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Chameettachal A, Mustafa F, Rizvi TA. Understanding Retroviral Life Cycle and its Genomic RNA Packaging. J Mol Biol 2023; 435:167924. [PMID: 36535429 DOI: 10.1016/j.jmb.2022.167924] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Members of the family Retroviridae are important animal and human pathogens. Being obligate parasites, their replication involves a series of steps during which the virus hijacks the cellular machinery. Additionally, many of the steps of retrovirus replication are unique among viruses, including reverse transcription, integration, and specific packaging of their genomic RNA (gRNA) as a dimer. Progress in retrovirology has helped identify several molecular mechanisms involved in each of these steps, but many are still unknown or remain controversial. This review summarizes our present understanding of the molecular mechanisms involved in various stages of retrovirus replication. Furthermore, it provides a comprehensive analysis of our current understanding of how different retroviruses package their gRNA into the assembling virions. RNA packaging in retroviruses holds a special interest because of the uniqueness of packaging a dimeric genome. Dimerization and packaging are highly regulated and interlinked events, critical for the virus to decide whether its unspliced RNA will be packaged as a "genome" or translated into proteins. Finally, some of the outstanding areas of exploration in the field of RNA packaging are highlighted, such as the role of epitranscriptomics, heterogeneity of transcript start sites, and the necessity of functional polyA sequences. An in-depth knowledge of mechanisms that interplay between viral and cellular factors during virus replication is critical in understanding not only the virus life cycle, but also its pathogenesis, and development of new antiretroviral compounds, vaccines, as well as retroviral-based vectors for human gene therapy.
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Affiliation(s)
- Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates. https://twitter.com/chameettachal
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
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Hyjek‐Składanowska M, Bajczyk M, Gołębiewski M, Nuc P, Kołowerzo‐Lubnau A, Jarmołowski A, Smoliński DJ. Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1155-1173. [PMID: 32369637 PMCID: PMC7540296 DOI: 10.1111/tpj.14792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 05/15/2023]
Abstract
In recent years, research has increasingly focused on the key role of post-transcriptional regulation of messenger ribonucleoprotein (mRNP) function and turnover. As a result of the complexity and dynamic nature of mRNPs, the full composition of a single mRNP complex remains unrevealed and mRNPs are poorly described in plants. Here we identify canonical Sm proteins as part of the cytoplasmic mRNP complex, indicating their function in the post-transcriptional regulation of gene expression in plants. Sm proteins comprise an evolutionarily ancient family of small RNA-binding proteins involved in pre-mRNA splicing. The latest research indicates that Sm could also impact on mRNA at subsequent stages of its life cycle. In this work we show that in the microsporocyte cytoplasm of Larix decidua, the European larch, Sm proteins accumulate within distinct cytoplasmic bodies, also containing polyadenylated RNA. To date, several types of cytoplasmic bodies involved in the post-transcriptional regulation of gene expression have been described, mainly in animal cells. Their role and molecular composition in plants remain less well established, however. A total of 222 mRNA transcripts have been identified as cytoplasmic partners for Sm proteins. The specific colocalization of these mRNAs with Sm proteins within cytoplasmic bodies has been confirmed via microscopic analysis. The results from this work support the hypothesis, that evolutionarily conserved Sm proteins have been adapted to perform a whole repertoire of functions related to the post-transcriptional regulation of gene expression in Eukaryota. This adaptation presumably enabled them to coordinate the interdependent processes of splicing element assembly, mRNA maturation and processing, and mRNA translation regulation, and its degradation.
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Affiliation(s)
- Malwina Hyjek‐Składanowska
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
- Present address:
Laboratory of Protein StructureInternational Institute of Molecular and Cell Biology4 Trojdena St.02‐109WarsawPoland
| | - Mateusz Bajczyk
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Marcin Gołębiewski
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
- Department of Plant Physiology and BiotechnologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
| | - Przemysław Nuc
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Agnieszka Kołowerzo‐Lubnau
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
| | - Artur Jarmołowski
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Dariusz Jan Smoliński
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
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Venters CC, Oh JM, Di C, So BR, Dreyfuss G. U1 snRNP Telescripting: Suppression of Premature Transcription Termination in Introns as a New Layer of Gene Regulation. Cold Spring Harb Perspect Biol 2019; 11:11/2/a032235. [PMID: 30709878 DOI: 10.1101/cshperspect.a032235] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent observations showed that nascent RNA polymerase II transcripts, pre-mRNAs, and noncoding RNAs are highly susceptible to premature 3'-end cleavage and polyadenylation (PCPA) from numerous intronic cryptic polyadenylation signals (PASs). The importance of this in gene regulation was not previously appreciated as PASs, despite their prevalence, were thought to be active in terminal exons at gene ends. Unexpectedly, antisense oligonucleotide interference with U1 snRNA base-pairing to 5' splice sites, which is necessary for U1 snRNP's (U1) function in splicing, caused widespread PCPA in metazoans. This uncovered U1's PCPA suppression activity, termed telescripting, as crucial for full-length transcription in thousands of vertebrate genes, providing a general role in transcription elongation control. Progressive intron-size expansion in metazoan evolution greatly increased PCPA vulnerability and dependence on U1 telescripting. We describe how these observations unfolded and discuss U1 telescripting's role in shaping the transcriptome.
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Affiliation(s)
- Christopher C Venters
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Jung-Min Oh
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Chao Di
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Byung Ran So
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Gideon Dreyfuss
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
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Jayaraman D, Kenyon JC. New windows into retroviral RNA structures. Retrovirology 2018; 15:11. [PMID: 29368653 PMCID: PMC5784592 DOI: 10.1186/s12977-018-0393-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/12/2018] [Indexed: 12/16/2022] Open
Abstract
Background The multiple roles of both viral and cellular RNAs have become increasingly apparent in recent years, and techniques to model them have become significantly more powerful, enabling faster and more accurate visualization of RNA structures. Main body Techniques such as SHAPE (selective 2’OH acylation analysed by primer extension) have revolutionized the field, and have been used to examine RNAs belonging to many and diverse retroviruses. Secondary structure probing reagents such as these have been aided by the development of faster methods of analysis either via capillary or next-generation sequencing, allowing the analysis of entire genomes, and of retroviral RNA structures within virions. Techniques to model the three-dimensional structures of these large RNAs have also recently developed. Conclusions The flexibility of retroviral RNAs, both structural and functional, is clear from the results of these new experimental techniques. Retroviral RNA structures and structural changes control many stages of the lifecycle, and both the RNA structures themselves and their interactions with ligands are potential new drug targets. In addition, our growing understanding of retroviral RNA structures is aiding our knowledge of cellular RNA form and function.
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Affiliation(s)
- Dhivya Jayaraman
- Department of Medicine, National University of Singapore, 14 Medical Drive, MD 6, Level 15, Singapore, 117599, Singapore
| | - Julia Claire Kenyon
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital Hills Rd, Cambridge, CB2 0QQ, UK. .,Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2 Blk MD4, Level 3, Singapore, 117545, Singapore. .,Homerton College, University of Cambridge, Hills Rd, Cambridge, CB2 8PH, UK.
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A purine-rich element in foamy virus pol regulates env splicing and gag/pol expression. Retrovirology 2017; 14:10. [PMID: 28166800 PMCID: PMC5294762 DOI: 10.1186/s12977-017-0337-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/31/2017] [Indexed: 12/21/2022] Open
Abstract
Background The foamy viral genome encodes four central purine-rich elements localized in the integrase-coding region of pol. Previously, we have shown that the first two of these RNA elements (A and B) are required for protease dimerization and activation. The D element functions as internal polypurine tract during reverse transcription. Peters et al., described the third element (C) as essential for gag expression suggesting that it might serve as an RNA export element for the unspliced genomic transcript. Results Here, we analysed env splicing and demonstrate that the described C element composed of three GAA repeats known to bind SR proteins regulates env splicing, thus balancing the amount of gag/pol mRNAs. Deletion of the C element effectively promotes a splice site switch from a newly identified env splice acceptor to the intrinsically strong downstream localised env 3′ splice acceptor permitting complete splicing of almost all LTR derived transcripts. We provide evidence that repression of this env splice acceptor is a prerequisite for gag expression. This repression is achieved by the C element, resulting in impaired branch point recognition and SF1/mBBP binding. Separating the branch point from the overlapping purine-rich C element, by insertion of only 20 nucleotides, liberated repression and fully restored splicing to the intrinsically strong env 3′ splice site. This indicated that the cis-acting element might repress splicing by blocking the recognition of essential splice site signals. Conclusions The foamy viral purine-rich C element regulates splicing by suppressing the branch point recognition of the strongest env splice acceptor. It is essential for the formation of unspliced gag and singly spliced pol transcripts. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0337-6) contains supplementary material, which is available to authorized users.
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Wagner TC, Bodem J. Sequence errors in foamy virus sequences in the GenBank database: resequencing of the prototypic foamy virus proviral plasmids. Arch Virol 2016; 162:1141-1144. [DOI: 10.1007/s00705-016-3206-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/18/2016] [Indexed: 11/29/2022]
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Hamann MV, Lindemann D. Foamy Virus Protein-Nucleic Acid Interactions during Particle Morphogenesis. Viruses 2016; 8:v8090243. [PMID: 27589786 PMCID: PMC5035957 DOI: 10.3390/v8090243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 12/24/2022] Open
Abstract
Compared with orthoretroviruses, our understanding of the molecular and cellular replication mechanism of foamy viruses (FVs), a subfamily of retroviruses, is less advanced. The FV replication cycle differs in several key aspects from orthoretroviruses, which leaves established retroviral models debatable for FVs. Here, we review the general aspect of the FV protein-nucleic acid interactions during virus morphogenesis. We provide a summary of the current knowledge of the FV genome structure and essential sequence motifs required for RNA encapsidation as well as Gag and Pol binding in combination with details about the Gag and Pol biosynthesis. This leads us to address open questions in FV RNA engagement, binding and packaging. Based on recent findings, we propose to shift the point of view from individual glycine-arginine-rich motifs having functions in RNA interactions towards envisioning the FV Gag C-terminus as a general RNA binding protein module. We encourage further investigating a potential new retroviral RNA packaging mechanism, which seems more complex in terms of the components that need to be gathered to form an infectious particle. Additional molecular insights into retroviral protein-nucleic acid interactions help us to develop safer, more specific and more efficient vectors in an era of booming genome engineering and gene therapy approaches.
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Affiliation(s)
- Martin V Hamann
- Institute of Virology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany.
- CRTD/DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Dirk Lindemann
- Institute of Virology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany.
- CRTD/DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany.
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Bouton C, Geldreich A, Ramel L, Ryabova LA, Dimitrova M, Keller M. Cauliflower mosaic virus Transcriptome Reveals a Complex Alternative Splicing Pattern. PLoS One 2015; 10:e0132665. [PMID: 26162084 PMCID: PMC4498817 DOI: 10.1371/journal.pone.0132665] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 06/18/2015] [Indexed: 12/23/2022] Open
Abstract
The plant pararetrovirus Cauliflower mosaic virus (CaMV) uses alternative splicing to generate several isoforms from its polycistronic pregenomic 35S RNA. This pro-cess has been shown to be essential for infectivity. Previous works have identified four splice donor sites and a single splice acceptor site in the 35S RNA 5' region and suggested that the main role of CaMV splicing is to downregulate expression of open reading frames (ORFs) I and II. In this study, we show that alternative splicing is a conserved process among CaMV isolates. In Cabb B-JI and Cabb-S isolates, splicing frequently leads to different fusion between ORFs, particularly between ORF I and II. The corresponding P1P2 fusion proteins expressed in E. coli interact with viral proteins P2 and P3 in vitro. However, they are detected neither during infection nor upon transient expression in planta, which suggests rapid degradation after synthesis and no important biological role in the CaMV infectious cycle. To gain a better understanding of the functional relevance of 35S RNA alternative splicing in CaMV infectivity, we inactivated the previously described splice sites. All the splicing mutants were as pathogenic as the corresponding wild-type isolate. Through RT-PCR-based analysis we demonstrate that CaMV 35S RNA exhibits a complex splicing pattern, as we identify new splice donor and acceptor sites whose selection leads to more than thirteen 35S RNA isoforms in infected turnip plants. Inactivating splice donor or acceptor sites is not lethal for the virus, since disrupted sites are systematically rescued by the activation of cryptic and/or seldom used splice sites. Taken together, our data depict a conserved, complex and flexible process, involving multiple sites, that ensures splicing of 35S RNA.
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Affiliation(s)
- Clément Bouton
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Angèle Geldreich
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Laëtitia Ramel
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Lyubov A. Ryabova
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Maria Dimitrova
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
- * E-mail: (MD); (MK)
| | - Mario Keller
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
- * E-mail: (MD); (MK)
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Koziol U, Radio S, Smircich P, Zarowiecki M, Fernández C, Brehm K. A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed in Echinococcus multilocularis Stem Cells. Genome Biol Evol 2015; 7:2136-53. [PMID: 26133390 PMCID: PMC4558846 DOI: 10.1093/gbe/evv126] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2015] [Indexed: 12/14/2022] Open
Abstract
Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we report the discovery of a novel family of small nonautonomous long terminal repeat retrotransposons (also known as terminal-repeat retrotransposons in miniature, TRIMs) which we have named ta-TRIM (taeniid TRIM). ta-TRIMs are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. These elements originated at the base of the taeniid tree and have expanded during taeniid diversification, including after the divergence of closely related species such as Echinococcus multilocularis and Echinococcus granulosus. They are massively expressed in larval stages, from a small proportion of full-length copies and from isolated terminal repeats that show transcriptional read-through into downstream regions, generating novel noncoding RNAs and transcriptional fusions to coding genes. In E. multilocularis, ta-TRIMs are specifically expressed in the germinative cells (the somatic stem cells) during asexual reproduction of metacestode larvae. This would provide a developmental mechanism for insertion of ta-TRIMs into cells that will eventually generate the adult germ line. Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes.
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Affiliation(s)
- Uriel Koziol
- Institute of Hygiene and Microbiology, University of Würzburg, Germany Sección Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Santiago Radio
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Magdalena Zarowiecki
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Cecilia Fernández
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Klaus Brehm
- Institute of Hygiene and Microbiology, University of Würzburg, Germany
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Rethwilm A. Specific RNA-protein interactions in the replication of foamy viruses (FVs). Curr Opin Virol 2013; 3:676-83. [PMID: 24119459 DOI: 10.1016/j.coviro.2013.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/10/2013] [Accepted: 09/10/2013] [Indexed: 11/25/2022]
Abstract
The FV pathway of replication is fundamentally different from what we know about the strategy employed by all known other retroviruses. This unique pathway involves some distinctive RNA-protein interactions, which range from nuclear RNA export to activation of reverse transcription late in the viral replication cycle. Some peculiarities of this replication strategy will be summarized here.
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Affiliation(s)
- Axel Rethwilm
- Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Str. 7, 97078 Würzburg, Germany.
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