophages exposed to AGEs. Methods Human Dll4 5' untranslated region (5'UTR) sequence was cloned and inserted into a bicistronic reporter plasmid. Human THP-1 macrophages transfected with the bicistronic reporter plasmids were exposed to AGEs. Dual-luciferase assay was used to detect internal ribosome entry site (IRES) activity contained in Dll4 5'UTR. Small interference RNA transfection was used to knock-down specific gene expression. Localization of protein was analyzed. Results AGEs exposure significantly induced IRES activity in Dll4 5' UTR in human macrophages. Internal potential promoter and ribosome read-through mechanisms were excluded. Inhibition of endoplasmic reticulum stress and specific silencing of protein kinase R-like endoplasmic reticulum kinase (PERK)/eukaryotic initiation factor 2α (eIF2α) signaling pathway activation reduced IRES activity in Dll4 5' UTR in human macrophages. Dll4 5' UTR IRES activity was also inhibited by targeted silencing of heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1). Moreover, specific inhibition of PERK/eIF2α signaling pathway led to deactivation of hnRNPA1, resulting to reduction of AGEs- induced Dll4 5' UTR IRES activity in human macrophages. Conclusions AGEs induced Dll4 5' UTR IRES activity in human macrophages which was dependent on endoplasmic reticulum stress PERK/eIF2α signaling pathway. hnRNPA1 acted the role as an ITAF was also indispensable for AGEs-induced Dll4 5'UTR IRES activity in human macrophages.
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Affiliation(s)
- Yanpeng Ma
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
- Atherosclerosis Integrated Chinese and Western Medicine Key Research Laboratory, Research Office of Shaanxi Administration of Traditional Chinese Medicine, Xi'an, 710003, China
- Affiliated Shaanxi Provincial People's Hospital, Northwestern Polytechnical University, Xi'an, 710068, China
| | - Shixiang Zheng
- Department of Critical Medicine, Fujian Medical University Union Hospital, Fuzhou, 350000, China
| | - Xiqiang Wang
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
- Atherosclerosis Integrated Chinese and Western Medicine Key Research Laboratory, Research Office of Shaanxi Administration of Traditional Chinese Medicine, Xi'an, 710003, China
- Affiliated Shaanxi Provincial People's Hospital, Northwestern Polytechnical University, Xi'an, 710068, China
| | - Ling Zhu
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
- Atherosclerosis Integrated Chinese and Western Medicine Key Research Laboratory, Research Office of Shaanxi Administration of Traditional Chinese Medicine, Xi'an, 710003, China
- Affiliated Shaanxi Provincial People's Hospital, Northwestern Polytechnical University, Xi'an, 710068, China
| | - Junkui Wang
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
- Atherosclerosis Integrated Chinese and Western Medicine Key Research Laboratory, Research Office of Shaanxi Administration of Traditional Chinese Medicine, Xi'an, 710003, China
- Affiliated Shaanxi Provincial People's Hospital, Northwestern Polytechnical University, Xi'an, 710068, China
| | - Shuo Pan
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
- Atherosclerosis Integrated Chinese and Western Medicine Key Research Laboratory, Research Office of Shaanxi Administration of Traditional Chinese Medicine, Xi'an, 710003, China
- Affiliated Shaanxi Provincial People's Hospital, Northwestern Polytechnical University, Xi'an, 710068, China
| | - Yong Zhang
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
- Atherosclerosis Integrated Chinese and Western Medicine Key Research Laboratory, Research Office of Shaanxi Administration of Traditional Chinese Medicine, Xi'an, 710003, China
- Affiliated Shaanxi Provincial People's Hospital, Northwestern Polytechnical University, Xi'an, 710068, China
| | - Zhongwei Liu
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
- Atherosclerosis Integrated Chinese and Western Medicine Key Research Laboratory, Research Office of Shaanxi Administration of Traditional Chinese Medicine, Xi'an, 710003, China
- Affiliated Shaanxi Provincial People's Hospital, Northwestern Polytechnical University, Xi'an, 710068, China
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2
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Liu F, Wang N, Huang Y, Wang Q, Shan H. Stem II-disrupting pseudoknot does not abolish ability of Senecavirus A IRES to initiate protein expression, but inhibits recovery of virus from cDNA clone. Vet Microbiol 2021; 255:109024. [PMID: 33713975 DOI: 10.1016/j.vetmic.2021.109024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
Senecavirus A (SVA) is classified into the genus Senecavirus in the family Picornaviridae. Its genome is a positive-sense, single-stranded and nonsegmented RNA, approximately 7300 nucleotides in length. A picornaviral genome is essentially an mRNA, which, albeit unmodified with 5' cap structure, can still initiate protein expression by the internal ribosome entry site (IRES). The SVA genome contains a hepatitis C virus-like IRES, in which a pseudoknot structure plays an important role in initiating protein expression. In this study, we constructed a set of SVA (CH-LX-01-2016 strain) minigenomes with all combinations of point mutations in its pseudoknot stem II (PKS-II). The results showed that any combination of point mutations could not significantly interfere with the IRES to initiate protein expression. Further, we constructed a full-length SVA cDNA clone, in which the PKS-II-forming cDNA motif was subjected to site-directed mutagenesis for totally disrupting the PKS-II formation in IRES. Such a modified SVA cDNA clone was transfected into BSR-T7/5 cells, consequently demonstrating that the PKS-II-disrupting IRES interfered neither with protein expression nor with antigenome replication, whereas a competent SVA could not be rescued from the cDNA clone. It was speculated that the mutated motif possibly disrupted a packaging signal for virion assembly, therefore causing the failure of SVA rescue.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Ning Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yilan Huang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
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3
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Ogawa A, Takamatsu M. Mutation of the start codon to enhance Cripavirus internal ribosome entry site-mediated translation in a wheat germ extract. Bioorg Med Chem Lett 2019; 29:126729. [PMID: 31607608 DOI: 10.1016/j.bmcl.2019.126729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 11/22/2022]
Abstract
Wheat germ extract (WGE) is one of the most widely used eukaryotic cell-free translation systems for easy synthesis of a broad range of proteins merely by adding template mRNAs. Its productivity has thus far been improved by removing translational inhibitors from the extract and stabilizing the template with terminal protectors. Nonetheless, there remains room for increasing the yield by designing a terminally protected template with higher susceptibility to translation. Given the fact that a 5' terminal protector is a strong inhibitor of the canonical translation, we herein focused on Cripavirus internal ribosome entry sites (IRESes), which allow for a unique translation initiation from a non-AUG start codon without the help of any initiation factors. We mutated their start codons to enhance the IRES-mediated translation efficiency in WGE. One of the mutants showed considerably higher efficiency, 3-4-fold higher than that of its wild type, and also 3-4-fold higher than the canonical translation efficiency by an IRES-free mRNA having one of the most effective canonical-translation enhancers. Because this mutated IRES is compatible with different types of genes and terminal protectors, we expect it will be widely used to synthesize proteins in WGE.
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Vincent HA, Ziehr B, Lenarcic EM, Moorman NJ. Human cytomegalovirus pTRS1 stimulates cap-independent translation. Virology 2019; 537:246-253. [PMID: 31539772 PMCID: PMC8281606 DOI: 10.1016/j.virol.2019.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 01/08/2023]
Abstract
Human cytomegalovirus (HCMV) manipulates multiple cellular processes to facilitate virus replication, including the control of mRNA translation. We previously showed that the HCMV TRS1 protein (pTRS1) promotes cap-dependent mRNA translation independent of its ability to antagonize the antiviral protein PKR. Here we find that pTRS1 enhances internal ribosome entry site (IRES) activity using a novel circular RNA reporter that lacks an mRNA cap and poly(A) tail. Additionally, pTRS1 expression increases the activity of cellular IRESs that control the expression of proteins needed for efficient HCMV replication. We find that the ability of pTRS1 to enhance cap-independent translation is separable from its ability to antagonize PKR, but requires the pTRS1 RNA binding domain. Together these data show that pTRS1 stimulates cap-independent translation and suggest a role for pTRS1 in alternative translation initiation pathways during HCMV infection.
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Affiliation(s)
- Heather A Vincent
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin Ziehr
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erik M Lenarcic
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nathaniel J Moorman
- Department of Microbiology & Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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5
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Giangaspero M, Steinbach F, Strong R, Decaro N, Buonavoglia C, Domenis L, Gargano P, Bailly X, Apicella C, Turno P. Characterization of internal ribosome entry sites according to secondary structure analysis to classify border disease virus strains. J Virol Methods 2020; 275:113704. [PMID: 31518634 DOI: 10.1016/j.jviromet.2019.113704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/18/2019] [Accepted: 07/18/2019] [Indexed: 11/24/2022]
Abstract
Applying palindromic nucleotide substitutions (PNS) method, variable loci of the internal ribosome entry site (IRES) secondary structure in the 5' untranslated region (UTR) of Border disease virus sequences were analysed allowing their allocation into ten IRES classes within the species. Sequence characteristics of Turkish and Chinese strains were highly divergent from other genogroups, indicating geographic segregation and micro-evolutive steps within the species. Observed heterogeneity in the BDV species has to be considered for potential implications on diagnostic tests, control and preventive measures.
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6
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Al-Allaf FA, Abduljaleel Z, Athar M, Taher MM, Khan W, Mehmet H, Colakogullari M, Apostolidou S, Bigger B, Waddington S, Coutelle C, Themis M, Al-Ahdal MN, Al-Mohanna FA, Al-Hassnan ZN, Bouazzaoui A. Modifying inter-cistronic sequence significantly enhances IRES dependent second gene expression in bicistronic vector: Construction of optimised cassette for gene therapy of familial hypercholesterolemia. Noncoding RNA Res 2018; 4:1-14. [PMID: 30891532 PMCID: PMC6404380 DOI: 10.1016/j.ncrna.2018.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 01/23/2023] Open
Abstract
Internal ribosome entry site (IRES) sequences have become a valuable tool in the construction of gene transfer and therapeutic vectors for multi-cistronic gene expression from a single mRNA transcript. The optimal conditions for effective use of this sequence to construct a functional expression vector are not precisely defined but it is generally assumed that the internal ribosome entry site dependent expression of the second gene in such as cassette is less efficient than the cap-dependent expression of the first gene. Mainly tailoring inter-cistronic sequence significantly enhances IRES dependent second gene expression in bicistronic vector further in construction of optimised cassette for gene therapy of familial hypercholesterolemia. We tailored the size of the inter-cistronic spacer sequence at the 5′ region of the internal ribosome entry site sequence using sequential deletions and demonstrated that the expression of the 3′ gene can be significantly increased to similar levels as the cap-dependent expression of the 5’ gene. Maximum expression efficiency of the downstream gene was obtained when the spacer is composed of 18–141 base pairs. In this case a single mRNA transcriptional unit containing both the first and the second Cistron was detected. Whilst constructs with spacer sequences of 216 bp or longer generate a single transcriptional unit containing only the first Cistron. This suggests that long spacers may affect transcription termination. When the spacer is 188 bp, both transcripts were produced simultaneously in most transfected cells, while a fraction of them expressed only the first but not the second gene. Expression analyses of vectors containing optimised cassettes clearly confirm that efficiency of gene transfer and biological activity of the expressed transgenic proteins in the transduced cells can be achieved. Furthermore, Computational analysis was carried out by molecular dynamics (MD) simulation to determine the most emerges as viable containing specific binding site and bridging of 5′ and 3′ ends involving direct RNA-RNA contacts and RNA-protein interactions. These results provide a mechanistic basis for translation stimulation and RNA resembling for the synergistic stimulation of cap-dependent translation.
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Affiliation(s)
- Faisal A Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia.,Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah, 21955, Saudi Arabia.,Gene Therapy Research Group, Department of Molecular and Cell Medicine, Faculty of Medicine, Imperial College London, South Kensington, London, SW7 2AZ, UK.,Institute of Reproductive and Developmental Biology, Division of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Zainularifeen Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia
| | - Mohammad Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia
| | - Mohiuddin M Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia
| | - Wajahatullah Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, PO Box 3124, Riyadh, 11426, Saudi Arabia
| | - Huseyin Mehmet
- Institute of Reproductive and Developmental Biology, Division of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Mukaddes Colakogullari
- Institute of Reproductive and Developmental Biology, Division of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Sophia Apostolidou
- Institute of Reproductive and Developmental Biology, Division of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Brian Bigger
- Gene Therapy Research Group, Department of Molecular and Cell Medicine, Faculty of Medicine, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Simon Waddington
- Gene Therapy Research Group, Department of Molecular and Cell Medicine, Faculty of Medicine, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Charles Coutelle
- Gene Therapy Research Group, Department of Molecular and Cell Medicine, Faculty of Medicine, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Michael Themis
- Gene Therapy Research Group, Department of Molecular and Cell Medicine, Faculty of Medicine, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Mohammed N Al-Ahdal
- Department of Infection and Immunity, King Faisal Specialist Hospital & Research Center, Riyadh, 11211, Saudi Arabia
| | - Futwan A Al-Mohanna
- Department of Cell Biology, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Zuhair N Al-Hassnan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Abdellatif Bouazzaoui
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia.,Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia
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7
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Suhail M, Sohrab SS, Qureshi A, Tarique M, Abdel-Hafiz H, Al-Ghamdi K, Qadri I. Association of HCV mutated proteins and host SNPs in the development of hepatocellular carcinoma. Infect Genet Evol 2018; 60:160-172. [PMID: 29501636 DOI: 10.1016/j.meegid.2018.02.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/14/2018] [Accepted: 02/28/2018] [Indexed: 12/13/2022]
Abstract
Hepatitis C virus plays a significant role in the development of hepatocellular carcinoma (HCC) globally. The pathogenic mechanisms of hepatocellular carcinoma with HCV infection are generally linked with inflammation, cytokines, fibrosis, cellular signaling pathways, and liver cell proliferation modulating pathways. HCV encoded proteins (Core, NS3, NS4, NS5A) interact with a broad range of hepatocytes derived factors to modulate an array of activities such as cell signaling, DNA repair, transcription and translational regulation, cell propagation, apoptosis, membrane topology. These four viral proteins are also implicated to show a strong conversion potential in tissue culture. Furthermore, Core and NS5A also trigger the accretion of the β-catenin pathway as a common target to contribute viral induced transformation. There is a strong association between HCV variants within Core, NS4, and NS5A and host single nucleotide polymorphisms (SNPs) with the HCC pathogenesis. Identification of such viral mutants and host SNPs is very critical to determine the risk of HCC and response to antiviral therapy. In this review, we highlight the association of key variants, mutated proteins, and host SNPs in development of HCV induced HCC. How such viral mutants may modulate the interaction with cellular host machinery is also discussed.
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Affiliation(s)
- Mohd Suhail
- King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, Jeddah 21589, Saudi Arabia
| | - Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, Jeddah 21589, Saudi Arabia
| | - Abid Qureshi
- Biomedical Informatics Centre, Sher-i-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J&K, India
| | - Mohd Tarique
- Department of Surgery, Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, United States
| | - Hany Abdel-Hafiz
- Dept of Medicine, University of Colorado Denver, Aurora, CO 80045, United States
| | - Khalid Al-Ghamdi
- Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ishtiaq Qadri
- Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia.
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8
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Lampe S, Kunze M, Scholz A, Brauß TF, Winslow S, Simm S, Keller M, Heidler J, Wittig I, Brüne B, Schmid T. Identification of the TXNIP IRES and characterization of the impact of regulatory IRES trans-acting factors. Biochim Biophys Acta Gene Regul Mech 2018; 1861:147-157. [PMID: 29378331 DOI: 10.1016/j.bbagrm.2018.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Sebastian Lampe
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Michael Kunze
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Anica Scholz
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Thilo F Brauß
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Sofia Winslow
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Stefan Simm
- Department of Molecular Cell Biology of Plants, Faculty of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mario Keller
- Department of Molecular Cell Biology of Plants, Faculty of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Juliana Heidler
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany.
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9
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Damiano F, Testini M, Tocci R, Gnoni GV, Siculella L. Translational control of human acetyl-CoA carboxylase 1 mRNA is mediated by an internal ribosome entry site in response to ER stress, serum deprivation or hypoxia mimetic CoCl 2. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:388-398. [PMID: 29343429 DOI: 10.1016/j.bbalip.2018.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 01/09/2018] [Accepted: 01/12/2018] [Indexed: 12/12/2022]
Abstract
Acetyl-CoA carboxylase 1 (ACC1) is a cytosolic enzyme catalyzing the rate limiting step in de novo fatty acid biosynthesis. There is mounting evidence showing that ACC1 is susceptible to dysregulation and that it is over-expressed in liver diseases associated with lipid accumulation and in several cancers. In the present study, ACC1 regulation at the translational level is reported. Using several experimental approaches, the presence of an internal ribosome entry site (IRES) has been established in the 5' untranslated region (5' UTR) of the ACC1 mRNA. Transfection experiments with the ACC1 5' UTR inserted in a dicistronic reporter vector show a remarkable increase in the downstream cistron translation, through a cap-independent mechanism. The endoplasmic reticulum (ER) stress condition and the related unfolded protein response (UPR), triggered by treatment with thapsigargin and tunicamycin, cause an increase of the cap-independent translation of ACC1 mRNA in HepG2 cells, despite the overall reduction in global protein synthesis. Other stress conditions, such as serum starvation and incubation with hypoxia mimetic agent CoCl2, up-regulate ACC1 expression in HepG2 cells at the translational level. Overall, these findings indicate that the presence of an IRES in the ACC1 5' UTR allows ACC1 mRNA translation in conditions that are inhibitory to cap-dependent translation. A potential involvement of the cap-independent translation of ACC1 in several pathologies, such as obesity and cancer, has been discussed.
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Affiliation(s)
- Fabrizio Damiano
- Laboratory of Biochemistry and Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Mariangela Testini
- Laboratory of Biochemistry and Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Romina Tocci
- Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), Hammersmith Hospital, London, UK
| | - Gabriele V Gnoni
- Laboratory of Biochemistry and Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Luisa Siculella
- Laboratory of Biochemistry and Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy.
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Abstract
Background Sequence variability in the hepatitis C virus (HCV) genome has led to the development and classification of six genotypes and a number of subtypes. The HCV 5′ untranslated region mainly comprises an internal ribosomal entry site (IRES) responsible for cap-independent synthesis of the viral polyprotein and is conserved among all HCV genotypes. Description Considering the possible high impact of variations in HCV IRES on viral protein production and thus virus replication, we decided to collect the available data on known nucleotide variants in the HCV IRES and their impact on IRES function in translation initiation. The HCV IRES variation database (HCVIVdb) is a collection of naturally occurring and engineered mutation entries for the HCV IRES. Each entry contains contextual information pertaining to the entry such as the HCV genotypic background and links to the original publication. Where available, quantitative data on the IRES efficiency in translation have been collated along with details on the reporter system used to generate the data. Data are displayed both in a tabular and graphical formats and allow direct comparison of results from different experiments. Together the data provide a central resource for researchers in the IRES and hepatitis C-oriented fields. Conclusion The collation of over 1900 mutations enables systematic analysis of the HCV IRES. The database is mainly dedicated to detailed comparative and functional analysis of all the HCV IRES domains, which can further lead to the development of site-specific drug designs and provide a guide for future experiments. HCVIVdb is available at http://www.hcvivdb.org. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0804-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evan W Floden
- Department of Genetics & Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anas Khawaja
- Department of Genetics & Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Václav Vopálenský
- Department of Genetics & Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Martin Pospíšek
- Department of Genetics & Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic
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11
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Ashraf A, Chakravarti A, Roy P, Kar P, Siddiqui O. Frequency of nucleotide sequence variations in the internal ribosome entry site region of hepatitis C virus RNA isolated from responding and non-responding patients with hepatitis C virus genotype 3 infection. Virusdisease 2016; 27:251-259. [PMID: 28466036 DOI: 10.1007/s13337-016-0335-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/27/2016] [Indexed: 01/18/2023] Open
Abstract
Located within 5' untranslated region of HCV RNA is internal ribosome entry site (IRES) which directs cap-independent translation of viral polyprotein. Mutations in IRES sequence have been shown to cause changes in efficiency of protein translation in vitro in few instances. No study has been done to investigate association between frequency of nucleotide sequence variations in IRES region of HCV-3 RNA and response to pegylated interferon-α plus ribavirin therapy. Hence, this study was planned to analyze relationship between frequency of nucleotide sequence variations of HCV-3 IRES region and response to therapy. Twenty-seven HCV-3 patients were studied, of whom 19 responded to therapy and 8 did not. Alanine aminotransferase and aspartate aminotransferase levels were significantly lower in responders compared to non-responders. HCV RNA detection and genotyping was performed by nested-PCR and RFLP respectively. Viral load quantification in pre and post therapy samples was done by real time PCR. The viral load was significantly lower in the patients after treatment as compared to before treatment. HCV IRES region from pre-treatment sera of 27 HCV-3 infected patients was amplified by nested PCR and sequenced. Secondary structure of IRES region of HCV-3 was predicted using the M fold Web Server. Mutational analysis revealed hot spot of mutations in HCV-3 IRES region from 40-80 and 210-280 nucleotides. Though more mutations were found in non-responders as compared to responders, this difference was statistically insignificant. Therefore, in addition to IRES region of HCV-3, some other host and viral factors may contribute to therapy outcome.
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Affiliation(s)
- Anzar Ashraf
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
| | - Anita Chakravarti
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
- 79, South Park Apartment, Kalkaji, New Delhi, Delhi 110019 India
| | - Priyamvada Roy
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
| | - Premashish Kar
- Department of Medicine, Maulana Azad Medical College and Associated Lok Nayak Hospital, New Delhi, Delhi 110002 India
| | - Oves Siddiqui
- Virology Laboratory, Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi 110002 India
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Kuo SC, Teng CY, Ho YJ, Chen YJ, Wu TY. Using Bicistronic Baculovirus Expression Vector System to Screen the Compounds That Interfere with the Infection of Chikungunya Virus. Methods Mol Biol 2016; 1426:263-72. [PMID: 27233279 DOI: 10.1007/978-1-4939-3618-2_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Chikungunya virus (CHIKV) is the etiologic agent of Chikungunya fever and has emerged in many countries over the past decade. There are no effective drugs for controlling the disease. A bicistronic baculovirus expression system was utilized to co-express CHIKV structural proteins C (capsid), E2 and E1 and the enhanced green fluorescence protein (EGFP) in Spodoptera frugiperda insect cells (Sf21). The EGFP-positive Sf21 cells fused with each other and with uninfected cells to form a syncytium is mediated by the CHIKV E1 allowing it to identify chemicals that can prevent syncytium formation. The compounds characterized by this method could be anti-CHIKV drugs.
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Affiliation(s)
- Szu-Cheng Kuo
- Institute of Prevention Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Chao-Yi Teng
- Bioengineering Group, Institute of Biologics, Development Center for Biotechnology, New Taipei, Taiwan
| | - Yi-Jung Ho
- Institute of Prevention Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Ying-Ju Chen
- Bioengineering Group, Institute of Biologics, Development Center for Biotechnology, New Taipei, Taiwan
| | - Tzong-Yuan Wu
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan.
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Chung YC, Hsieh FC, Lin YJ, Wu TY, Lin CW, Lin CT, Tang NY, Jinn TR. Magnesium lithospermate B and rosmarinic acid, two compounds present in Salvia miltiorrhiza, have potent antiviral activity against enterovirus 71 infections. Eur J Pharmacol 2015; 755:127-33. [PMID: 25773498 DOI: 10.1016/j.ejphar.2015.02.046] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 02/23/2015] [Accepted: 02/26/2015] [Indexed: 12/15/2022]
Abstract
The aim of this study was to identify the active ingredients responsible for the anti-EV71 activity produced by Salvia miltiorrhiza extracts. A pGS-EV71 IRES-based bicistronic reporter assay platform was used for rapid analysis of compounds that could specifically inhibit EV71 viral IRES-mediated translation. The analysis identified 2 caffeic acid derivatives, magnesium lithospermate B (MLB) and rosmarinic acid (RA), which suppressed EV71 IRES-mediated translation at concentrations of 30μg/ml. We also found that MLB and RA inhibited EV71 infection when they were added to RD cells during the viral absorption stage. MLB had a low IC50 value of 0.09mM and a high TI value of 10.52. In contrast, RA had an IC50 value of 0.50mM with a TI value of 2.97. MLB and RA (100µg/ml) also reduced EV71 viral particle production and significantly decreased VP1 protein production. We propose that these two derivatives inhibit EV71 viral entry into cells and viral IRES activity, thereby reducing viral particle production and viral RNA expression and blocking viral VP1 protein translation. This study provides useful information for the development of anti-EV71 assays and reagents by demonstrating a convenient EV71 IRES-based bicistronic assay platform to screen for anti-EV71 IRES activity, and also reports 2 compounds, MLB and RA, which are responsible for the anti-EV71 activity of S. miltiorrhiza.
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Affiliation(s)
- Yi-Ching Chung
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan, ROC
| | - Feng-Chia Hsieh
- Biopesticide Department, Agricultural Chemicals and Toxic Substances Research Institute, Taichung 41300, Taiwan, ROC
| | - Ying-Ju Lin
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan, ROC
| | - Tzong-Yuan Wu
- Department of Science Technology, Chung Yuan Christian University, Chung Li 32023, Taiwan, ROC
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan, ROC
| | - Ching-Ting Lin
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan, ROC
| | - Nou-Ying Tang
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan, ROC
| | - Tzyy-Rong Jinn
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan, ROC.
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Renaud-Gabardos E, Hantelys F, Morfoisse F, Chaufour X, Garmy-Susini B, Prats AC. Internal ribosome entry site-based vectors for combined gene therapy. World J Exp Med 2015; 5:11-20. [PMID: 25699230 PMCID: PMC4308528 DOI: 10.5493/wjem.v5.i1.11] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 11/25/2014] [Accepted: 12/19/2014] [Indexed: 02/06/2023] Open
Abstract
Gene therapy appears as a promising strategy to treat incurable diseases. In particular, combined gene therapy has shown improved therapeutic efficiency. Internal ribosome entry sites (IRESs), RNA elements naturally present in the 5’ untranslated regions of a few mRNAs, constitute a powerful tool to co-express several genes of interest. IRESs are translational enhancers allowing the translational machinery to start protein synthesis by internal initiation. This feature allowed the design of multi-cistronic vectors expressing several genes from a single mRNA. IRESs exhibit tissue specificity, and drive translation in stress conditions when the global cell translation is blocked, which renders them useful for gene transfer in hypoxic conditions occurring in ischemic diseases and cancer. IRES-based viral and non viral vectors have been used successfully in preclinical and clinical assays of combined gene therapy and resulted in therapeutic benefits for various pathologies including cancers, cardiovascular diseases and degenerative diseases.
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Abstract
Hepatitis C virus (HCV) infection is a rapidly increasing global health problem with an estimated 170 million people infected worldwide. HCV is a hepatotropic, positive-sense RNA virus of the family Flaviviridae. As a positive-sense RNA virus, the HCV genome itself must serve as a template for translation, replication and packaging. The viral RNA must therefore be a dynamic structure that is able to readily accommodate structural changes to expose different regions of the genome to viral and cellular proteins to carry out the HCV life cycle. The ∼ 9600 nucleotide viral genome contains a single long open reading frame flanked by 5' and 3' non-coding regions that contain cis-acting RNA elements important for viral translation, replication and stability. Additional cis-acting RNA elements have also been identified in the coding sequences as well as in the 3' end of the negative-strand replicative intermediate. Herein, we provide an overview of the importance of these cis-acting RNA elements in the HCV life cycle.
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Affiliation(s)
- Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Jasmin Chahal
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Peter Sarnow
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States.
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Cheng X, Gao XC, Wang JP, Yang XY, Wang Y, Li BS, Kang FB, Li HJ, Nan YM, Sun DX. Tricistronic hepatitis C virus subgenomic replicon expressing double transgenes. World J Gastroenterol 2014; 20:18284-18295. [PMID: 25561795 PMCID: PMC4277965 DOI: 10.3748/wjg.v20.i48.18284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 08/28/2014] [Accepted: 10/15/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To construct a tricistronic hepatitis C virus (HCV) replicon with double internal ribosome entry sites (IRESes) of only 22 nucleotides for each, substituting the encephalomyocarditis virus (EMCV) IRESes, which are most often used as the translation initiation element to form HCV replicons.
METHODS: The alternative 22-nucleotide IRES, RNA-binding motif protein 3 IRES (Rbm3 IRES), was used to form a tricistronic HCV replicon, to facilitate constructing HCV-harboring stable cell lines and successive antiviral screening using a luciferase marker. Briefly, two sequential Rbm3 IRESes were inserted into bicistronic pUC19-HCV plasmid, consequently forming a tricistronic HCV replicon (pHCV-rep-NeoR-hRluc), initiating the translation of humanized Renilla luciferase and HCV non-structural gene, along with HCV authentic IRES initiating the translation of neomycin resistance gene. The sH7 cell lines, in which the novel replicon RNA stably replicated, were constructed by neomycin and luciferase activity screening. The intracellular HCV replicon RNA, expression of inserted foreign genes and HCV non-structural gene, as well as response to anti-HCV agents, were measured in sH7 cells and cells transiently transfected with tricistronic replicon RNA.
RESULTS: The intracellular HCV replicon RNA and expression of inserted foreign genes and HCV non-structural gene in sH7 cells and cells transiently transfected with tricistronic replicon RNA were comparable to those in cells stably or transiently transfected with traditional bicistronic HCV replicons. The average relative light unit in pHCV-rep-NeoR-hRluc group was approximately 2-fold of those in the pUC19-HCV-hRLuc and Tri-JFH1 groups (1.049 × 108± 2.747 × 107vs 5.368 × 107± 1.016 × 107, P < 0.05; 1.049 × 108± 2.747 × 107vs 5.243 × 107± 1.194 × 107, P < 0.05), suggesting that the translation initiation efficiency of the first Rbm3 IRES in the two sequential IRESes was stronger than the HCV authentic IRES and EMCV IRES. The fold changes of 72 h/4 h relative light units in the pHCV-rep-NeoR-hRluc and pUC19-HCV-hRLuc groups were similar (159.619 ± 9.083 vs 163.536 ± 24.031, P = 0.7707), and were both higher than the fold change in the Tri-JFH1 group 159.619± 9.083 vs 140.811 ± 9.882, P < 0.05; 163.536 ± 24.031 vs 140.811 ± 9.882, P < 0.05), suggesting that the replication potency of the Rbm3 IRES tricistronic replicon matched the replication of bicistronic replicon and exceeded the potency of EMCV IRES replicon. Replication of tricistronic replicons was suppressed by ribavirin, simvastatin, atorvastatin, telaprevir and boceprevir. Interferon-alpha 2b could not block replication of the novel replicon RNA in sH7 cells. After interferon stimulation, MxA mRNA and protein levels were lower in sH7 than in parental cells.
CONCLUSION: Tricistronic HCV replicon with double Rbm3 IRESes could be applied to evaluate the replication inhibition efficacy of anti-HCV agents.
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Romero-López C, Berzal-Herranz A. Structure-function relationship in viral RNA genomes: The case of hepatitis C virus. World J Med Genet 2014; 4:6-18. [DOI: 10.5496/wjmg.v4.i2.6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/23/2014] [Accepted: 04/03/2014] [Indexed: 02/06/2023] Open
Abstract
The acquisition of a storage information system beyond the nucleotide sequence has been a crucial issue for the propagation and dispersion of RNA viruses. This system is composed by highly conserved, complex structural units in the genomic RNA, termed functional RNA domains. These elements interact with other regions of the viral genome and/or proteins to direct viral translation, replication and encapsidation. The genomic RNA of the hepatitis C virus (HCV) is a good model for investigating about conserved structural units. It contains functional domains, defined by highly conserved structural RNA motifs, mostly located in the 5’-untranslatable regions (5’UTRs) and 3’UTR, but also occupying long stretches of the coding sequence. Viral translation initiation is mediated by an internal ribosome entry site located at the 5’ terminus of the viral genome and regulated by distal functional RNA domains placed at the 3’ end. Subsequent RNA replication strongly depends on the 3’UTR folding and is also influenced by the 5’ end of the HCV RNA. Further increase in the genome copy number unleashes the formation of homodimers by direct interaction of two genomic RNA molecules, which are finally packed and released to the extracellular medium. All these processes, as well as transitions between them, are controlled by structural RNA elements that establish a complex, direct and long-distance RNA-RNA interaction network. This review summarizes current knowledge about functional RNA domains within the HCV RNA genome and provides an overview of the control exerted by direct, long-range RNA-RNA contacts for the execution of the viral cycle.
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Chan SW. Establishment of chronic hepatitis C virus infection: Translational evasion of oxidative defence. World J Gastroenterol 2014; 20:2785-2800. [PMID: 24659872 PMCID: PMC3961964 DOI: 10.3748/wjg.v20.i11.2785] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/03/2013] [Accepted: 01/15/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) causes a clinically important disease affecting 3% of the world population. HCV is a single-stranded, positive-sense RNA virus belonging to the genus Hepacivirus within the Flaviviridae family. The virus establishes a chronic infection in the face of an active host oxidative defence, thus adaptation to oxidative stress is key to virus survival. Being a small RNA virus with a limited genomic capacity, we speculate that HCV deploys a different strategy to evade host oxidative defence. Instead of counteracting oxidative stress, it utilizes oxidative stress to facilitate its own survival. Translation is the first step in the replication of a plus strand RNA virus so it would make sense if the virus can exploit the host oxidative defence in facilitating this very first step. This is particularly true when HCV utilizes an internal ribosome entry site element in translation, which is distinctive from that of cap-dependent translation of the vast majority of cellular genes, thus allowing selective translation of genes under conditions when global protein synthesis is compromised. Indeed, we were the first to show that HCV translation was stimulated by an important pro-oxidant-hydrogen peroxide in hepatocytes, suggesting that HCV is able to adapt to and utilize the host anti-viral response to facilitate its own translation thus allowing the virus to thrive under oxidative stress condition to establish chronicity. Understanding how HCV translation is regulated under oxidative stress condition will advance our knowledge on how HCV establishes chronicity. As chronicity is the initiator step in disease progression this will eventually lead to a better understanding of pathogenicity, which is particularly relevant to the development of anti-virals and improved treatments of HCV patients using anti-oxidants.
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