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Huang X, Du Z. Elaborated pseudoknots that stimulate -1 programmed ribosomal frameshifting or stop codon readthrough in RNA viruses. J Biomol Struct Dyn 2023:1-13. [PMID: 38095458 PMCID: PMC11176267 DOI: 10.1080/07391102.2023.2292296] [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: 07/18/2023] [Accepted: 11/25/2023] [Indexed: 05/08/2024]
Abstract
Pseudoknots assume various functions including stimulation of -1 programmed ribosomal frameshifting (PRF) or stop codon readthrough (SCR) in RNA viruses. These pseudoknots vary greatly in sizes and structural complexities. Recent biochemical and structural studies confirm the three-stemmed pseudoknots as the -1 PRF stimulators in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related coronaviruses. We reexamined previously reported -1 PRF or SCR stimulating pseudoknots, especially those containing a relatively long connecting loop between the two pseudoknot-forming stems, for their ability to form elaborated structures. Many potential elaborated pseudoknots were identified that contain one or more of the following extra structural elements: stem-loop, embedded pseudoknot, kissing hairpins, and additional loop-loop interactions. The elaborated pseudoknots are found in several different virus families that utilize either the -1 PRF or SCR recoding mechanisms. Model-building studies were performed to not only establish the structural feasibility of the elaborated pseudoknots but also reveal potential additional structural features that cannot be readily inferred from the predicted secondary structures. Some of the structures, such as embedded double pseudoknots and compact loop-loop pseudoknots mediated by the previously established common pseudoknot motif-1 (CPK-1), represent the first of its kind in the literatures. By advancing discovery of new functional RNA structures, we significantly expand the repertoire of known elaborated pseudoknots that could potentially play a role in -1 PRF and SCR regulation. These results contribute to a better understanding of RNA structures in general, facilitating the design of engineering RNA molecules with certain desired functions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xiaolan Huang
- School of Computing, Southern Illinois University at Carbondale, IL 62901, USA
| | - Zhihua Du
- School of Chemical and Biomolecular Sciences, Southern Illinois University at Carbondale, IL 62901, USA
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Qiao Q, Yan Y, Guo J, Du S, Zhang J, Jia R, Ren H, Qiao Y, Li Q. A review on architecture of the gag-pol ribosomal frameshifting RNA in human immunodeficiency virus: a variability survey of virus genotypes. J Biomol Struct Dyn 2016; 35:1629-1653. [PMID: 27485859 DOI: 10.1080/07391102.2016.1194231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Programmed '-1' ribosomal frameshifting is necessary for expressing the pol gene overlapped from a gag of human immunodeficiency virus. A viral RNA structure that requires base pairing across the overlapping sequence region suggests a mechanism of regulating ribosome and helicase traffic during expression. To get precise roles of an element around the frameshift site, a review on architecture of the frameshifting RNA is performed in combination of reported information with augments of a representative set of 19 viral samples. In spite of a different length for the viral RNAs, a canonical comparison on the element sequence allocation is performed for viewing variability associations between virus genotypes. Additionally, recent and historical insights recognized in frameshifting regulation are looked back as for indel and single nucleotide polymorphism of RNA. As specially noted, structural changes at a frameshift site, the spacer sequence, and a three-helix junction element, as well as two Watson-Crick base pairs near a bulge and a C-G pair close a loop, are the most vital strategies for the virus frameshifting regulations. All of structural changes, which are dependent upon specific sequence variations, facilitate an elucidation about the RNA element conformation-dependent mechanism for frameshifting. These facts on disrupting base pair interactions also allow solving the problem of competition between ribosome and helicase on a same RNA template, common to single-stranded RNA viruses. In a broad perspective, each new insight of frameshifting regulation in the competition systems introduced by the RNA element construct changes will offer a compelling target for antiviral therapy.
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Affiliation(s)
- Qi Qiao
- a School of Pharmaceutical Sciences, Xiamen University , Fujian 361102 , P.R. China
| | - Yanhua Yan
- b Department of Bioscience , Luliang University , Shanxi 033001 , P.R. China
| | - Jinmei Guo
- c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China
| | - Shuqiang Du
- c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China
| | - Jiangtao Zhang
- b Department of Bioscience , Luliang University , Shanxi 033001 , P.R. China
| | - Ruyue Jia
- c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China
| | - Haimin Ren
- c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China
| | - Yuanbiao Qiao
- d Graduate Institute of Pharmaceutical Chemistry, Luliang University , Shanxi 033001 , P.R. China
| | - Qingshan Li
- e School of Pharmaceutical Sciences , Shanxi Medical University , Shanxi 030001 , P.R. China
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Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
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Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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Guerrero S, Batisse J, Libre C, Bernacchi S, Marquet R, Paillart JC. HIV-1 replication and the cellular eukaryotic translation apparatus. Viruses 2015; 7:199-218. [PMID: 25606970 PMCID: PMC4306834 DOI: 10.3390/v7010199] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/12/2015] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic translation is a complex process composed of three main steps: initiation, elongation, and termination. During infections by RNA- and DNA-viruses, the eukaryotic translation machinery is used to assure optimal viral protein synthesis. Human immunodeficiency virus type I (HIV-1) uses several non-canonical pathways to translate its own proteins, such as leaky scanning, frameshifting, shunt, and cap-independent mechanisms. Moreover, HIV-1 modulates the host translation machinery by targeting key translation factors and overcomes different cellular obstacles that affect protein translation. In this review, we describe how HIV-1 proteins target several components of the eukaryotic translation machinery, which consequently improves viral translation and replication.
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Affiliation(s)
- Santiago Guerrero
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
| | - Julien Batisse
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
| | - Camille Libre
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
| | - Serena Bernacchi
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
| | - Roland Marquet
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
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