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Kim J. Circular RNAs: Novel Players in Cancer Mechanisms and Therapeutic Strategies. Int J Mol Sci 2024; 25:10121. [PMID: 39337606 PMCID: PMC11432211 DOI: 10.3390/ijms251810121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 09/19/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that have emerged as pivotal players in gene regulation. Our understanding of circRNAs has greatly expanded over the last decade, with studies elucidating their biology and exploring their therapeutic applications. In this review, we provide an overview of the current understanding of circRNA biogenesis, outline their mechanisms of action in cancer, and assess their clinical potential as biomarkers. Furthermore, we discuss circRNAs as a potential therapeutic strategy, including recent advances in circRNA production and translation, along with proof-of-concept preclinical studies of cancer vaccines.
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Affiliation(s)
- Jimi Kim
- Department of Life Sciences, Gachon University, Seongnam 13120, Republic of Korea;
- Department of Health Science and Technology, GAIHST, Lee Gil Ya Cancer and Diabetes Institute, Incheon 21999, Republic of Korea
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2
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Xu C, Jiang Y, Wang M, Cheng A, Zhang W, Ou X, Sun D, Yang Q, Wu Y, Tian B, He Y, Wu Z, Zhang S, Zhao X, Huang J, Zhu D, Chen S, Liu M, Jia R. Duck hepatitis A virus utilizes PCBP2 to facilitate viral translation and replication. Vet Res 2024; 55:110. [PMID: 39300570 PMCID: PMC11414061 DOI: 10.1186/s13567-024-01369-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 08/07/2024] [Indexed: 09/22/2024] Open
Abstract
Duck hepatitis A virus type 1 (DHAV-1) is an important member of the Picornaviridae family that causes highly fatal hepatitis in ducklings. Since picornaviruses have small genomes with limited coding capacity, they must utilize host proteins for viral cap-independent translation and RNA replication. Here, we report the role of duck poly(rC)-binding protein 2 (PCBP2) in regulating the replication and translation of DHAV-1. During DHAV-1 infection, PCBP2 expression was upregulated. A biotinylated RNA pull-down assay revealed that PCBP2 positively regulates DHAV-1 translation through specific interactions with structural domains II and III of the DHAV-1 internal ribosome entry site (IRES). Further studies revealed that PCBP2 promotes DHAV-1 replication via an interaction of its KH1 domain (aa 1-92) with DHAV-1 3Dpol. Thus, our studies demonstrated the specific role of PCBP2 in regulating DHAV-1 translation and replication, revealing a novel mechanism by which host‒virus interactions regulate viral translation and replication. These findings contribute to further understanding of the pathogenesis of picornavirus infections.
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Affiliation(s)
- Chenxia Xu
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yurui Jiang
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingshu Wang
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Anchun Cheng
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China.
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China.
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China.
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Wei Zhang
- Sinopharm Yangzhou VAC Biological Engineering Co., Ltd., Yangzhou, 225100, China
| | - Xumin Ou
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Di Sun
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiao Yang
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ying Wu
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bin Tian
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu He
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhen Wu
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shaqiu Zhang
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinxin Zhao
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Juan Huang
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dekang Zhu
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shun Chen
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mafeng Liu
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Renyong Jia
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, 611130, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
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3
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Triller J, Prots I, Jäck HM, Wittmann J. An Enhanced Retroviral Vector for Efficient Genetic Manipulation and Selection in Mammalian Cells. Biomolecules 2024; 14:1131. [PMID: 39334897 PMCID: PMC11430422 DOI: 10.3390/biom14091131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/22/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024] Open
Abstract
Introducing genetic material into hard-to-transfect mammalian cell lines and primary cells is often best achieved through retroviral infection. An ideal retroviral vector should offer a compact, selectable, and screenable marker while maximizing transgene delivery capacity. However, a previously published retroviral vector featuring an EGFP/Puromycin fusion protein failed to meet these criteria in our experiments. We encountered issues such as low infection efficiency, weak EGFP fluorescence, and selection against infected cells. To address these shortcomings, we developed a novel retroviral vector based on the Moloney murine leukemia virus. This vector includes a compact bifunctional EGFP and Puromycin resistance cassette connected by a 2A peptide. Our extensively tested vector demonstrated superior EGFP expression, efficient Puromycin selection, and no growth penalty in infected cells compared with the earlier design. These benefits were consistent across multiple mammalian cell types, underscoring the versatility of our vector. In summary, our enhanced retroviral vector offers a robust solution for efficient infection, reliable detection, and effective selection in mammalian cells. Its improved performance and compact design make it an ideal choice for a wide range of applications involving precise genetic manipulation and characterization in cell-based studies.
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Affiliation(s)
- Jana Triller
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center of Molecular Medicine (NFZ), Friedrich-Alexander-Universität Erlangen-Nürnberg, Glückstraße 6, D-91054 Erlangen, Germany
| | - Iryna Prots
- Department of Operative Dentistry and Periodontology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Glückstraße 11, D-91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center of Molecular Medicine (NFZ), Friedrich-Alexander-Universität Erlangen-Nürnberg, Glückstraße 6, D-91054 Erlangen, Germany
| | - Jürgen Wittmann
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center of Molecular Medicine (NFZ), Friedrich-Alexander-Universität Erlangen-Nürnberg, Glückstraße 6, D-91054 Erlangen, Germany
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4
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Whittaker A, Goss DJ. Modeling the structure and DAP5-binding site of the FGF-9 5'-UTR RNA utilized in cap-independent translation. RNA (NEW YORK, N.Y.) 2024; 30:1184-1198. [PMID: 38866431 PMCID: PMC11331406 DOI: 10.1261/rna.080013.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024]
Abstract
Cap-independent or eukaryotic initiation factor (eIF) 4E-independent, translation initiation in eukaryotes requires scaffolding protein eIF4G or its homolog, death-associated protein 5 (DAP5). eIF4G associates with the 40S ribosomal subunit, recruiting the ribosome to the RNA transcript. A subset of RNA transcripts, such as fibroblast growth factor 9 (FGF-9), contain 5' untranslated regions (5' UTRs) that directly bind DAP5 or eIF4GI. For viral mRNA, eIF recruitment usually utilizes RNA structure, such as a pseudoknot or stem-loops, and the RNA-helicase eIF4A is required for DAP5- or 4G-mediated translation, suggesting these 5' UTRs are structured. However, for cellular IRES-like translation, no consensus RNA structures or sequences have yet been identified for eIF binding. However, the DAP5-binding site within the FGF-9 5' UTR is unknown. Moreover, DAP5 binds to other, dissimilar 5' UTRs, some of which require an unpaired, accessible 5' end to stimulate cap-independent translation. Using SHAPE-seq, we modeled the 186 nt FGF-9 5'-UTR RNA's complex secondary structure in vitro. Further, DAP5 footprinting, toeprinting, and UV cross-linking experiments identify DAP5-RNA interactions. Modeling of FGF-9 5'-UTR tertiary structure aligns DAP5-interacting nucleotides on one face of the predicted structure. We propose that RNA structure involving tertiary folding, rather than a conserved sequence or secondary structure, acts as a DAP5-binding site. DAP5 appears to contact nucleotides near the start codon. Our findings offer a new perspective in the hunt for cap-independent translational enhancers. Structural, rather than sequence-specific, eIF-binding sites may act as attractive chemotherapeutic targets or as dosage tools for mRNA-based therapies.
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Affiliation(s)
- Amanda Whittaker
- PhD Program in Biochemistry, The Graduate Center, CUNY, New York, New York 10016, USA
- Department of Chemistry, Hunter College, CUNY, New York, New York 10065, USA
| | - Dixie J Goss
- PhD Program in Biochemistry, The Graduate Center, CUNY, New York, New York 10016, USA
- Department of Chemistry, Hunter College, CUNY, New York, New York 10065, USA
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5
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Landa CR, Ariza-Mateos A, Briones C, Perales C, Wagner A, Domingo E, Gómez J. Adapting the rhizome concept to an extended definition of viral quasispecies and the implications for molecular evolution. Sci Rep 2024; 14:17914. [PMID: 39095425 PMCID: PMC11297277 DOI: 10.1038/s41598-024-68760-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from "symbiotic" relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain.
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Affiliation(s)
- Carlos Raico Landa
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Avd. Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Ascensión Ariza-Mateos
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Avd. Conocimiento 17, 18016, Armilla, Granada, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Celia Perales
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain
| | | | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Jordi Gómez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Avd. Conocimiento 17, 18016, Armilla, Granada, Spain.
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Duenas MA, Craig RJ, Gallaher SD, Moseley JL, Merchant SS. Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.605010. [PMID: 39091764 PMCID: PMC11291117 DOI: 10.1101/2024.07.24.605010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Advances in sequencing technology have unveiled examples of nucleus-encoded polycistronic genes, once considered rare. Exclusively polycistronic transcripts are prevalent in green algae, although the mechanism by which multiple polypeptides are translated from a single transcript is unknown. Here, we used bioinformatic and in vivo mutational analyses to evaluate competing mechanistic models for polycistronic expression in green algae. High-confidence manually curated datasets of bicistronic loci from two divergent green algae, Chlamydomonas reinhardtii and Auxenochlorella protothecoides, revealed 1) a preference for weak Kozak-like sequences for ORF 1 and 2) an underrepresentation of potential initiation codons before ORF 2, which are suitable conditions for leaky scanning to allow ORF 2 translation. We used mutational analysis in Auxenochlorella protothecoides to test the mechanism. In vivo manipulation of the ORF 1 Kozak-like sequence and start codon altered reporter expression at ORF 2, with a weaker Kozak-like sequence enhancing expression and a stronger one diminishing it. A synthetic bicistronic dual reporter demonstrated inversely adjustable activity of green fluorescent protein expressed from ORF 1 and luciferase from ORF 2, depending on the strength of the ORF 1 Kozak-like sequence. Our findings demonstrate that translation of multiple ORFs in green algal bicistronic transcripts is consistent with episodic leaky ribosome scanning of ORF 1 to allow translation at ORF 2. This work has implications for the potential functionality of upstream open reading frames found across eukaryotic genomes and for transgene expression in synthetic biology applications.
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Affiliation(s)
- Marco A. Duenas
- Department of Plant and Microbial Biology, University of California Berkeley, University of California, Berkeley, CA 94720, USA
| | - Rory J. Craig
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Sean D. Gallaher
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey L. Moseley
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Sabeeha S. Merchant
- Department of Plant and Microbial Biology, University of California Berkeley, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology and Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, CA, USA
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7
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Dehaen N, Van Hul M, Mignion L, Kouakou AN, Cani PD, Jordan BF. Luciferase transduction and selection protocol for reliable in vivo bioluminescent measurements in cancer research. Heliyon 2024; 10:e33356. [PMID: 39035528 PMCID: PMC11259842 DOI: 10.1016/j.heliyon.2024.e33356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/23/2024] Open
Abstract
Bioluminescence imaging has become an essential non-invasive tool in cancer research for monitoring various cellular processes and tumor progression in vivo. In this article, we aimed to propose a transduction and selection protocol for reliable in vivo bioluminescent measurements in immunocompetent mouse models. Using two different heterogenous luciferase-expressing cell models, we underlined factors influencing transduction. The protocol was tested through an in vitro luciferase activity assay as well as using in vivo longitudinal monitoring of metastases formation (In Vivo Imaging System®). The data were cross validated with histological assessment. Our results demonstrated stable and proportional in vitro and in vivo bioluminescent signals correlating with actual metastatic burden. Furthermore, ex vivo analysis confirmed the accuracy of bioluminescent imaging in quantifying metastatic surface area. This protocol should ensure reliable and reproducible measurements in cancer research utilizing luciferase-positive cell lines, confirming the validity and accuracy of preclinical studies in immunocompetent models.
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Affiliation(s)
- Natacha Dehaen
- Biomedical Magnetic Resonance group (REMA), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Metabolism and Nutrition Research Group (MNUT), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Matthias Van Hul
- Metabolism and Nutrition Research Group (MNUT), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), WELBIO department, WEL Research Institute, Wavre, Belgium
| | - Lionel Mignion
- Biomedical Magnetic Resonance group (REMA), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Nuclear and Electron Spin Technologies (NEST) Platform, Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Axell-Natalie Kouakou
- Biomedical Magnetic Resonance group (REMA), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Metabolism and Nutrition Research Group (MNUT), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Bioanalysis and Pharmacology of Bioactive Lipids (BPBL), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Patrice D. Cani
- Metabolism and Nutrition Research Group (MNUT), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), WELBIO department, WEL Research Institute, Wavre, Belgium
- Institute of Experimental and Clinical Research (IREC), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Bénédicte F. Jordan
- Biomedical Magnetic Resonance group (REMA), Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Nuclear and Electron Spin Technologies (NEST) Platform, Louvain Drug Research Institute (LDRI), UCLouvain, Université catholique de Louvain, Brussels, Belgium
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8
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Li Y, Zhang L, Wang L, Li J, Zhao Y, Liu F, Wang Q. Structure and function of type IV IRES in picornaviruses: a systematic review. Front Microbiol 2024; 15:1415698. [PMID: 38855772 PMCID: PMC11157119 DOI: 10.3389/fmicb.2024.1415698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
The Picornaviridae is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a core of RNA genome. A typical genome of picornavirus harbors a well-conserved and highly structured RNA element known as the internal ribosome entry site (IRES), functionally essential for viral replication and protein translation. Based on differences in their structures and mechanisms of action, picornaviral IRESs have been categorized into five types: type I, II, III, IV, and V. Compared with the type IV IRES, the others not only are structurally complicated, but also involve multiple initiation factors for triggering protein translation. The type IV IRES, often referred to as hepatitis C virus (HCV)-like IRES due to its structural resemblance to the HCV IRES, exhibits a simpler and more compact structure than those of the other four. The increasing identification of picornaviruses with the type IV IRES suggests that this IRES type seems to reveal strong retention and adaptation in terms of viral evolution. Here, we systematically reviewed structural features and biological functions of the type IV IRES in picornaviruses. A comprehensive understanding of the roles of type IV IRESs will contribute to elucidating the replication mechanism and pathogenesis of picornaviruses.
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Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- Qingdao Center for Animal Disease Control and Prevention, Qingdao, China
| | - Lei Zhang
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, China
| | - Jing Li
- Market Supervision Administration of Huangdao District, Qingdao, China
| | - Yanwei Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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9
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Schatz C, Knabl L, Lee HK, Seeboeck R, von Laer D, Lafon E, Borena W, Mangge H, Prüller F, Qerimi A, Wilflingseder D, Posch W, Haybaeck J. Machine Learning to Identify Critical Biomarker Profiles in New SARS-CoV-2 Variants. Microorganisms 2024; 12:798. [PMID: 38674742 PMCID: PMC11052335 DOI: 10.3390/microorganisms12040798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
The global dissemination of SARS-CoV-2 resulted in the emergence of several variants, including Alpha, Alpha + E484K, Beta, and Omicron. Our research integrated the study of eukaryotic translation factors and fundamental components in general protein synthesis with the analysis of SARS-CoV-2 variants and vaccination status. Utilizing statistical methods, we successfully differentiated between variants in infected individuals and, to a lesser extent, between vaccinated and non-vaccinated infected individuals, relying on the expression profiles of translation factors. Additionally, our investigation identified common causal relationships among the translation factors, shedding light on the interplay between SARS-CoV-2 variants and the host's translation machinery.
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Affiliation(s)
- Christoph Schatz
- Tyrolpath Obrist Brunhuber GmbH, 6311 Zams, Austria (L.K.)
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria;
| | - Ludwig Knabl
- Tyrolpath Obrist Brunhuber GmbH, 6311 Zams, Austria (L.K.)
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Rita Seeboeck
- Department Life Sciences, IMC University of Applied Sciences Krems, 3500 Krems, Austria;
- Clinical Institute of Pathology, University Hospital St. Poelten, Karl Landsteiner University of Health Science, 3100 St. Poelten, Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Peter-Mayr-Strasse 4b, 6020 Innsbruck, Austria (W.B.)
| | - Eliott Lafon
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria (D.W.); (W.P.)
| | - Wegene Borena
- Institute of Virology, Medical University of Innsbruck, Peter-Mayr-Strasse 4b, 6020 Innsbruck, Austria (W.B.)
| | - Harald Mangge
- Clinical Institute for Medical and Chemical Laboratory Diagnosis (CIMCL), Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Florian Prüller
- Clinical Institute for Medical and Chemical Laboratory Diagnosis (CIMCL), Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Adelina Qerimi
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria;
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria (D.W.); (W.P.)
- Department of Pathobiology, Infectiology, Veterinary University of Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria (D.W.); (W.P.)
| | - Johannes Haybaeck
- Department of Pathology, Saint Vincent Hospital Zams, 6511 Zams, Austria
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
- Department of Pathology, Laborteam, 9403 Goldach, Switzerland
- Department of Pathology, University Medical Centre Maribor, 2000 Maribor, Slovenia
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10
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Liu J, Liu L, Zeng S, Meng X, Lei N, Yang H, Li R, Mu X, Guo X. Inhibition of EV71 replication by an interferon-stimulated gene product L3HYPDH. Virus Res 2024; 342:199336. [PMID: 38342315 PMCID: PMC10875296 DOI: 10.1016/j.virusres.2024.199336] [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: 12/05/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/13/2024]
Abstract
Enterovirus 71 (EV71) is the common causative agent of hand-foot-mouth disease (HFMD). Despite evidence in mice model suggested that the interferon (IFN) signaling pathways play a role in defending against this virus, knowledge on the IFN-mediated antiviral response is still limited. Here we identified an IFN-stimulated gene (ISG) called L3HYPDH, whose expression inhibits EV71 replication. Mapping assay indicated that amino acids 61-120 and 295-354 are critical for its optimal antiviral activity. Mechanismly, L3HYPDH specifically inhibits protein translation mediated by EV71 internal ribosome entry site (IRES). Our data thus uncovered a new mechanism utilized by the host cell to restrict EV71 replication.
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Affiliation(s)
- Jian Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Logen Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Shinuan Zeng
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Xiaobin Meng
- Meizhou People's Hospital, Meizhou 514031, China
| | - Nanfeng Lei
- Meizhou People's Hospital, Meizhou 514031, China
| | - Hai Yang
- Meizhou People's Hospital, Meizhou 514031, China
| | - Runcai Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Xin Mu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin 300072, China.
| | - Xuemin Guo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China; Meizhou People's Hospital, Meizhou 514031, China; Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou 514031, China.
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11
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Yan J, Oyler-Castrillo P, Ravisankar P, Ward CC, Levesque S, Jing Y, Simpson D, Zhao A, Li H, Yan W, Goudy L, Schmidt R, Solley SC, Gilbert LA, Chan MM, Bauer DE, Marson A, Parsons LR, Adamson B. Improving prime editing with an endogenous small RNA-binding protein. Nature 2024; 628:639-647. [PMID: 38570691 PMCID: PMC11023932 DOI: 10.1038/s41586-024-07259-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3' ends of CRISPR-Cas guide RNAs1. To identify cellular determinants of prime editing, we developed scalable prime editing reporters and performed genome-scale CRISPR-interference screens. From these screens, a single factor emerged as the strongest mediator of prime editing: the small RNA-binding exonuclease protection factor La. Further investigation revealed that La promotes prime editing across approaches (PE2, PE3, PE4 and PE5), edit types (substitutions, insertions and deletions), endogenous loci and cell types but has no consistent effect on genome-editing approaches that rely on standard, unextended guide RNAs. Previous work has shown that La binds polyuridine tracts at the 3' ends of RNA polymerase III transcripts2. We found that La functionally interacts with the 3' ends of polyuridylated prime editing guide RNAs (pegRNAs). Guided by these results, we developed a prime editor protein (PE7) fused to the RNA-binding, N-terminal domain of La. This editor improved prime editing with expressed pegRNAs and engineered pegRNAs (epegRNAs), as well as with synthetic pegRNAs optimized for La binding. Together, our results provide key insights into how prime editing components interact with the cellular environment and suggest general strategies for stabilizing exogenous small RNAs therein.
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Affiliation(s)
- Jun Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Paul Oyler-Castrillo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Carl C Ward
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Sébastien Levesque
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yangwode Jing
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Danny Simpson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Anqi Zhao
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hui Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Weihao Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Laine Goudy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Sabrina C Solley
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Luke A Gilbert
- Arc Institute, Palo Alto, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Michelle M Chan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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12
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Wu J, Sun C, Guan J, Abdullah SW, Wang X, Ren M, Qiao L, Sun S, Guo H. Nuclear ribonucleoprotein RALY downregulates foot-and-mouth disease virus replication but antagonized by viral 3C protease. Microbiol Spectr 2024; 12:e0365823. [PMID: 38323828 PMCID: PMC10913732 DOI: 10.1128/spectrum.03658-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
The internal ribosome entry site (IRES) element constitutes a cis-acting RNA regulatory sequence that recruits the ribosomal initiation complex in a cap-independent manner, assisted by various RNA-binding proteins and IRES trans-acting factors. Foot-and-mouth disease virus (FMDV) contains a functional IRES element and takes advantage of this element to subvert host translation machinery. Our study identified a novel mechanism wherein RALY, a member of the heterogeneous nuclear ribonucleoproteins (hnRNP) family belonging to RNA-binding proteins, binds to the domain 3 of FMDV IRES via its RNA recognition motif residue. This interaction results in the downregulation of FMDV replication by inhibiting IRES-driven translation. Furthermore, our findings reveal that the inhibitory effect exerted by RALY on FMDV replication is not attributed to the FMDV IRES-mediated assembly of translation initiation complexes but rather to the impediment of 80S ribosome complex formation after binding with 40S ribosomes. Conversely, 3Cpro of FMDV counteracts RALY-mediated inhibition by the ubiquitin-proteasome pathway. Therefore, these results indicate that RALY, as a novel critical IRES-binding protein, inhibits FMDV replication by blocking the formation of 80S ribosome, providing a deeper understanding of how viruses recruit and manipulate host factors. IMPORTANCE The translation of FMDV genomic RNA driven by IRES element is a crucial step for virus infections. Many host proteins are hijacked to regulate FMDV IRES-dependent translation, but the regulatory mechanism remains unknown. Here, we report for the first time that cellular RALY specifically interacts with the IRES of FMDV and negatively regulates viral replication by blocking 80S ribosome assembly on FMDV IRES. Conversely, RALY-mediated inhibition is antagonized by the viral 3C protease by the ubiquitin-proteasome pathway. These results would facilitate further understanding of virus-host interactions and translational control during viral infection.
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Affiliation(s)
- Jin'en Wu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Chao Sun
- Division of Livestock Infectious Diseases, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Junyong Guan
- Division of Livestock Infectious Diseases, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Sahibzada Waheed Abdullah
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuefei Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mei Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Lu Qiao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shiqi Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huichen Guo
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
- School of Animal Science, Yangtze University, Jingzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
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13
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Shehata SI, Watkins JM, Burke JM, Parker R. Mechanisms and consequences of mRNA destabilization during viral infections. Virol J 2024; 21:38. [PMID: 38321453 PMCID: PMC10848536 DOI: 10.1186/s12985-024-02305-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
During viral infection there is dynamic interplay between the virus and the host to regulate gene expression. In many cases, the host induces the expression of antiviral genes to combat infection, while the virus uses "host shut-off" systems to better compete for cellular resources and to limit the induction of the host antiviral response. Viral mechanisms for host shut-off involve targeting translation, altering host RNA processing, and/or inducing the degradation of host mRNAs. In this review, we discuss the diverse mechanisms viruses use to degrade host mRNAs. In addition, the widespread degradation of host mRNAs can have common consequences including the accumulation of RNA binding proteins in the nucleus, which leads to altered RNA processing, mRNA export, and changes to transcription.
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Affiliation(s)
- Soraya I Shehata
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Monty Watkins
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
| | - James M Burke
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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14
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Ojha M, Vogt J, Das NK, Redmond E, Singh K, Banna HA, Sadat T, Koirala D. Structure of saguaro cactus virus 3' translational enhancer mimics 5' cap for eIF4E binding. Proc Natl Acad Sci U S A 2024; 121:e2313677121. [PMID: 38241435 PMCID: PMC10823258 DOI: 10.1073/pnas.2313677121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
The genomes of several plant viruses contain RNA structures at their 3' ends called cap-independent translation enhancers (CITEs) that bind the host protein factors such as mRNA 5' cap-binding protein eIF4E for promoting cap-independent genome translation. However, the structural basis of such 5' cap-binding protein recognition by the uncapped RNA remains largely unknown. Here, we have determined the crystal structure of a 3' CITE, panicum mosaic virus-like translation enhancer (PTE) from the saguaro cactus virus (SCV), using a Fab crystallization chaperone. The PTE RNA folds into a three-way junction architecture with a pseudoknot between the purine-rich R domain and pyrimidine-rich Y domain, which organizes the overall structure to protrude out a specific guanine nucleotide, G18, from the R domain that comprises a major interaction site for the eIF4E binding. The superimposable crystal structures of the wild-type, G18A, G18C, and G18U mutants suggest that the PTE scaffold is preorganized with the flipped-out G18 ready to dock into the eIF4E 5' cap-binding pocket. The binding studies with wheat and human eIF4Es using gel electrophoresis and isothermal titration calorimetry, and molecular docking computation for the PTE-eIF4E complex demonstrated that the PTE structure essentially mimics the mRNA 5' cap for eIF4E binding. Such 5' cap mimicry by the uncapped and structured viral RNA highlights how viruses can exploit RNA structures to mimic the host protein-binding partners and bypass the canonical mechanisms for their genome translation, providing opportunities for a better understanding of virus-host interactions and non-canonical translation mechanisms found in many pathogenic RNA viruses.
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Affiliation(s)
- Manju Ojha
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD21250
| | - Jeff Vogt
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD21250
| | - Naba Krishna Das
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD21250
| | - Emily Redmond
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD21250
| | - Karndeep Singh
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD21250
- HHMI, University of Maryland Baltimore County, Baltimore, MD21250
| | - Hasan Al Banna
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD21250
| | - Tasnia Sadat
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD21250
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD21250
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15
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Abram QH, Landry BN, Wang AB, Kothe RF, Hauch HC, Sagan SM. The myriad roles of RNA structure in the flavivirus life cycle. RNA Biol 2024; 21:14-30. [PMID: 38797925 PMCID: PMC11135854 DOI: 10.1080/15476286.2024.2357857] [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] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
As positive-sense RNA viruses, the genomes of flaviviruses serve as the template for all stages of the viral life cycle, including translation, replication, and infectious particle production. Yet, they encode just 10 proteins, suggesting that the structure and dynamics of the viral RNA itself helps shepherd the viral genome through these stages. Herein, we highlight advances in our understanding of flavivirus RNA structural elements through the lens of their impact on the viral life cycle. We highlight how RNA structures impact translation, the switch from translation to replication, negative- and positive-strand RNA synthesis, and virion assembly. Consequently, we describe three major themes regarding the roles of RNA structure in flavivirus infections: 1) providing a layer of specificity; 2) increasing the functional capacity; and 3) providing a mechanism to support genome compaction. While the interactions described herein are specific to flaviviruses, these themes appear to extend more broadly across RNA viruses.
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Affiliation(s)
- Quinn H. Abram
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Breanna N. Landry
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alex B. Wang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ronja F. Kothe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Hannah C.H. Hauch
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Selena M. Sagan
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
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16
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Abedeera SM, Davila-Calderon J, Haddad C, Henry B, King J, Penumutchu S, Tolbert BS. The Repurposing of Cellular Proteins during Enterovirus A71 Infection. Viruses 2023; 16:75. [PMID: 38257775 PMCID: PMC10821071 DOI: 10.3390/v16010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
Viruses pose a great threat to people's lives. Enterovirus A71 (EV-A71) infects children and infants all over the world with no FDA-approved treatment to date. Understanding the basic mechanisms of viral processes aids in selecting more efficient drug targets and designing more effective antivirals to thwart this virus. The 5'-untranslated region (5'-UTR) of the viral RNA genome is composed of a cloverleaf structure and an internal ribosome entry site (IRES). Cellular proteins that bind to the cloverleaf structure regulate viral RNA synthesis, while those that bind to the IRES also known as IRES trans-acting factors (ITAFs) regulate viral translation. In this review, we survey the cellular proteins currently known to bind the 5'-UTR and influence viral gene expression with emphasis on comparing proteins' functions and localizations pre- and post-(EV-A71) infection. A comprehensive understanding of how the host cell's machinery is hijacked and reprogrammed by the virus to facilitate its replication is crucial for developing effective antivirals.
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Affiliation(s)
- Sudeshi M. Abedeera
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Jesse Davila-Calderon
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Barrington Henry
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Josephine King
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA; (J.D.-C.); (C.H.); (J.K.)
| | - Srinivasa Penumutchu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
| | - Blanton S. Tolbert
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.M.A.); (B.H.); (S.P.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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17
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Truniger V, Pechar GS, Aranda MA. Advances in Understanding the Mechanism of Cap-Independent Cucurbit Aphid-Borne Yellows Virus Protein Synthesis. Int J Mol Sci 2023; 24:17598. [PMID: 38139425 PMCID: PMC10744285 DOI: 10.3390/ijms242417598] [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: 10/30/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Non-canonical translation mechanisms have been described for many viral RNAs. In the case of several plant viruses, their protein synthesis is controlled by RNA elements in their genomic 3'-ends that are able to enhance cap-independent translation (3'-CITE). The proposed general mechanism of 3'-CITEs includes their binding to eukaryotic translation initiation factors (eIFs) that reach the 5'-end and AUG start codon through 5'-3'-UTR-interactions. It was previously shown that cucurbit aphid-borne yellows virus (CABYV) has a 3'-CITE, which varies in sequence and structure depending on the phylogenetic group to which the isolate belongs, possibly as a result of adaptation to the different geographical regions. In this work, the cap-independent translation mechanisms of two CABYV 3'-CITEs belonging to the Mediterranean (CMTE) and Asian (CXTE) groups, respectively, were studied. In vivo cap-independent translation assays show that these 3'-CITEs require the presence of the CABYV short genomic 5'-UTR with at least 40% adenines in cis and an accessible 5'-end for its activity. Additionally, they suggest that the eIF4E-independent CABYV 3'-CITE activities may not require either eIF4A or the eIF4F complex, but may depend on eIF4G and PABP. By pulling down host proteins using RNA baits containing both 5'- and 3'-CABYV-UTRs, 80 RNA binding proteins were identified. These interacted preferentially with either CMTE, CXTE, or both. One of these proteins, specifically interacting with the RNA containing CMTE, was HSP70.2. Preliminary results suggested that HSP70.2 may be involved in CMTE- but not CXTE-mediated cap-independent translation activity.
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Affiliation(s)
- Verónica Truniger
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Murcia, Spain; (G.S.P.); (M.A.A.)
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18
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Boros Á, Pankovics P, László Z, Urbán P, Herczeg R, Gáspár G, Tóth F, Reuter G. The genomic and epidemiological investigations of enteric viruses of domestic caprine ( Capra hircus) revealed the presence of multiple novel viruses related to known strains of humans and ruminant livestock species. Microbiol Spectr 2023; 11:e0253323. [PMID: 37823638 PMCID: PMC10714811 DOI: 10.1128/spectrum.02533-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Compared with other domestic animals, the virome and viral diversity of small ruminants especially in caprine are less studied even of its zoonotic potential. In this study, the enteric virome of caprine was investigated in detail using next-generation sequencing and reverse transcription PCR techniques. The complete or nearly complete genomes of seven novel viruses were determined which show a close phylogenetic relationship to known human and ruminant viruses. The high similarity between the identified caprine tusavirus (family Parvoviridae) and an unassigned CRESS DNA virus with closely related human strains could indicate the (reverse) zoonotic potential of these viruses. Others, like astroviruses (family Astroviridae), enteroviruses, or novel caripiviruses (named after the term caprine picornavirus) of family Picornaviridae found mostly in multiple co-infections in caprine and ovine, could indicate the cross-species transmission capabilities of these viruses between small ruminants.
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Affiliation(s)
- Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Zoltán László
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | - Róbert Herczeg
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | - Gábor Gáspár
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Fruzsina Tóth
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
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19
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Gentry RC, Ide NA, Comunale VM, Hartwick EW, Kinz-Thompson CD, Gonzalez RL. The mechanism of mRNA activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567265. [PMID: 38014128 PMCID: PMC10680758 DOI: 10.1101/2023.11.15.567265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
During translation initiation, messenger RNA molecules must be identified and activated for loading into a ribosome. In this rate-limiting step, the heterotrimeric protein eukaryotic initiation factor eIF4F must recognize and productively interact with the 7-methylguanosine cap at the 5' end of the messenger RNA and subsequently activate the message. Despite its fundamental, regulatory role in gene expression, the molecular events underlying cap recognition and messenger RNA activation remain mysterious. Here, we generate a unique, single-molecule fluorescence imaging system to interrogate the dynamics with which eIF4F discriminates productive and non-productive locations on full-length, native messenger RNA molecules. At the single-molecule level, we observe stochastic sampling of eIF4F along the length of the messenger RNA and identify allosteric communication between the eIF4F subunits which ultimately drive cap-recognition and subsequent activation of the message. Our experiments uncover novel functions for each subunit of eIF4F and we conclude by presenting a model for messenger RNA activation which precisely defines the composition of the activated message. This model provides a general framework for understanding how messenger RNA molecules may be discriminated from one another, and how other RNA-binding proteins may control the efficiency of translation initiation.
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Affiliation(s)
- Riley C Gentry
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Nicholas A Ide
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | - Erik W Hartwick
- Department of Chemistry, Columbia University, New York, NY, USA
- Current Address: BioChemistry Krios Electron Microscopy Facility, Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Colin D Kinz-Thompson
- Department of Chemistry, Columbia University, New York, NY, USA
- Current Address: Department of Chemistry, Rutgers University-Newark, Newark, NJ 07102
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20
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Lee KH. Internal ribosomal entry site-mediated translational activity of nitric oxide synthase 2. Anim Cells Syst (Seoul) 2023; 27:321-328. [PMID: 38414531 PMCID: PMC10898816 DOI: 10.1080/19768354.2023.2275613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/22/2023] [Indexed: 02/29/2024] Open
Abstract
The internal ribosome entry site (IRES) is a unique structure found in the 5' untranslated region (5'-UTR) of specific messenger RNAs (mRNAs) that allows ribosomes to bind and initiate translation without the need for a cap structure. In this study, we investigated the presence and functional properties of the IRES activity of nitric oxide synthase 2 (NOS2) mRNA, which encodes an enzyme that produces nitric oxide in response to various stimuli such as inflammation. Nitric oxide is a signaling molecule that plays a crucial role in various physiological processes, including immune responses and neuronal signaling. Our results showed the existence of IRES activity in the 5'-UTR of Nos2 mRNA in various cell types. IRES-mediated translation of NOS2 mRNA was higher in neuronal cells and its activity increased in response to lipopolysaccharide (LPS). Despite inhibition of cap-dependent translation, nitrite production was partially maintained. These results demonstrate the presence of IRES activity in the 5'-UTR of NOS2 mRNA and suggest that IRES-mediated translation plays a key role in controlling nitric oxide production in response to LPS, an inflammatory stimulus.
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Affiliation(s)
- Kyung-Ha Lee
- Department of Molecular Biology, Pusan National University, Busan, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, Republic of Korea
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21
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Ariza-Mateos A, Briones C, Perales C, Bayo-Jiménez MT, Domingo E, Gómez J. Viruses as archaeological tools for uncovering ancient molecular relationships. Ann N Y Acad Sci 2023; 1529:3-13. [PMID: 37801367 DOI: 10.1111/nyas.15071] [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] [Indexed: 10/08/2023]
Abstract
The entry of a virus into the host cell always implies the alteration of certain intracellular molecular relationships, some of which may involve the recovery of ancient cellular activities. In this sense, viruses are archaeological tools for identifying unexpressed activities in noninfected cells. Among these, activities that hinder virus propagation may represent cellular defense mechanisms, for example, activities that mutagenize the viral genome such as ADAR-1 or APOBEC activities. Instead, those that facilitate virus propagation can be interpreted as the result of viral adaptation to-or mimicking-cellular structures, enabling the virus to perform anthropomorphic activities, including hijacking, manipulating, and reorganizing cellular factors for their own benefit. The alternative we consider here is that some of these second set of cellular activities were already in the uninfected cell but silenced, under the negative control of the cell or lineage, and that they represent a necessary precondition for viral infection. For example, specifically loading an amino acid at the 3'-end of the mRNA of some plant viruses by aminoacyl-tRNA synthetases has proved essential for virus infection despite this reaction not occurring with cellular mRNAs. Other activities of this type are discussed here, together with the biological context in which they acquire a coherent meaning, that is, genetic latency and molecular conflict.
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Affiliation(s)
- Ascensión Ariza-Mateos
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
| | - María Teresa Bayo-Jiménez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Jordi Gómez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
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22
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Fang JC, Liu MJ. Translation initiation at AUG and non-AUG triplets in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111822. [PMID: 37574140 DOI: 10.1016/j.plantsci.2023.111822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/22/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
In plants and other eukaryotes, precise selection of translation initiation site (TIS) on mRNAs shapes the proteome in response to cellular events or environmental cues. The canonical translation of mRNAs initiates at a 5' proximal AUG codon in a favorable context. However, the coding and non-coding regions of plant genomes contain numerous unannotated alternative AUG and non-AUG TISs. Determining how and why these unexpected and prevalent TISs are activated in plants has emerged as an exciting research area. In this review, we focus on the selection of plant TISs and highlight studies that revealed previously unannotated TISs used in vivo via comparative genomics and genome-wide profiling of ribosome positioning and protein N-terminal ends. The biological signatures of non-AUG TIS-initiated open reading frames (ORFs) in plants are also discussed. We describe what is understood about cis-regulatory RNA elements and trans-acting eukaryotic initiation factors (eIFs) in the site selection for translation initiation by featuring the findings in plants along with supporting findings in non-plant species. The prevalent, unannotated TISs provide a hidden reservoir of ORFs that likely help reshape plant proteomes in response to developmental or environmental cues. These findings underscore the importance of understanding the mechanistic basis of TIS selection to functionally annotate plant genomes, especially for crops with large genomes.
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Affiliation(s)
- Jhen-Cheng Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ming-Jung Liu
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan.
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23
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Sherlock ME, Langeberg CJ, Segar KE, Kieft JS. A conserved class of viral RNA structures regulate translation reinitiation through dynamic ribosome interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560040. [PMID: 37808774 PMCID: PMC10557763 DOI: 10.1101/2023.09.29.560040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Certain viral RNAs encode proteins downstream of the main protein coding region, expressed through "termination-reinitiation" events, dependent on RNA structure. RNA elements located upstream of the first stop codon within these viral mRNAs bind the ribosome, preventing ribosome recycling and inducing reinitiation. We used bioinformatic methods to identify new examples of viral reinitiation-stimulating RNAs and experimentally verified their secondary structure and function. We determined the structure of a representative viral RNA-ribosome complex using cryoEM. 3D classification and variability analyses reveal that the viral RNA structure can sample a range of conformations while remaining tethered to the ribosome, which enabling the ribosome to find a reinitiation start site within a limited range of mRNA sequence. Evaluating the conserved features and constraints of this entire RNA class in the context of the cryoEM reconstruction provides insight into mechanisms enabling reinitiation, a translation regulation strategy employed by many other viral and eukaryotic systems.
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24
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Lewicka A, Roman C, Jones S, Disare M, Rice P, Piccirilli J. Crystal structure of a cap-independent translation enhancer RNA. Nucleic Acids Res 2023; 51:8891-8907. [PMID: 37548413 PMCID: PMC10484670 DOI: 10.1093/nar/gkad649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/14/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023] Open
Abstract
In eukaryotic messenger RNAs, the 5' cap structure binds to the translation initiation factor 4E to facilitate early stages of translation. Although many plant viruses lack the 5' cap structure, some contain cap-independent translation elements (CITEs) in their 3' untranslated region. The PTE (Panicum mosaic virus translation element) class of CITEs contains a G-rich asymmetric bulge and a C-rich helical junction that were proposed to interact via formation of a pseudoknot. SHAPE analysis of PTE homologs reveals a highly reactive guanosine residue within the G-rich region proposed to mediate eukaryotic initiation factor 4E (eIF4E) recognition. Here we have obtained the crystal structure of the PTE from Pea enation mosaic virus 2 (PEMV2) RNA in complex with our structural chaperone, Fab BL3-6. The structure reveals that the G-rich and C-rich regions interact through a complex network of interactions distinct from those expected for a pseudoknot. The motif, which contains a short parallel duplex, provides a structural mechanism for how the guanosine is extruded from the core stack to enable eIF4E recognition. Homologous PTE elements harbor a G-rich bulge and a three-way junction and exhibit covariation at crucial positions, suggesting that the PEMV2 tertiary architecture is conserved among these homologs.
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Affiliation(s)
- Anna Lewicka
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Christina Roman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Stacey Jones
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Michael Disare
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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25
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Saetzler V, Riet T, Schienke A, Henschel P, Freitag K, Haake A, Heppner FL, Buitrago-Molina LE, Noyan F, Jaeckel E, Hardtke-Wolenski M. Development of Beta-Amyloid-Specific CAR-Tregs for the Treatment of Alzheimer's Disease. Cells 2023; 12:2115. [PMID: 37626926 PMCID: PMC10453937 DOI: 10.3390/cells12162115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a neurodegenerative disease that remains uncured. Its pathogenesis is characterized by the formation of β-amyloid (Aβ) plaques. The use of antigen-specific regulatory T cells (Tregs) through adoptive transfer has shown promise for the treatment of many inflammatory diseases, although the effectiveness of polyspecific Tregs is limited. Obtaining a sufficient number of antigen-specific Tregs from patients remains challenging. AIMS AND METHODS To address this problem, we used an antibody-like single-chain variable fragment from a phage library and subsequently generated a chimeric antigen receptor (CAR) targeting β-amyloid. RESULTS The β-amyloid-specific CARs obtained were stimulated by both recombinant and membrane-bound Aβ isolated from the murine brain. The generated CAR-Tregs showed a normal Treg phenotype, were antigen-specific activatable, and had suppressive capacity. CONCLUSION This study highlights the potential of CAR technology to generate antigen-specific Tregs and presents novel approaches for developing functional CARs.
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Affiliation(s)
- Valerie Saetzler
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany; (V.S.); (T.R.); (A.S.); (P.H.); (L.E.B.-M.); (F.N.); (E.J.)
| | - Tobias Riet
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany; (V.S.); (T.R.); (A.S.); (P.H.); (L.E.B.-M.); (F.N.); (E.J.)
- Department I of Internal Medicine, Tumor Genetics, University Hospital of Cologne and Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Andrea Schienke
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany; (V.S.); (T.R.); (A.S.); (P.H.); (L.E.B.-M.); (F.N.); (E.J.)
| | - Pierre Henschel
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany; (V.S.); (T.R.); (A.S.); (P.H.); (L.E.B.-M.); (F.N.); (E.J.)
| | - Kiara Freitag
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (K.F.); (A.H.); (F.L.H.)
- German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, 10117 Berlin, Germany
| | - Alexander Haake
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (K.F.); (A.H.); (F.L.H.)
- German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, 10117 Berlin, Germany
| | - Frank L. Heppner
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (K.F.); (A.H.); (F.L.H.)
- German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, 10117 Berlin, Germany
| | - Laura Elisa Buitrago-Molina
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany; (V.S.); (T.R.); (A.S.); (P.H.); (L.E.B.-M.); (F.N.); (E.J.)
| | - Fatih Noyan
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany; (V.S.); (T.R.); (A.S.); (P.H.); (L.E.B.-M.); (F.N.); (E.J.)
| | - Elmar Jaeckel
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany; (V.S.); (T.R.); (A.S.); (P.H.); (L.E.B.-M.); (F.N.); (E.J.)
- Department of Liver Transplantation, Multi Organ Transplant Program, University Health Network, University of Toronto, Toronto, ON M5T 0S8, Canada
| | - Matthias Hardtke-Wolenski
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany; (V.S.); (T.R.); (A.S.); (P.H.); (L.E.B.-M.); (F.N.); (E.J.)
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
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26
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Ornelas MY, Thomas AY, Johnson Rosas LI, Medina GN, Mehta AP. Characterization, Directed Evolution, and Targeting of DNA Virus-Encoded RNA Capping Enzymes Using Phenotypic Yeast Platforms. ACS Chem Biol 2023; 18:1808-1820. [PMID: 37498174 PMCID: PMC11024868 DOI: 10.1021/acschembio.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The constant and the sudden emergence of zoonotic human and animal viruses is a significant threat to human health, the world economy, and the world food supply. This has necessitated the development of broad-spectrum therapeutic strategies to combat these emerging pathogens. Mechanisms that are essential for viral replication and propagation have been successfully targeted in the past to develop broad-spectrum therapeutics that can be readily repurposed to combat new zoonotic pathogens. Because of the importance of viral RNA capping enzymes to viral replication and pathogenesis, as well as their presence in both DNA and RNA viruses, these viral proteins have been a long-standing therapeutic target. Here, we use genome sequencing information and yeast-based platforms (YeRC0M) to identify, characterize, and target viral genome-encoded essential RNA capping enzymes from emerging strains of DNA viruses, i.e., Monkeypox virus and African Swine Fever Virus, which are a significant threat to human and domestic animal health. We first identified and biochemically characterized these viral RNA capping enzymes and their necessary protein domains. We observed significant differences in functional protein domains and organization for RNA capping enzymes from emerging DNA viruses in comparison to emerging RNA viruses. We also observed several differences in the biochemical properties of these viral RNA capping enzymes using our phenotypic yeast-based approaches (YeRC0M) as compared to the previous in vitro studies. Further, using directed evolution, we were able to identify inactivation and attenuation mutations in these essential viral RNA capping enzymes; these data could have implications on virus biocontainment as well as live attenuated vaccine development. We also developed methods that would facilitate high-throughput phenotypic screening to identify broad-spectrum inhibitors that selectively target viral RNA capping enzymes over host RNA capping enzymes. As demonstrated here, our approaches to identify, characterize, and target viral genome-encoded essential RNA capping enzymes are highly modular and can be readily adapted for targeting emerging viral pathogens as well as their variants that emerge in the future.
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Affiliation(s)
- Marya Y Ornelas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, Illinois 61801, United States
| | - Angela Y Thomas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, Illinois 61801, United States
| | - L Idalee Johnson Rosas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, Illinois 61801, United States
| | - Gisselle N Medina
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, New York 11944, United States
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, Kansas 66502, United States
| | - Angad P Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Matthews Avenue, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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27
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Solodushko V, Fouty B. Terminal hairpins improve protein expression in IRES-initiated mRNA in the absence of a cap and polyadenylated tail. Gene Ther 2023; 30:620-627. [PMID: 36828937 PMCID: PMC9951143 DOI: 10.1038/s41434-023-00391-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/26/2023]
Abstract
Synthesizing mRNA in vitro is a standard and simple procedure. Adding the 5' cap and 3' polyadenylated (poly(A)) tail to make this mRNA functional for use as a vaccine or therapy increases the time and cost of production and usually decreases the yield, however. We designed mRNA that lacked a cap and poly(A) tail but included an internal ribosomal entry site (IRES) to initiate protein translation. To protect the 5' and 3' ends of mRNA from exonucleases, we added stable terminal hairpins. When compared against typical mRNA (i.e., mRNA that contained a cap and poly(A) tail but lacked hairpins), expression of the delivered reporter protein in HEK293 cells was similar. Using a triple instead of a single hairpin at each end increased protein expression even more. This method has the potential to simplify the production and reduce the cost of synthesizing exogenous mRNA for use as biologics or vaccines.
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Affiliation(s)
- Victor Solodushko
- Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
| | - Brian Fouty
- Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- Department of Internal Medicine, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Division of Pulmonary and Critical Care Medicine, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
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28
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Lidsky PV, Yuan J, Lashkevich KA, Dmitriev SE, Andino R. Monitoring integrated stress response in live Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548942. [PMID: 37502856 PMCID: PMC10369977 DOI: 10.1101/2023.07.13.548942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cells exhibit stress responses to various environmental changes. Among these responses, the integrated stress response (ISR) plays a pivotal role as a crucial stress signaling pathway. While extensive ISR research has been conducted on cultured cells, our understanding of its implications in multicellular organisms remains limited, largely due to the constraints of current techniques that hinder our ability to track and manipulate the ISR in vivo. To overcome these limitations, we have successfully developed an internal ribosome entry site (IRES)-based fluorescent reporter system. This innovative reporter enables us to label Drosophila cells, within the context of a living organism, that exhibit eIF2 phosphorylation-dependent translational shutoff - a characteristic feature of the ISR and viral infections. Through this methodology, we have unveiled tissue- and cell-specific regulation of stress response in Drosophila flies and have even been able to detect stressed tissues in vivo during virus and bacterial infections. To further validate the specificity of our reporter, we have engineered ISR-null eIF2αS50A mutant flies for stress response analysis. Our results shed light on the tremendous potential of this technique for investigating a broad range of developmental, stress, and infection-related experimental conditions. Combining the reporter tool with ISR-null mutants establishes Drosophila as an exceptionally powerful model for studying the ISR in the context of multicellular organisms.
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Affiliation(s)
- Peter V Lidsky
- University of California San Francisco, San Francisco, CA, 94158
| | - Jing Yuan
- University of California San Francisco, San Francisco, CA, 94158
| | - Kseniya A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Raul Andino
- University of California San Francisco, San Francisco, CA, 94158
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Miścicka A, Lu K, Abaeva IS, Pestova TV, Hellen CUT. Initiation of translation on nedicistrovirus and related intergenic region IRESs by their factor-independent binding to the P site of 80S ribosomes. RNA (NEW YORK, N.Y.) 2023; 29:1051-1068. [PMID: 37041031 PMCID: PMC10275262 DOI: 10.1261/rna.079599.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/27/2023] [Indexed: 06/18/2023]
Abstract
Initiation of translation on many viral mRNAs occurs by noncanonical mechanisms that involve 5' end-independent binding of ribosomes to an internal ribosome entry site (IRES). The ∼190-nt-long intergenic region (IGR) IRES of dicistroviruses such as cricket paralysis virus (CrPV) initiates translation without Met-tRNAi Met or initiation factors. Advances in metagenomics have revealed numerous dicistrovirus-like genomes with shorter, structurally distinct IGRs, such as nedicistrovirus (NediV) and Antarctic picorna-like virus 1 (APLV1). Like canonical IGR IRESs, the ∼165-nt-long NediV-like IGRs comprise three domains, but they lack key canonical motifs, including L1.1a/L1.1b loops (which bind to the L1 stalk of the ribosomal 60S subunit) and the apex of stem-loop V (SLV) (which binds to the head of the 40S subunit). Domain 2 consists of a compact, highly conserved pseudoknot (PKIII) that contains a UACUA loop motif and a protruding CrPV-like stem--loop SLIV. In vitro reconstitution experiments showed that NediV-like IRESs initiate translation from a non-AUG codon and form elongation-competent 80S ribosomal complexes in the absence of initiation factors and Met-tRNAi Met Unlike canonical IGR IRESs, NediV-like IRESs bind directly to the peptidyl (P) site of ribosomes leaving the aminoacyl (A) site accessible for decoding. The related structures of NediV-like IRESs and their common mechanism of action indicate that they exemplify a distinct class of IGR IRES.
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Affiliation(s)
- Anna Miścicka
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Kristen Lu
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Irina S Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
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Sherlock ME, Baquero Galvis L, Vicens Q, Kieft JS, Jagannathan S. Principles, mechanisms, and biological implications of translation termination-reinitiation. RNA (NEW YORK, N.Y.) 2023; 29:865-884. [PMID: 37024263 PMCID: PMC10275272 DOI: 10.1261/rna.079375.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/28/2023] [Indexed: 06/11/2023]
Abstract
The gene expression pathway from DNA sequence to functional protein is not as straightforward as simple depictions of the central dogma might suggest. Each step is highly regulated, with complex and only partially understood molecular mechanisms at play. Translation is one step where the "one gene-one protein" paradigm breaks down, as often a single mature eukaryotic mRNA leads to more than one protein product. One way this occurs is through translation reinitiation, in which a ribosome starts making protein from one initiation site, translates until it terminates at a stop codon, but then escapes normal recycling steps and subsequently reinitiates at a different downstream site. This process is now recognized as both important and widespread, but we are only beginning to understand the interplay of factors involved in termination, recycling, and initiation that cause reinitiation events. There appear to be several ways to subvert recycling to achieve productive reinitiation, different types of stresses or signals that trigger this process, and the mechanism may depend in part on where the event occurs in the body of an mRNA. This perspective reviews the unique characteristics and mechanisms of reinitiation events, highlights the similarities and differences between three major scenarios of reinitiation, and raises outstanding questions that are promising avenues for future research.
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Affiliation(s)
- Madeline E Sherlock
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Laura Baquero Galvis
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
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31
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Cheng J, Li G, Wang W, Stovall DB, Sui G, Li D. Circular RNAs with protein-coding ability in oncogenesis. Biochim Biophys Acta Rev Cancer 2023; 1878:188909. [PMID: 37172651 DOI: 10.1016/j.bbcan.2023.188909] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023]
Abstract
As ubiquitously expressed transcripts in eukaryotes, circular RNAs (circRNAs) are covalently closed and lack a 5'-cap and 3'-polyadenylation (poly (A)) tail. Initially, circRNAs were considered non-coding RNA (ncRNA), and their roles as sponging molecules to adsorb microRNAs have been extensively reported. However, in recent years, accumulating evidence has demonstrated that circRNAs could encode functional polypeptides through the initiation of translation mediated by internal ribosomal entry sites (IRESs) or N6-methyladenosine (m6A). In this review, we collectively discuss the biogenesis, cognate mRNA products, regulatory mechanisms, aberrant expression and biological phenotypes or clinical relevance of all currently reported, cancer-relevant protein-coding circRNAs. Overall, we provide a comprehensive overview of circRNA-encoded proteins and their physiological and pathological functions.
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Affiliation(s)
- Jiahui Cheng
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Guangyue Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Daniel B Stovall
- College of Arts and Sciences, Winthrop University, Rock Hill, SC 29733, United States
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin 150040, China.
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China.
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Liu C, Shi Q, Huang X, Koo S, Kong N, Tao W. mRNA-based cancer therapeutics. Nat Rev Cancer 2023:10.1038/s41568-023-00586-2. [PMID: 37311817 DOI: 10.1038/s41568-023-00586-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 06/15/2023]
Abstract
Due to the fact that mRNA technology allows the production of diverse vaccines and treatments in a shorter time frame and with reduced expense compared to conventional approaches, there has been a surge in the use of mRNA-based therapeutics in recent years. With the aim of encoding tumour antigens for cancer vaccines, cytokines for immunotherapy, tumour suppressors to inhibit tumour development, chimeric antigen receptors for engineered T cell therapy or genome-editing proteins for gene therapy, many of these therapeutics have shown promising efficacy in preclinical studies, and some have even entered clinical trials. Given the evidence supporting the effectiveness and safety of clinically approved mRNA vaccines, coupled with growing interest in mRNA-based therapeutics, mRNA technology is poised to become one of the major pillars in cancer drug development. In this Review, we present in vitro transcribed mRNA-based therapeutics for cancer treatment, including the characteristics of the various types of synthetic mRNA, the packaging systems for efficient mRNA delivery, preclinical and clinical studies, current challenges and future prospects in the field. We anticipate the translation of promising mRNA-based treatments into clinical applications, to ultimately benefit patients.
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Affiliation(s)
- Chuang Liu
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Qiangqiang Shi
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Xiangang Huang
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Seyoung Koo
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Na Kong
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
| | - Wei Tao
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Jemelkova J, Stuchlova Horynova M, Kosztyu P, Zachova K, Zadrazil J, Galuszkova D, Takahashi K, Novak J, Raska M. GalNAc-T14 may Contribute to Production of Galactose-Deficient Immunoglobulin A1, the Main Autoantigen in IgA Nephropathy. Kidney Int Rep 2023; 8:1068-1075. [PMID: 37180502 PMCID: PMC10166743 DOI: 10.1016/j.ekir.2023.02.1072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/13/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction Immunoglobulin A1 (IgA1) with galactose-deficient O-glycans (Gd-IgA1) play a key role in the pathogenesis of IgA nephropathy (IgAN). Mucosal-tissue infections increase IL-6 production and, in patients with IgAN, are often associated with macroscopic hematuria. IgA1-secreting cell lines derived from the circulation of patients with IgAN, compared to those of healthy controls (HCs), produce more IgA1 that has O-glycans with terminal or sialylated N-acetylgalactosamine (GalNAc). GalNAc residues are added to IgA1 hinge region by some of the 20 GalNAc transferases, the O-glycosylation-initiating enzymes. Expression of GALNT2, encoding GalNAc-T2, the main enzyme initiating IgA1 O-glycosylation, is similar in cells derived from patients with IgAN and HCs. In this report, we extend our observations of GALNT14 overexpression in IgA1-producing cell lines from patients with IgAN. Methods GALNT14 expression was analyzed in peripheral blood mononuclear cells (PBMCs) from patients with IgAN and from HCs. Moreover, the effect of GALNT14 overexpression or knock-down on Gd-IgA1 production in Dakiki cells was assessed. Results GALNT14 was overexpressed in PBMCs from patients with IgAN. IL-6 increased GALNT14 expression in PBMCs from patients with IgAN and HCs. We used IgA1-producing cell line Dakiki, a previously reported model of Gd-IgA1-producing cells, and showed that overexpression of GalNAc-T14 enhanced galactose deficiency of IgA1, whereas siRNA-mediated GalNAc-T14 knock-down reduced it. GalNAc-T14 was localized in trans-Golgi network, as expected. Conclusions Overexpression of GALNT14 due to inflammatory signals during mucosal infections may contribute to overproduction of Gd-IgA1 in patients with IgAN.
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Affiliation(s)
- Jana Jemelkova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Milada Stuchlova Horynova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Petr Kosztyu
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Katerina Zachova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Josef Zadrazil
- Department of Internal Medicine III Nephrology, Rheumatology and Endocrinology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Dana Galuszkova
- Department of Transfusion Medicine, University Hospital Olomouc, Olomouc, Czech Republic
| | - Kazuo Takahashi
- Department of Biomedical Molecular Sciences, School of Medicine, Fujita Health University, Nagoya, Aichi, Japan
| | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Milan Raska
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
- Department of Immunology, University Hospital Olomouc, Olomouc, Czech Republic
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Laiton-Donato K, Guzmán C, Perdomo-Balaguera E, Sarmiento L, Torres-Fernandez O, Ruiz HA, Rosales-Munar A, Peláez-Carvajal D, Navas MC, Wong MC, Junglen S, Ajami NJ, Parra-Henao G, Usme-Ciro JA. Novel Putative Tymoviridae-like Virus Isolated from Culex Mosquitoes in Colombia. Viruses 2023; 15:v15040953. [PMID: 37112933 PMCID: PMC10143313 DOI: 10.3390/v15040953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
The family Tymoviridae comprises positive-sense RNA viruses, which mainly infect plants. Recently, a few Tymoviridae-like viruses have been found in mosquitoes, which feed on vertebrate sources. We describe a novel Tymoviridae-like virus, putatively named, Guachaca virus (GUAV), isolated from Culex pipiens and Culex quinquefasciatus species of mosquitoes and collected in the rural area of Santa Marta, Colombia. After a cytopathic effect was observed in C6/36 cells, RNA was extracted and processed through the NetoVIR next-generation sequencing protocol, and data were analyzed through the VirMAP pipeline. Molecular and phenotypic characterization of the GUAV was achieved using a 5'/3' RACE, transmission electron microscopy, amplification in vertebrate cells, and phylogenetic analysis. A cytopathic effect was observed in C6/36 cells three days post-infection. The GUAV genome was successfully assembled, and its polyadenylated 3' end was corroborated. GUAV shared only 54.9% amino acid identity with its closest relative, Ek Balam virus, and was grouped with the latter and other unclassified insect-associated tymoviruses in a phylogenetic analysis. GUAV is a new member of a family previously described as comprising plant-infecting viruses, which seem to infect and replicate in mosquitoes. The sugar- and blood-feeding behavior of the Culex spp., implies a sustained contact with plants and vertebrates and justifies further studies to unravel the ecological scenario for transmission.
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Affiliation(s)
- Katherine Laiton-Donato
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
- Grupo Genómica de Microorganismos Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Camila Guzmán
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Erik Perdomo-Balaguera
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
- Secretaría de Salud Distrital, Programa de Enfermedades Transmitidas por Vectores, Santa Marta 470004, Colombia
| | - Ladys Sarmiento
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Orlando Torres-Fernandez
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Héctor Alejandro Ruiz
- Grupo Genómica de Microorganismos Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Alicia Rosales-Munar
- Grupo Genómica de Microorganismos Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Dioselina Peláez-Carvajal
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Maria-Cristina Navas
- Grupo de Gastrohepatología, Facultad de Medicina, Universidad de Antioquia, Medellin 050010, Colombia
| | - Matthew C Wong
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Viroworks, Houston, TX 77030, USA
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Nadim J Ajami
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Viroworks, Houston, TX 77030, USA
| | - Gabriel Parra-Henao
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
| | - José A Usme-Ciro
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
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Sabei A, Caldas Baia TG, Saffar R, Martin J, Frezza E. Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes. J Chem Inf Model 2023; 63:2554-2572. [PMID: 36972178 DOI: 10.1021/acs.jcim.2c01509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
We investigated the capability of internal normal modes to reproduce RNA flexibility and predict observed RNA conformational changes and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified representation of the RNA structure and its potential energy. Three data sets were also created to investigate different aspects. Despite all the approximations, our study shows that iNMA is a suitable method to take into account RNA flexibility and describe its conformational changes opening the route to its applicability in any integrative approach where these properties are crucial.
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Abstract
Viruses lack the properties to replicate independently due to the limited resources encoded in their genome; therefore, they hijack the host cell machinery to replicate and survive. Picornaviruses get the prerequisite for effective protein synthesis through specific sequences known as internal ribosome entry sites (IRESs). In the past 2 decades, significant progress has been made in identifying different types of IRESs in picornaviruses. This review will discuss the past and current findings related to the five different types of IRESs and various internal ribosome entry site trans-acting factors (ITAFs) that either promote or suppress picornavirus translation and replication. Some IRESs are inefficient and thus require ITAFs. To achieve their full efficiency, they recruit various ITAFs, which enable them to translate more effectively and efficiently, except type IV IRES, which does not require any ITAFs. Although there are two kinds of ITAFs, one promotes viral IRES-dependent translation, and the second type restricts. Picornaviruses IRESs are classified into five types based on their use of sequence, ITAFs, and initiation factors. Some ITAFs regulate IRES activity by localizing to the viral replication factories in the cytoplasm. Also, some drugs, chemicals, and herbal extracts also regulate viral IRES-dependent translation and replication. Altogether, this review will elaborate on our understanding of the past and recent advancements in the IRES-dependent translation and replication of picornaviruses. IMPORTANCE The family Picornaviridae is divided into 68 genera and 158 species. The viruses belonging to this family range from public health importance, such as poliovirus, enterovirus A71, and hepatitis A virus, to animal viruses of great economic importance, such as foot-and-mouth disease virus. The genomes of picornaviruses contain 5' untranslated regions (5' UTRs), which possess crucial and highly structured stem-loops known as IRESs. IRES assemble the ribosomes and facilitate the cap-independent translation. Virus-host interaction is a hot spot for researchers, which warrants deep insight into understanding viral pathogenesis better and discovering new tools and ways for viral restriction to improve human and animal health. The cap-independent translation in the majority of picornaviruses is modulated by ITAFs, which bind to various IRES regions to initiate the translation. The discoveries of ITAFs substantially contributed to understanding viral replication behavior and enhanced our knowledge about virus-host interaction more effectively than ever before. This review discussed the various types of IRESs found in Picornaviridae, past and present discoveries regarding ITAFs, and their mechanism of action. The herbal extracts, drugs, and chemicals, which indicated their importance in controlling viruses, were also summarized. In addition, we discussed the movement of ITAFs from the nucleus to viral replication factories. We believe this review will stimulate researchers to search for more novel ITAFs, drugs, herbal extracts, and chemicals, enhancing the understanding of virus-host interaction.
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Ponticelli M, Bellone ML, Parisi V, Iannuzzi A, Braca A, de Tommasi N, Russo D, Sileo A, Quaranta P, Freer G, Pistello M, Milella L. Specialized metabolites from plants as a source of new multi-target antiviral drugs: a systematic review. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2023; 22:1-79. [PMID: 37359711 PMCID: PMC10008214 DOI: 10.1007/s11101-023-09855-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/30/2023] [Indexed: 06/28/2023]
Abstract
Viral infections have always been the main global health challenge, as several potentially lethal viruses, including the hepatitis virus, herpes virus, and influenza virus, have affected human health for decades. Unfortunately, most licensed antiviral drugs are characterized by many adverse reactions and, in the long-term therapy, also develop viral resistance; for these reasons, researchers have focused their attention on investigating potential antiviral molecules from plants. Natural resources indeed offer a variety of specialized therapeutic metabolites that have been demonstrated to inhibit viral entry into the host cells and replication through the regulation of viral absorption, cell receptor binding, and competition for the activation of intracellular signaling pathways. Many active phytochemicals, including flavonoids, lignans, terpenoids, coumarins, saponins, alkaloids, etc., have been identified as potential candidates for preventing and treating viral infections. Using a systematic approach, this review summarises the knowledge obtained to date on the in vivo antiviral activity of specialized metabolites extracted from plant matrices by focusing on their mechanism of action.
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Affiliation(s)
- Maria Ponticelli
- Department of Science, University of Basilicata, Viale Dell’ateneo Lucano 10, 85100 Potenza, Italy
| | - Maria Laura Bellone
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
- Ph.D. Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Valentina Parisi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
- Ph.D. Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Annamaria Iannuzzi
- Department of Pharmacy, University of Pisa, Via Bonanno 33, 56126 Pisa, Italy
- Interdepartmental Research Center “Nutraceuticals and Food for Health”, University of Pisa, 56100 Pisa, Italy
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Alessandra Braca
- Department of Pharmacy, University of Pisa, Via Bonanno 33, 56126 Pisa, Italy
- Interdepartmental Research Center “Nutraceuticals and Food for Health”, University of Pisa, 56100 Pisa, Italy
- Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Nunziatina de Tommasi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Daniela Russo
- Department of Science, University of Basilicata, Viale Dell’ateneo Lucano 10, 85100 Potenza, Italy
| | - Annalisa Sileo
- Department of Science, University of Basilicata, Viale Dell’ateneo Lucano 10, 85100 Potenza, Italy
| | | | - Giulia Freer
- Virology Unit, Pisa University Hospital, Pisa, Italy
| | | | - Luigi Milella
- Department of Science, University of Basilicata, Viale Dell’ateneo Lucano 10, 85100 Potenza, Italy
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Chen R, Wang SK, Belk JA, Amaya L, Li Z, Cardenas A, Abe BT, Chen CK, Wender PA, Chang HY. Engineering circular RNA for enhanced protein production. Nat Biotechnol 2023; 41:262-272. [PMID: 35851375 PMCID: PMC9931579 DOI: 10.1038/s41587-022-01393-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/14/2022] [Indexed: 01/07/2023]
Abstract
Circular RNAs (circRNAs) are stable and prevalent RNAs in eukaryotic cells that arise from back-splicing. Synthetic circRNAs and some endogenous circRNAs can encode proteins, raising the promise of circRNA as a platform for gene expression. In this study, we developed a systematic approach for rapid assembly and testing of features that affect protein production from synthetic circRNAs. To maximize circRNA translation, we optimized five elements: vector topology, 5' and 3' untranslated regions, internal ribosome entry sites and synthetic aptamers recruiting translation initiation machinery. Together, these design principles improve circRNA protein yields by several hundred-fold, provide increased translation over messenger RNA in vitro, provide more durable translation in vivo and are generalizable across multiple transgenes.
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Affiliation(s)
- Robert Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Sean K Wang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Laura Amaya
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Zhijian Li
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Angel Cardenas
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Brian T Abe
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Chun-Kan Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul A Wender
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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39
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Wu GH, Lee KM, Kao CY, Shih SR. The internal ribosome entry site determines the neurotropic potential of enterovirus A71. Microbes Infect 2023; 25:105107. [PMID: 36708870 DOI: 10.1016/j.micinf.2023.105107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023]
Abstract
The mechanisms underlying tissue-specific replication of enteroviruses are currently unclear. Although enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16) are both common pathogens that cause hand-foot-mouth disease, they display quite different neurotropic properties. Herein, we characterized the role of the internal ribosomal entry site (IRES) in determining neurovirulence using an oral inoculation model of EV-A71. The receptor transgenic (hSCARB2-Tg) mice developed neurological symptoms after being infected with a mouse-adapted EV-A71 strain (MP4) via different administrative routes. Intragastric administration of the MP4 strain caused pathological changes such as neuronal loss and neuropil vacuolation, whereas replacing EV-A71 IRES with CV-A16 abolished the neuropathological phenotypes. The attenuated neurotropic potential of IRES-swapped EV-A71 was observed even in mice that received intraperitoneal and intracerebral inoculations. Fewer chimeric MP4 viral RNAs and proteins were detected in the mouse tissues, regardless of the inoculation route. Tissue-specific replication can be reflected in cell-based characterization. While chimeric MP4 virus replicated poorly in human intestinal C2BBe1 and neuroblastoma SH-SY5Y cells, its replication in susceptible rhabdomyosarcoma cells was not affected. Overall, our results demonstrated that the IRES determined the neurotropic potential of EV-A71 and CV-A16, emphasizing the importance of the IRES in tissue tropism, along with the host receptors.
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Affiliation(s)
- Guan-Hong Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan
| | - Kuo-Ming Lee
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan; Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan; Division of Pediatric Infectious Diseases, Chang Gung Memorial Hospital, Linkou, Taoyuan, 333 Taiwan
| | - Chia-Yu Kao
- Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan
| | - Shin-Ru Shih
- Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, 333 Taiwan; Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 333 Taiwan; Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, 333 Taiwan.
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40
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Takallou S, Puchacz N, Allard D, Said KB, Nokhbeh MR, Samanfar B, Golshani A. IRES-mediated translation in bacteria. Biochem Biophys Res Commun 2023; 641:110-115. [PMID: 36527744 DOI: 10.1016/j.bbrc.2022.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Despite the similarity in fundamental goals of translation initiation between different domains of life, it is one of the most phylogenetically diverse steps of the central dogma of molecular biology. In a classical view, the translation signals for prokaryotes and eukaryotes are distinct from each other. This idea was challenged by the finding that the Internal Ribosome Entry Site (IRES) belonging to Plautia stali intestine virus (PSIV) could bypass the domain-specific boundaries and effectively initiate translation in E. coli. This finding led us to investigate whether the ability of PSIV IRES to initiate translation in E. coli is specific to this IRES and also to study features that allow this viral IRES to mediate prokaryotic translation initiation. We observed that certain IRESs may also possess the ability to initiate E. coli translation. Our results also indicated that the structural integrity of the PSIV IRES in translation in prokaryotes does not appear to be as critical as it is in eukaryotes. We also demonstrated that two regions of the PSIV IRES with complementarity to 16S ribosomal RNA are important for the ability of this IRES to initiate translation in E. coli.
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Affiliation(s)
- Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Nathalie Puchacz
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Danielle Allard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Kamaledin B Said
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Saudi Arabia.
| | | | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, Ontario, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada.
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
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41
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Jiao L, Liu Y, Yu XY, Pan X, Zhang Y, Tu J, Song YH, Li Y. Ribosome biogenesis in disease: new players and therapeutic targets. Signal Transduct Target Ther 2023; 8:15. [PMID: 36617563 PMCID: PMC9826790 DOI: 10.1038/s41392-022-01285-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 01/10/2023] Open
Abstract
The ribosome is a multi-unit complex that translates mRNA into protein. Ribosome biogenesis is the process that generates ribosomes and plays an essential role in cell proliferation, differentiation, apoptosis, development, and transformation. The mTORC1, Myc, and noncoding RNA signaling pathways are the primary mediators that work jointly with RNA polymerases and ribosome proteins to control ribosome biogenesis and protein synthesis. Activation of mTORC1 is required for normal fetal growth and development and tissue regeneration after birth. Myc is implicated in cancer development by enhancing RNA Pol II activity, leading to uncontrolled cancer cell growth. The deregulation of noncoding RNAs such as microRNAs, long noncoding RNAs, and circular RNAs is involved in developing blood, neurodegenerative diseases, and atherosclerosis. We review the similarities and differences between eukaryotic and bacterial ribosomes and the molecular mechanism of ribosome-targeting antibiotics and bacterial resistance. We also review the most recent findings of ribosome dysfunction in COVID-19 and other conditions and discuss the consequences of ribosome frameshifting, ribosome-stalling, and ribosome-collision. We summarize the role of ribosome biogenesis in the development of various diseases. Furthermore, we review the current clinical trials, prospective vaccines for COVID-19, and therapies targeting ribosome biogenesis in cancer, cardiovascular disease, aging, and neurodegenerative disease.
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Affiliation(s)
- Lijuan Jiao
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yuzhe Liu
- grid.452829.00000000417660726Department of Orthopedics, the Second Hospital of Jilin University, Changchun, Jilin 130000 P. R. China
| | - Xi-Yong Yu
- grid.410737.60000 0000 8653 1072Key Laboratory of Molecular Target & Clinical Pharmacology and the NMPA State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong 511436 P. R. China
| | - Xiangbin Pan
- grid.506261.60000 0001 0706 7839Department of Structural Heart Disease, National Center for Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China ,Key Laboratory of Cardiovascular Appratus Innovation, Beijing, 100037 P. R. China
| | - Yu Zhang
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Junchu Tu
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, P. R. China. .,State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, P. R. China.
| | - Yangxin Li
- Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu, 215123, P. R. China.
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42
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Li Y, Wei L, Cheng A, Wang M, Ou X, Mao S, Tian B, Yang Q, Wu Y, Zhang S, Huang J, Gao Q, Sun D, Zhao X, Jia R, Liu M, Zhu D, Chen S, Yu Y, Zhang L, Pan L. Specific DNAzymes cleave the 300-618 nt of 5'UTR to inhibit DHAV-1 translation and replication. Front Microbiol 2022; 13:1064612. [PMID: 36578574 PMCID: PMC9791187 DOI: 10.3389/fmicb.2022.1064612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
DNAzymes effectively inhibit the expression of viral genes. Duck hepatitis A virus type-1 (DHAV-1) genomic RNA carries an internal ribosome entry site (IRES). The IRES initiates the translation of DHAV-1 via a mechanism that differs from that of cap-dependent translation. Therefore, it is an attractive target for the treatment of DHAV-1. In this study, we designed 6 DNAzymes (Dzs) specifically targeting 300-618 nt sequence in the DHAV-1 5'untranslated region (UTR; a predicted IRES-like element). In the presence of divalent metal ions, three designed DNAzymes (DZ369, DZ454, and DZ514) efficiently cleaved the 300-618 nt sequence of the DHAV-1 5'UTR RNA. The activity of the Dzs was particularly dependent on Mg2+ ions. Subsequently, the translation inhibitory activity of these Dzs was determined by western blotting experiments. The Dzs effectively inhibited the translation mediated by the 300-618 nt of DHAV-1 5'UTR in duck embryo fibroblasts (DEFs). Importantly, DZ454 showed the strongest inhibitory effect, and its inhibition was time and dose dependent. However, none of the Dzs showed significant inhibition of cap-dependent translation. These results suggest that these Dzs show specificity for target RNA. Moreover, DZ454 inhibited the replication of DHAV-1. In conclusion, the designed DNAzymes can be used as inhibitors of DHAV-1 RNA translation and replication, providing new insights useful for the development of anti-DHAV-1 drugs.
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Affiliation(s)
- Yanglin Li
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Wei
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,*Correspondence: Mingshu Wang,
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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43
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Ornelas MY, Thomas AY, Johnson Rosas LI, Scoville RO, Mehta AP. Synthetic Platforms for Characterizing and Targeting of SARS-CoV-2 Genome Capping Enzymes. ACS Synth Biol 2022; 11:3759-3771. [PMID: 36331143 PMCID: PMC9662071 DOI: 10.1021/acssynbio.2c00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Indexed: 11/06/2022]
Abstract
Essential viral enzymes have been successfully targeted to combat the diseases caused by emerging pathogenic RNA viruses (e.g., viral RNA-dependent RNA polymerase). Because of the conserved nature of such viral enzymes, therapeutics targeting these enzymes have the potential to be repurposed to combat emerging diseases, e.g., remdesivir, which was initially developed as a potential Ebola treatment, then was repurposed for COVID-19. Our efforts described in this study target another essential and highly conserved, but relatively less explored, step in RNA virus translation and replication, i.e., capping of the viral RNA genome. The viral genome cap structure disguises the genome of most RNA viruses to resemble the mRNA cap structure of their host and is essential for viral translation, propagation, and immune evasion. Here, we developed a synthetic, phenotypic yeast-based complementation platform (YeRC0M) for molecular characterization and targeting of SARS-CoV-2 genome-encoded RNA cap-0 (guanine-N7)-methyltransferase (N7-MTase) enzyme (nsp14). In YeRC0M, the lack of yeast mRNA capping N7-MTase in yeast, which is an essential gene in yeast, is complemented by the expression of functional viral N7-MTase or its variants. Using YeRC0M, we first identified important protein domains and amino acid residues that are essential for SARS-CoV-2 nsp14 N7-MTase activity. We also expanded YeRC0M to include key nsp14 variants observed in emerging variants of SARS-CoV-2 (e.g., delta variant of SARS-CoV-2 encodes nsp14 A394V and nsp14 P46L). We also combined YeRC0M with directed evolution to identify attenuation mutations in SARS-CoV-2 nsp14. Because of the high sequence similarity of nsp14 in emerging coronaviruses, these observations could have implications on live attenuated vaccine development strategies. These data taken together reveal key domains in SARS-CoV-2 nsp14 that can be targeted for therapeutic strategies. We also anticipate that these readily tractable phenotypic platforms can also be used for the identification of inhibitors of viral RNA capping enzymes as antivirals.
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Affiliation(s)
- Marya Y. Ornelas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Angela Y. Thomas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - L. Idalee Johnson Rosas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Riley O. Scoville
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Angad P. Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign
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44
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Wang X, Zhu J, Zhang D, Liu G. Ribosomal control in RNA virus-infected cells. Front Microbiol 2022; 13:1026887. [PMID: 36419416 PMCID: PMC9677555 DOI: 10.3389/fmicb.2022.1026887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Viruses are strictly intracellular parasites requiring host cellular functions to complete their reproduction cycle involving virus infection of host cell, viral genome replication, viral protein translation, and virion release. Ribosomes are protein synthesis factories in cells, and viruses need to manipulate ribosomes to complete their protein synthesis. Viruses use translation initiation factors through their own RNA structures or cap structures, thereby inducing ribosomes to synthesize viral proteins. Viruses also affect ribosome production and the assembly of mature ribosomes, and regulate the recognition of mRNA by ribosomes, thereby promoting viral protein synthesis and inhibiting the synthesis of host antiviral immune proteins. Here, we review the remarkable mechanisms used by RNA viruses to regulate ribosomes, in particular, the mechanisms by which RNA viruses induce the formation of specific heterogeneous ribosomes required for viral protein translation. This review provides valuable insights into the control of viral infection and diseases from the perspective of viral protein synthesis.
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45
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Lu SC, Barry MA. Locked and loaded: engineering and arming oncolytic adenoviruses to enhance anti-tumor immune responses. Expert Opin Biol Ther 2022; 22:1359-1378. [DOI: 10.1080/14712598.2022.2139601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
| | - Michael A Barry
- Division of Infectious Diseases, Department of Medicine
- Department of Immunology
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
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46
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Sadic M, Schneider WM, Katsara O, Medina GN, Fisher A, Mogulothu A, Yu Y, Gu M, de los Santos T, Schneider RJ, Dittmann M. DDX60 selectively reduces translation off viral type II internal ribosome entry sites. EMBO Rep 2022; 23:e55218. [PMID: 36256515 PMCID: PMC9724679 DOI: 10.15252/embr.202255218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 11/05/2022] Open
Abstract
Co-opting host cell protein synthesis is a hallmark of many virus infections. In response, certain host defense proteins limit mRNA translation globally, albeit at the cost of the host cell's own protein synthesis. Here, we describe an interferon-stimulated helicase, DDX60, that decreases translation from viral internal ribosome entry sites (IRESs). DDX60 acts selectively on type II IRESs of encephalomyocarditis virus (EMCV) and foot and mouth disease virus (FMDV), but not by other IRES types or by 5' cap. Correspondingly, DDX60 reduces EMCV and FMDV (type II IRES) replication, but not that of poliovirus or bovine enterovirus 1 (BEV-1; type I IRES). Furthermore, replacing the IRES of poliovirus with a type II IRES is sufficient for DDX60 to inhibit viral replication. Finally, DDX60 selectively modulates the amount of translating ribosomes on viral and in vitro transcribed type II IRES mRNAs, but not 5' capped mRNA. Our study identifies a novel facet in the repertoire of interferon-stimulated effector genes, the selective downregulation of translation from viral type II IRES elements.
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Affiliation(s)
| | | | | | - Gisselle N Medina
- Plum Island Animal Disease Center, ARSUSDAGreenportNYUSA,National Bio and Agro‐Defense Facility (NBAF), ARSUSDAManhattanKSUSA
| | | | - Aishwarya Mogulothu
- Plum Island Animal Disease Center, ARSUSDAGreenportNYUSA,Department of Pathobiology and Veterinary ScienceUniversity of ConnecticutStorrsCTUSA
| | - Yingpu Yu
- The Rockefeller UniversityNew YorkNYUSA
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47
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Wu Z, Yu X, Zhang S, He Y, Guo W. Mechanism underlying circRNA dysregulation in the TME of digestive system cancer. Front Immunol 2022; 13:951561. [PMID: 36238299 PMCID: PMC9550895 DOI: 10.3389/fimmu.2022.951561] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Circular RNAs (circRNAs) are a new series of noncoding RNAs (ncRNAs) that have been reported to be expressed in eukaryotic cells and have a variety of biological functions in the regulation of cancer pathogenesis and progression. The TME, as a microscopic ecological environment, consists of a variety of cells, including tumor cells, immune cells and other normal cells, ECM and a large number of signaling molecules. The crosstalk between circRNAs and the TME plays a complicated role in affecting the malignant behaviors of digestive system cancers. Herein, we summarize the mechanisms underlying aberrant circRNA expression in the TME of the digestive system cancers, including immune surveillance, angiogenesis, EMT, and ECM remodelling. The regulation of the TME by circRNA is expected to be a new therapeutic method.
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Affiliation(s)
- Zeyu Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Wenzhi Guo, ; Yuting He,
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Wenzhi Guo, ; Yuting He,
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Dionisi S, Piera K, Baumschlager A, Khammash M. Implementation of a Novel Optogenetic Tool in Mammalian Cells Based on a Split T7 RNA Polymerase. ACS Synth Biol 2022; 11:2650-2661. [PMID: 35921263 PMCID: PMC9396705 DOI: 10.1021/acssynbio.2c00067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Optogenetic tools are widely used to control gene expression
dynamics
both in prokaryotic and eukaryotic cells. These tools are used in
a variety of biological applications from stem cell differentiation
to metabolic engineering. Despite some tools already available in
bacteria, no light-inducible system currently exists to control gene
expression independently from mammalian transcriptional and/or translational
machineries thus working orthogonally to endogenous regulatory mechanisms.
Such a tool would be particularly important in synthetic biology,
where orthogonality is advantageous to achieve robust activation of
synthetic networks. Here we implement, characterize, and optimize
a new optogenetic tool in mammalian cells based on a previously published
system in bacteria called Opto-T7RNAPs. The tool is orthogonal to
the cellular machinery for transcription and consists of a split T7
RNA polymerase coupled with the blue light-inducible magnets system
(mammalian OptoT7–mOptoT7). In our study we exploited the T7
polymerase’s viral origins to tune our system’s expression
level, reaching up to an almost 20-fold change activation over the
dark control. mOptoT7 is used here to generate mRNA for protein expression,
shRNA for protein inhibition, and Pepper aptamer for RNA visualization.
Moreover, we show that mOptoT7 can mitigate the gene expression burden
when compared to another optogenetic construct. These properties make
mOptoT7 a powerful new tool to use when orthogonality and viral RNA
species (that lack endogenous RNA modifications) are desired.
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Affiliation(s)
- Sara Dionisi
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Karol Piera
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Armin Baumschlager
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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Condé L, Allatif O, Ohlmann T, de Breyne S. Translation of SARS-CoV-2 gRNA Is Extremely Efficient and Competitive despite a High Degree of Secondary Structures and the Presence of an uORF. Viruses 2022; 14:1505. [PMID: 35891485 PMCID: PMC9322171 DOI: 10.3390/v14071505] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 infection generates up to nine different sub-genomic mRNAs (sgRNAs), in addition to the genomic RNA (gRNA). The 5'UTR of each viral mRNA shares the first 75 nucleotides (nt.) at their 5'end, called the leader, but differentiates by a variable sequence (0 to 190 nt. long) that follows the leader. As a result, each viral mRNA has its own specific 5'UTR in term of length, RNA structure, uORF and Kozak context; each one of these characteristics could affect mRNA expression. In this study, we have measured and compared translational efficiency of each of the ten viral transcripts. Our data show that most of them are very efficiently translated in all translational systems tested. Surprisingly, the gRNA 5'UTR, which is the longest and the most structured, was also the most efficient to initiate translation. This property is conserved in the 5'UTR of SARS-CoV-1 but not in MERS-CoV strain, mainly due to the regulation imposed by the uORF. Interestingly, the translation initiation mechanism on the SARS-CoV-2 gRNA 5'UTR requires the cap structure and the components of the eIF4F complex but showed no dependence in the presence of the poly(A) tail in vitro. Our data strongly suggest that translation initiation on SARS-CoV-2 mRNAs occurs via an unusual cap-dependent mechanism.
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Affiliation(s)
| | | | - Théophile Ohlmann
- CIRI, Centre International de Recherche en Infectiologie, (Team Ohlmann), Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007 Lyon, France; (L.C.); (O.A.)
| | - Sylvain de Breyne
- CIRI, Centre International de Recherche en Infectiologie, (Team Ohlmann), Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, F-69007 Lyon, France; (L.C.); (O.A.)
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50
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Sáez Moreno D, Udi Q, Azeredo J, Domingues L. Towards T7 RNA polymerase (T7RNAP)-based expression system in yeast: challenges and opportunities. Bioengineered 2022; 13:14947-14959. [PMID: 37105766 DOI: 10.1080/21655979.2023.2180579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
During the last decades, we have witnessed unprecedented advances in biological engineering and synthetic biology. These disciplines aim to take advantage of gene pathway regulation and gene expression in different organisms, to enable cells to perform desired functions. Yeast has been widely utilized as a model for the study of eukaryotic protein expression while bacteriophage T7RNAP and its promoter constitute the preferred system for prokaryotic protein expression (such as pET-based expression systems). The ability to integrate a T7RNAP-based expression system in yeast could allow for a better understanding of gene regulation in eukaryotic cells, and potentially increase the efficiency and processivity of yeast as an expression system. However, the attempts for the creation of such a system have been unsuccessful to date. This review aims to: (i) summarize the efforts that, for many years, have been devoted to the creation of a T7RNAP-based yeast expression system and ii) provide an overview of the latest advances in knowledge of eukaryotic transcription and translation that could lead to the construction of a successful T7RNAP expression system in yeast. The completion of this new expression system would allow to further expand the toolkit of yeast in synthetic biology and ultimately contribute to boost yeast usage as a key cell factory in sustainable biorefinery and circular economy.
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Affiliation(s)
- David Sáez Moreno
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, 4835-198, Guimarães, Braga, Portugal
| | - Qimron Udi
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joana Azeredo
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, 4835-198, Guimarães, Braga, Portugal
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, 4835-198, Guimarães, Braga, Portugal
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