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Geng G, Yu C, Yuan X. Variable eIF4E-binding sites and their synergistic effect on cap-independent translation in a novel IRES of wheat yellow mosaic virus RNA2 isolates. Int J Biol Macromol 2024; 254:128062. [PMID: 37967597 DOI: 10.1016/j.ijbiomac.2023.128062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
Some viral proteins are translated cap-independently via the internal ribosome entry site (IRES), which maintains conservative characteristic among different isolates of the same virus species. However, IRES activity showed a 7-fold variance in RNA2 of wheat yellow mosaic virus (WYMV) HC and LYJN isolates in this study. Based on RNA structure probing and mutagenesis assay, the loosened middle stem of H1 and the hepta-nucleotide top loop of H2 in the LYJN isolate synergistically ensured higher IRES activity than that in the HC isolate. In addition, the conserved top loop of H1 ensured basic IRES activity in HC and LYJN isolates. WYMV RNA2 5'-UTR specifically interacted with the wheat eIF4E, accomplished by the top loop of H1 in the HC isolate or the top loop of H1 and H2 in the LYJN isolate. The high IRES activity of the WYMV RNA2 LYJN isolate was regulated by two eIF4E-binding sites, which showed a synergistic effect mediated by the proximity of the H1 and H2 top loops owing to the flexibility of the middle stem in H1. This report presents a novel evolution pattern of IRES, which altered the number of eIF4E-binding sites to regulate IRES activity.
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Affiliation(s)
- Guowei Geng
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Shandong Province Key Laboratory of Agricultural Microbiology, Tai'an 271018, PR China
| | - Chengming Yu
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Shandong Province Key Laboratory of Agricultural Microbiology, Tai'an 271018, PR China
| | - Xuefeng Yuan
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Shandong Province Key Laboratory of Agricultural Microbiology, Tai'an 271018, PR China.
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Exploration of wheat yellow mosaic virus-responsive miRNAs and their targets in wheat by miRNA and degradome sequencing. J Biosci 2021. [DOI: 10.1007/s12038-021-00207-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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3
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Semkum P, Kaewborisuth C, Thangthamniyom N, Theerawatanasirikul S, Lekcharoensuk C, Hansoongnern P, Ramasoota P, Lekcharoensuk P. A Novel Plasmid DNA-Based Foot and Mouth Disease Virus Minigenome for Intracytoplasmic mRNA Production. Viruses 2021; 13:1047. [PMID: 34205958 PMCID: PMC8229761 DOI: 10.3390/v13061047] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022] Open
Abstract
Picornaviruses are non-enveloped, single-stranded RNA viruses that cause highly contagious diseases, such as polio and hand, foot-and-mouth disease (HFMD) in human, and foot-and-mouth disease (FMD) in animals. Reverse genetics and minigenome of picornaviruses mainly depend on in vitro transcription and RNA transfection; however, this approach is inefficient due to the rapid degradation of RNA template. Although DNA-based reverse genetics systems driven by mammalian RNA polymerase I and/or II promoters display the advantage of rescuing the engineered FMDV, the enzymatic functions are restricted in the nuclear compartment. To overcome these limitations, we successfully established a novel DNA-based vector, namely pKLS3, an FMDV minigenome containing the minimum cis-acting elements of FMDV essential for intracytoplasmic transcription and translation of a foreign gene. A combination of pKLS3 minigenome and the helper plasmids yielded the efficient production of uncapped-green florescent protein (GFP) mRNA visualized in the transfected cells. We have demonstrated the application of the pKLS3 for cell-based antiviral drug screening. Not only is the DNA-based FMDV minigenome system useful for the FMDV research and development but it could be implemented for generating other picornavirus minigenomes. Additionally, the prospective applications of this viral minigenome system as a vector for DNA and mRNA vaccines are also discussed.
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Affiliation(s)
- Ploypailin Semkum
- Interdisciplinary Graduate Program in Genetic Engineering, The Graduate School, Kasetsart University, Bangkok 10900, Thailand;
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.H.)
- Center for Advanced Studies in Agriculture and Food, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
| | - Challika Kaewborisuth
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Nattarat Thangthamniyom
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.H.)
| | - Sirin Theerawatanasirikul
- Department of Anatomy, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
| | - Chalermpol Lekcharoensuk
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
| | - Payuda Hansoongnern
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.H.)
| | - Pongrama Ramasoota
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Porntippa Lekcharoensuk
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (N.T.); (P.H.)
- Center for Advanced Studies in Agriculture and Food, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
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Construction and biological characterization of an infectious full-length cDNA clone of a Chinese isolate of Wheat yellow mosaic virus. Virology 2021; 556:101-109. [PMID: 33561697 DOI: 10.1016/j.virol.2021.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/22/2022]
Abstract
Wheat yellow mosaic virus (family Potyviridae; genus Bymovirus), is an important soil-borne virus that causes serious economic losses in wheat. In this study, we constructed infectious cDNA clones of WYMV genomic RNAs under the control of 35S or SP6 promoter for versatile usage (agroinfiltration or in vitro RNA transcription). Our results showed that an Agrobacterium-mediated inoculation system enabled WYMV to infect the leaves of Nicotiana benthamiana without causing WYMV systemic infection. However, in vitro transcripts from infectious cDNA clones using the SP6 promoter promoted WYMV systemic infection of wheat plants, which was then developed for further assays. The optimal temperature for virus multiplication and systemic infection of wheat was 8 °C. Additionally, a synergistic effect between WYMV and Chinese wheat mosaic virus (CWMV) was also detected. This is the first report of the construction of a Chinese isolate of WYMV and should facilitate the investigation of viral pathogenesis.
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Altmäe S, Molina NM, Sola-Leyva A. Omission of non-poly(A) viral transcripts from the tissue level atlas of the healthy human virome. BMC Biol 2020; 18:179. [PMID: 33239005 PMCID: PMC7690156 DOI: 10.1186/s12915-020-00907-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022] Open
Abstract
A recent paper in BMC Biology entitled “A tissue level atlas of the healthy human virome” by Kumata et al. describes a meta-transcriptomic analysis of RNA-sequencing datasets from the Genotype-Tissue Expression (GTEx) Project. Using a workflow that maps the GTEx sequences to the human genome, then screens unmapped sequences to detect viral transcripts, the authors present a quantitative analysis of the presence of different viruses in the non-diseased tissues of over 500 individuals and assess the impact of these viruses on host gene expression. Here we draw attention to an issue not acknowledged in this study. Namely, by relying solely on GTEx datasets, which are enriched for transcripts with poly(A) tails, the analysis will have missed non-poly(A) viral transcripts, rendering this tissue level atlas of the virome incomplete. A commentary on Kumata et al. (BMC Biol 18:55, 2020).
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Affiliation(s)
- Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071, Granada, Spain. .,Instituto de Investigación Biosanitaria ibs.GRANADA, 18014, Granada, Spain. .,Competence Centre on Health Technologies, 50411, Tartu, Estonia.
| | - Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071, Granada, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, 18014, Granada, Spain
| | - Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071, Granada, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, 18014, Granada, Spain
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