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Kumar S, Verma R, Saha S, Agrahari AK, Shukla S, Singh ON, Berry U, Anurag, Maiti TK, Asthana S, Ranjith-Kumar CT, Surjit M. RNA-Protein Interactome at the Hepatitis E Virus Internal Ribosome Entry Site. Microbiol Spectr 2023; 11:e0282722. [PMID: 37382527 PMCID: PMC10434006 DOI: 10.1128/spectrum.02827-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/11/2023] [Indexed: 06/30/2023] Open
Abstract
Multiple processes exist in a cell to ensure continuous production of essential proteins either through cap-dependent or cap-independent translation processes. Viruses depend on the host translation machinery for viral protein synthesis. Therefore, viruses have evolved clever strategies to use the host translation machinery. Earlier studies have shown that genotype 1 hepatitis E virus (g1-HEV) uses both cap-dependent and cap-independent translation machineries for its translation and proliferation. Cap-independent translation in g1-HEV is driven by an 87-nucleotide-long RNA element that acts as a noncanonical, internal ribosome entry site-like (IRESl) element. Here, we have identified the RNA-protein interactome of the HEV IRESl element and characterized the functional significance of some of its components. Our study identifies the association of HEV IRESl with several host ribosomal proteins, demonstrates indispensable roles of ribosomal protein RPL5 and DHX9 (RNA helicase A) in mediating HEV IRESl activity, and establishes the latter as a bona fide internal translation initiation site. IMPORTANCE Protein synthesis is a fundamental process for survival and proliferation of all living organisms. The majority of cellular proteins are produced through cap-dependent translation. Cells also use a variety of cap-independent translation processes to synthesize essential proteins during stress. Viruses depend on the host cell translation machinery to synthesize their own proteins. Hepatitis E virus (HEV) is a major cause of hepatitis worldwide and has a capped positive-strand RNA genome. Viral nonstructural and structural proteins are synthesized through a cap-dependent translation process. An earlier study from our laboratory reported the presence of a fourth open reading frame (ORF) in genotype 1 HEV, which produces the ORF4 protein using a cap-independent internal ribosome entry site-like (IRESl) element. In the current study, we identified the host proteins that associate with the HEV-IRESl RNA and generated the RNA-protein interactome. Through a variety of experimental approaches, our data prove that HEV-IRESl is a bona fide internal translation initiation site.
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Affiliation(s)
- Shiv Kumar
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Rohit Verma
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Sandhini Saha
- Laboratory of Functional Proteomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Ashish Kumar Agrahari
- Noncommunicable Disease Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Shivangi Shukla
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Oinam Ningthemmani Singh
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Umang Berry
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Anurag
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Tushar Kanti Maiti
- Laboratory of Functional Proteomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Shailendra Asthana
- Noncommunicable Disease Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - C. T. Ranjith-Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Milan Surjit
- Virology Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
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Shi B, Song Q, Luo X, Song J, Xia D, Xia Z, Liu M, Wang W, Wang R, Du H, Wei Q, Han J. Identification of an IRES within the coding region of the structural protein of human rhinovirus 16. J Med Virol 2021; 94:2653-2661. [PMID: 34873729 DOI: 10.1002/jmv.27507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/13/2021] [Accepted: 12/02/2021] [Indexed: 11/07/2022]
Abstract
As an alternative mechanism for cap-dependent (m7GpppN) translation, internal ribosome entry site (IRES)-dependent translation has been observed in the 5' untranslated regions (5' UTR) and coding regions of a number of viral and eukaryotic mRNAs. In this study, a series of 5' terminal truncated structural protein genes that were fused with GFP was used to screen for potential IRESs, and IRESs were identified using a bicistronic luciferase vector or GFP expression vector possessing a hairpin structure. Our results revealed that a putative IRES was located between nt 1982 and 2281 in the VP3 coding region of the human rhinovirus 16 (HRV16) genomes. We also demonstrated that effective IRES-initiated protein expression in vitro did not occur through splicing sites or cryptic promoters. We confirmed that thapsigargin (TG), an inducer of endoplasmic reticulum stress (ERS), facilitated increased IRES activity in a dose-dependent manner. Additionally, the secondary structure of the IRES was predicted online using the RNAfold web server.
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Affiliation(s)
- Bingtian Shi
- Center for Viral Resource, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Qinqin Song
- Center for Viral Resource, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xiaonuan Luo
- Department of Pathology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, Guangdong, China
| | - Juan Song
- Center for Viral Resource, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Dong Xia
- Center for Viral Resource, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Zhiqiang Xia
- Center for Viral Resource, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Mi Liu
- Center for Viral Resource, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Wenjun Wang
- Center for Viral Resource, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Ruifang Wang
- Center for Viral Resource, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Haijun Du
- Center for Viral Resource, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Qiang Wei
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Han
- Center for Viral Resource, State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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