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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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Hanson HM, Willkomm NA, Yang H, Mansky LM. Human Retrovirus Genomic RNA Packaging. Viruses 2022; 14:1094. [PMID: 35632835 PMCID: PMC9142903 DOI: 10.3390/v14051094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 02/07/2023] Open
Abstract
Two non-covalently linked copies of the retrovirus genome are specifically recruited to the site of virus particle assembly and packaged into released particles. Retroviral RNA packaging requires RNA export of the unspliced genomic RNA from the nucleus, translocation of the genome to virus assembly sites, and specific interaction with Gag, the main viral structural protein. While some aspects of the RNA packaging process are understood, many others remain poorly understood. In this review, we provide an update on recent advancements in understanding the mechanism of RNA packaging for retroviruses that cause disease in humans, i.e., HIV-1, HIV-2, and HTLV-1, as well as advances in the understanding of the details of genomic RNA nuclear export, genome translocation to virus assembly sites, and genomic RNA dimerization.
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Affiliation(s)
- Heather M. Hanson
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA;
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
| | - Nora A. Willkomm
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- DDS-PhD Dual Degree Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- Comparative Molecular Biosciences Graduate Program, University of Minnesota—Twin Cities, St. Paul, MN 55455, USA
| | - Louis M. Mansky
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA;
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- DDS-PhD Dual Degree Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Comparative Molecular Biosciences Graduate Program, University of Minnesota—Twin Cities, St. Paul, MN 55455, USA
- Masonic Cancer Center, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
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Wu W, Hatterschide J, Syu YC, Cantara WA, Blower RJ, Hanson HM, Mansky LM, Musier-Forsyth K. Human T-cell leukemia virus type 1 Gag domains have distinct RNA-binding specificities with implications for RNA packaging and dimerization. J Biol Chem 2018; 293:16261-16276. [PMID: 30217825 DOI: 10.1074/jbc.ra118.005531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/13/2018] [Indexed: 12/14/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the first retrovirus that has conclusively been shown to cause human diseases. In HIV-1, specific interactions between the nucleocapsid (NC) domain of the Gag protein and genomic RNA (gRNA) mediate gRNA dimerization and selective packaging; however, the mechanism for gRNA packaging in HTLV-1, a deltaretrovirus, is unclear. In other deltaretroviruses, the matrix (MA) and NC domains of Gag are both involved in gRNA packaging, but MA binds nucleic acids with higher affinity and has more robust chaperone activity, suggesting that this domain may play a primary role. Here, we show that the MA domain of HTLV-1, but not the NC domain, binds short hairpin RNAs derived from the putative gRNA packaging signal. RNA probing of the HTLV-1 5' leader and cross-linking studies revealed that the primer-binding site and a region within the putative packaging signal form stable hairpins that interact with MA. In addition to a previously identified palindromic dimerization initiation site (DIS), we identified a new DIS in HTLV-1 gRNA and found that both palindromic sequences bind specifically the NC domain. Surprisingly, a mutant partially defective in dimer formation in vitro exhibited a significant increase in RNA packaging into HTLV-1-like particles, suggesting that efficient RNA dimerization may not be strictly required for RNA packaging in HTLV-1. Moreover, the lifecycle of HTLV-1 and other deltaretroviruses may be characterized by NC and MA functions that are distinct from those of the corresponding HIV-1 proteins, but together provide the functions required for viral replication.
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Affiliation(s)
- Weixin Wu
- From the Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus Ohio 43210 and
| | - Joshua Hatterschide
- From the Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus Ohio 43210 and
| | - Yu-Ci Syu
- From the Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus Ohio 43210 and
| | - William A Cantara
- From the Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus Ohio 43210 and
| | | | - Heather M Hanson
- Institute for Molecular Virology.,Molecular, Cellular, Developmental Biology and Genetics Graduate Program, and
| | - Louis M Mansky
- Institute for Molecular Virology.,Molecular, Cellular, Developmental Biology and Genetics Graduate Program, and.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Karin Musier-Forsyth
- From the Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus Ohio 43210 and
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Dubois N, Marquet R, Paillart JC, Bernacchi S. Retroviral RNA Dimerization: From Structure to Functions. Front Microbiol 2018; 9:527. [PMID: 29623074 PMCID: PMC5874298 DOI: 10.3389/fmicb.2018.00527] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/08/2018] [Indexed: 01/18/2023] Open
Abstract
The genome of the retroviruses is a dimer composed by two homologous copies of genomic RNA (gRNA) molecules of positive polarity. The dimerization process allows two gRNA molecules to be non-covalently linked together through intermolecular base-pairing. This step is critical for the viral life cycle and is highly conserved among retroviruses with the exception of spumaretroviruses. Furthermore, packaging of two gRNA copies into viral particles presents an important evolutionary advantage for immune system evasion and drug resistance. Recent studies reported RNA switches models regulating not only gRNA dimerization, but also translation and packaging, and a spatio-temporal characterization of viral gRNA dimerization within cells are now at hand. This review summarizes our current understanding on the structural features of the dimerization signals for a variety of retroviruses (HIVs, MLV, RSV, BLV, MMTV, MPMV…), the mechanisms of RNA dimer formation and functional implications in the retroviral cycle.
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Affiliation(s)
- Noé Dubois
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Roland Marquet
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Serena Bernacchi
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
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Yu H, Li T, Qiao W, Chen Q, Geng Y. Guanine tetrad and palindromic sequence play critical roles in the RNA dimerization of bovine foamy virus. Arch Virol 2007; 152:2159-67. [PMID: 17712597 DOI: 10.1007/s00705-007-1047-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Accepted: 07/18/2007] [Indexed: 10/22/2022]
Abstract
Retroviruses are unique in having a diploid genome. However, the RNA sequences and structures that link the two RNA molecules are different. To identify the dimer linkage site of bovine foamy virus (BFV), complementary DNAs were used to interfere with RNA dimerization of BFV. We found that two sites, designated SI and SII, within a 53-base RNA fragment, were essential for BFV dimerization in vitro. SI consists of a potential guanine tetrad (GGGGC), which overlaps the primer binding site, while SII contains 15 nucleotides including a palindromic sequence, UCCCUAGGGA. Masking either of the sites completely abolished RNA dimer formation. Furthermore, a deletion of SII was introduced into a BFV infectious DNA clone; we found that deletion of SII significantly increased expression of BFV transactivator Borf-1. Interestingly, we also found that this deletion abolished viral infectivity. These results suggest that dimerization might play a unique role in the BFV life cycle.
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Affiliation(s)
- H Yu
- College of Life Sciences, Nankai University, Tianjin, PR China
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Monie TP, Greatorex JS, Zacharias M, Lever AML. The human T-cell lymphotropic virus type-I dimerization initiation site forms a hairpin loop, unlike previously characterized retroviral dimerization motifs. Biochemistry 2004; 43:6085-90. [PMID: 15147192 DOI: 10.1021/bi030237i] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of genomic RNA dimers during the retroviral life cycle is essential for optimal viral replication and infectivity. The sequences and RNA structures responsible for this interaction are located in the untranslated 5' leader RNA, along with other cis-acting signals. Dimer formation occurs by specific interaction between identical structural motifs. It is believed that an initial kissing hairpin forms following self-recognition by autocomplementary RNA loops, leading to formation of an extended stable duplex. The dimerization initiation site (DIS) of the deltaretrovirus human T-cell lymphotropic virus type-I (HTLV-I) has been previously localized to a 14-nucleotide sequence predicted to contain an RNA stem loop. Biochemical probing of the monomeric RNA structure using RNAse T1, RNAse V1, RNAse U2, lead acetate, and dimethyl sulfate has led to the generation of the first structural map of the HTLV-I DIS. A comprehensive data set of individual nucleotide modifications reveals that the structural motif responsible for HTLV-I RNA dimerization forms a trinucleotide RNA loop, unlike any previously characterized retroviral dimerization motif. Molecular modeling demonstrates that this can be formed by an unusual C:synG base pair closing the loop. Comparative phylogeny indicates that such a motif may also exist in other deltaretroviruses.
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Affiliation(s)
- Tom P Monie
- Department of Medicine, University of Cambridge, Level 5, Addenbrooke's Hospital, UK
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Greatorex J. The retroviral RNA dimer linkage: different structures may reflect different roles. Retrovirology 2004; 1:22. [PMID: 15317659 PMCID: PMC516450 DOI: 10.1186/1742-4690-1-22] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Accepted: 08/18/2004] [Indexed: 11/16/2022] Open
Abstract
Retroviruses are unique among virus families in having dimeric genomes. The RNA sequences and structures that link the two RNA molecules vary, and these differences provide clues as to the role of this feature in the viral lifecycles. This review draws upon examples from different retroviral families. Differences and similarities in both secondary and tertiary structure are discussed. The implication of varying roles for the dimer linkage in related viruses is considered.
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Affiliation(s)
- Jane Greatorex
- Division of Infectious Diseases, Dept. of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 2QQ, UK.
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Paillart JC, Shehu-Xhilaga M, Marquet R, Mak J. Dimerization of retroviral RNA genomes: an inseparable pair. Nat Rev Microbiol 2004; 2:461-72. [PMID: 15152202 DOI: 10.1038/nrmicro903] [Citation(s) in RCA: 232] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jean-Christophe Paillart
- UPR 9002 du CNRS affiliée à l'Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France
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Ren X, Gavory G, Li H, Ying L, Klenerman D, Balasubramanian S. Identification of a new RNA.RNA interaction site for human telomerase RNA (hTR): structural implications for hTR accumulation and a dyskeratosis congenita point mutation. Nucleic Acids Res 2004; 31:6509-15. [PMID: 14602909 PMCID: PMC275565 DOI: 10.1093/nar/gkg871] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The enzyme telomerase is a ribonucleoprotein that has a critical role in the maintenance of stable telomeres in organisms that possess linear chromosomes. Using a recently developed single molecule fluorescence coincidence method, we have studied the RNA component of telomerase (hTR) and directly observed multimerisation of hTR in solution. RNA mutagenesis and blocking oligonucleotides were employed to identify the single-stranded internal loop J7b/8a as an important and specific hTR.hTR interaction site. This observation was confirmed by studies on a model RNA fragment (hTR(380-444)), comprising part of the H/ACA domain, the internal loop J7b/8a and the CR7 domain, that was found to dimerise. Substitution mutagenesis within the proposed RNA.RNA interaction site of hTR(380-444) resulted in a loss of dimerisation potential and insertion of the dyskeratosis congenita mutation C408G led to a significant reduction in dimer formation. Together, these results suggest that this RNA.RNA interaction site may be functionally relevant.
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Affiliation(s)
- Xiaojun Ren
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Abstract
RNA loop-loop interactions are frequently used to trigger initial recognition between two RNA molecules. In this review, we present selected well-documented cases that illustrate the diversity of biological processes using RNA loop-loop recognition properties. The first one is related to natural antisense RNAs that play a variety of regulatory functions in bacteria and their extra-chromosomal elements. The second one concerns the dimerization of HIV-1 genomic RNA, which is responsible for the encapsidation of a diploid RNA genome. The third one concerns RNA interactions involving double-loop interactions. These are used by the bicoid mRNA to form dimers, a property that appears to be important for mRNA localization in drosophila embryo, and by bacteriophage phi29 pRNA which forms hexamers that participate in the translocation of the DNA genome through the portal vertex of the capsid. Despite the high diversity of systems and mechanisms, some common features can be highlighted. (1) Efficient recognition requires rapid bi-molecular binding rates, regardless of the RNA pairing scheme. (2) The initial recognition is favored by particular conformations of the loops enabling a proper presentation of nucleotides (generally a restricted number) that initiate the recognition process. (3) The fate of the initial reversible loop-loop complex is dictated by both functional and structural constraints. RNA structures have evolved either to "freeze" the initial complex, or to convert it into a more stable one, which involves propagation of intermolecular interactions along topologically feasible pathways. Stabilization of the initial complex may also be assisted by proteins and/or formation of additional contacts.
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Affiliation(s)
- Christine Brunel
- UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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Abstract
Retroviral virions each contain two identical genomic RNA strands that are stably but noncovalently joined in parallel near their 5' ends. For certain viruses, this dimerization has been shown to depend on a unique RNA stem-loop locus, called the dimer initiation site (DIS), that efficiently homodimerizes through a palindromic base sequence in its loop. Previous studies with Moloney murine leukemia virus (Mo-MuLV) identified two alternative DIS loci that can each independently support RNA dimerization in vitro but whose relative contributions are unknown. We now report that both of these loci contribute to the assembly of the Mo-MuLV dimer. Using targeted deletions, point mutagenesis, and antisense oligonucleotides, we found that each of the two stem-loops forms as predicted and contributes independently to dimerization in vitro through a mechanism involving autocomplementary interactions of its loop. Disruption of either DIS locus individually reduced both the yield and the thermal stability of the in vitro dimers, whereas disruption of both eliminated dimerization altogether. Similarly, the thermal stability of virion-derived dimers was impaired by deletion of both DIS elements, and point mutations in either element produced defects in viral replication that correlated with their effects on in vitro RNA dimerization. These findings support the view that in some retroviruses, dimer initiation and stability involve two or more closely linked DIS loci which together align the nascent dimer strands in parallel and in register.
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Affiliation(s)
- Hinh Ly
- Department of Pathology, University of California, San Francisco, California 94143-0511, USA
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