1
|
Baby J, Gull B, Ahmad W, Baki HA, Khader TA, Panicker NG, Akhlaq S, Rizvi TA, Mustafa F. The Host miR-17-92 Cluster Negatively Regulates Mouse Mammary Tumor Virus (MMTV) Replication Primarily Via Cluster Member miR-92a. J Mol Biol 2024; 436:168738. [PMID: 39117177 DOI: 10.1016/j.jmb.2024.168738] [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: 02/15/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024]
Abstract
The mouse mammary tumor virus (MMTV) is a well-known causative agent of breast cancer in mice. Previously, we have shown that MMTV dysregulates expression of the host miR-17-92 cluster in MMTV-infected mammary glands and MMTV-induced tumors. This cluster, better known as oncomiR-1, is frequently dysregulated in cancers, particularly breast cancer. In this study, our aim was to uncover a functional interaction between MMTV and the cluster. Our results reveal that MMTV expression led to dysregulation of the cluster in both mammary epithelial HC11 and HEK293T cells with the expression of miR-92a cluster member being affected the most. Conversely, overexpression of the whole or partial cluster significantly repressed MMTV expression. Notably, overexpression of cluster member miR-92a alone repressed MMTV expression to the same extent as overexpression of the complete/partial cluster. Inhibition of miR-92a led to nearly a complete restoration of MMTV expression, while deletion/substitution of the miR-92a seed sequence rescued MMTV expression. Dual luciferase assays identified MMTV genomic RNA as the potential target of miR-92a. These results show that the miR-17-92 cluster acts as part of the cell's well-known miRNA-based anti-viral response to thwart incoming MMTV infection. Thus, this study provides the first evidence highlighting the biological significance of host miRNAs in regulating MMTV replication and potentially influencing tumorigenesis.
Collapse
Affiliation(s)
- Jasmin Baby
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Bushra Gull
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Waqar Ahmad
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Hala Abdul Baki
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Thanumol Abdul Khader
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE; ASPIRE Research Institute in Precision Medicine, Abu Dhabi, UAE.
| | - Neena G Panicker
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Shaima Akhlaq
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE.
| | - Tahir A Rizvi
- Department of Microbiology and Immunology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE; Zayed Center for Health Sciences (ZCHS), UAE University, Al Ain, UAE; ASPIRE Research Institute in Precision Medicine, Abu Dhabi, UAE.
| | - Farah Mustafa
- Department of Biochemistry and Molecular Biology, College of Medicine & Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain, UAE; Zayed Center for Health Sciences (ZCHS), UAE University, Al Ain, UAE; ASPIRE Research Institute in Precision Medicine, Abu Dhabi, UAE.
| |
Collapse
|
2
|
Prabhu SG, Pillai VN, Ali LM, Vivet-Boudou V, Chameettachal A, Bernacchi S, Mustafa F, Marquet R, Rizvi TA. MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals. PLoS Biol 2024; 22:e3002827. [PMID: 39361708 PMCID: PMC11449360 DOI: 10.1371/journal.pbio.3002827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/30/2024] [Indexed: 10/05/2024] Open
Abstract
The packaging of genomic RNA (gRNA) into retroviral particles relies on the specific recognition by the Gag precursor of packaging signals (Psi), which maintain a complex secondary structure through long-range interactions (LRIs). However, it remains unclear whether the binding of Gag to Psi alone is enough to promote RNA packaging and what role LRIs play in this process. Using mouse mammary tumor virus (MMTV), we investigated the effects of mutations in 4 proposed LRIs on gRNA structure and function. Our findings revealed the presence of an unsuspected extended LRI, and hSHAPE revealed that maintaining a wild-type-like Psi structure is crucial for efficient packaging. Surprisingly, filter-binding assays demonstrated that most mutants, regardless of their packaging capability, exhibited significant binding to Pr77Gag, suggesting that Gag binding to Psi is insufficient for efficient packaging. Footprinting experiments indicated that efficient RNA packaging is promoted when Pr77Gag binds to 2 specific sites within Psi, whereas binding elsewhere in Psi does not lead to efficient packaging. Taken together, our results suggest that the 3D structure of the Psi/Pr77Gag complex regulates the assembly of viral particles around gRNA, enabling effective discrimination against other viral and cellular RNAs that may also bind Gag efficiently.
Collapse
Affiliation(s)
- Suresha G Prabhu
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Vineeta N Pillai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Lizna Mohamed Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Farah Mustafa
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Research Institute in Precision Medicine, Abu Dhabi, United Arab Emirates
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Research Institute in Precision Medicine, Abu Dhabi, United Arab Emirates
| |
Collapse
|
3
|
Krishnan A, Ali LM, Prabhu SG, Pillai VN, Chameettachal A, Vivet-Boudou V, Bernacchi S, Mustafa F, Marquet R, Rizvi TA. Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging. RNA (NEW YORK, N.Y.) 2023; 30:68-88. [PMID: 37914398 PMCID: PMC10726167 DOI: 10.1261/rna.079840.123] [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: 09/15/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023]
Abstract
The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous regions within the 5' end of the gRNA that assumes a higher order structure harboring several structural motifs. To better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ sequences using genetic, biochemical, and structure-function relationship approaches. Our mutational analysis revealed that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput selective 2' hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences, with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained nucleotides 80-92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA-Pr50Gag interactions. Delineating sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of FIV-based vectors for human gene therapy.
Collapse
Affiliation(s)
- Anjana Krishnan
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Lizna M Ali
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Suresha G Prabhu
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Vineeta N Pillai
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Akhil Chameettachal
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67084 Strasbourg cedex, France
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67084 Strasbourg cedex, France
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Research Institute in Precision Medicine, Abu Dhabi, United Arab Emirates
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67084 Strasbourg cedex, France
| | - Tahir A Rizvi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Research Institute in Precision Medicine, Abu Dhabi, United Arab Emirates
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Pillai VN, Ali LM, Prabhu SG, Krishnan A, Tariq S, Mustafa F, Rizvi TA. Expression, purification, and functional characterization of soluble recombinant full-length simian immunodeficiency virus (SIV) Pr55 Gag. Heliyon 2023; 9:e12892. [PMID: 36685375 PMCID: PMC9853374 DOI: 10.1016/j.heliyon.2023.e12892] [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: 08/03/2022] [Revised: 12/14/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
The simian immunodeficiency virus (SIV) precursor polypeptide Pr55Gag drives viral assembly and facilitates specific recognition and packaging of the SIV genomic RNA (gRNA) into viral particles. While several studies have tried to elucidate the role of SIV Pr55Gag by expressing its different components independently, studies using full-length SIV Pr55Gag have not been conducted, primarily due to the unavailability of purified and biologically active full-length SIV Pr55Gag. We successfully expressed soluble, full-length SIV Pr55Gag with His6-tag in bacteria and purified it using affinity and gel filtration chromatography. In the process, we identified within Gag, a second in-frame start codon downstream of a putative Shine-Dalgarno-like sequence resulting in an additional truncated form of Gag. Synonymously mutating this sequence allowed expression of full-length Gag in its native form. The purified Gag assembled into virus-like particles (VLPs) in vitro in the presence of nucleic acids, revealing its biological functionality. In vivo experiments also confirmed formation of functional VLPs, and quantitative reverse transcriptase PCR demonstrated efficient packaging of SIV gRNA by these VLPs. The methodology we employed ensured the availability of >95% pure, biologically active, full-length SIV Pr55Gag which should facilitate future studies to understand protein structure and RNA-protein interactions involved during SIV gRNA packaging.
Collapse
Affiliation(s)
- Vineeta N. Pillai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates
| | - Lizna Mohamed Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates
| | - Suresha G. Prabhu
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates
| | - Anjana Krishnan
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates
| | - Saeed Tariq
- Department of Anatomy, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates,Corresponding author. Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), P.O. Box 15551, 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 Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates,Corresponding author. Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), P.O. Box 15551, Al Ain, United Arab Emirates.
| |
Collapse
|
6
|
A Stretch of Unpaired Purines in the Leader Region of Simian Immunodeficiency Virus (SIV) Genomic RNA is Critical for its Packaging into Virions. J Mol Biol 2021; 433:167293. [PMID: 34624298 DOI: 10.1016/j.jmb.2021.167293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/22/2022]
Abstract
Simian immunodeficiency virus (SIV) is an important lentivirus used as a non-human primate model to study HIV replication, and pathogenesis of human AIDS, as well as a potential vector for human gene therapy. This study investigated the role of single-stranded purines (ssPurines) as potential genomic RNA (gRNA) packaging determinants in SIV replication. Similar ssPurines have been implicated as important motifs for gRNA packaging in many retroviruses like, HIV-1, MPMV, and MMTV by serving as Gag binding sites during virion assembly. In examining the secondary structure of the SIV 5' leader region, as recently deduced using SHAPE methodology, we identified four specific stretches of ssPurines (I-IV) in the region that harbors major packaging determinants of SIV. The significance of these ssPurine motifs were investigated by mutational analysis coupled with a biologically relevant single round of replication assay. These analyses revealed that while ssPurine II was essential, the others (ssPurines I, III, & IV) did not significantly contribute to SIV gRNA packaging. Any mutation in the ssPurine II, such as its deletion or substitution, or other mutations that caused base pairing of ssPurine II loop resulted in near abrogation of RNA packaging, further substantiating the crucial role of ssPurine II and its looped conformation in SIV gRNA packaging. Structure prediction analysis of these mutants further corroborated the biological results and further revealed that the unpaired nature of ssPurine II is critical for its function during SIV RNA packaging perhaps by enabling it to function as a specific binding site for SIV Gag.
Collapse
|
7
|
Chameettachal A, Vivet-Boudou V, Pitchai F, Pillai V, Ali L, Krishnan A, Bernacchi S, Mustafa F, Marquet R, Rizvi T. A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag. Nucleic Acids Res 2021; 49:4668-4688. [PMID: 33836091 PMCID: PMC8096270 DOI: 10.1093/nar/gkab223] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 12/22/2022] Open
Abstract
Retroviral RNA genome (gRNA) harbors cis-acting sequences that facilitate its specific packaging from a pool of other viral and cellular RNAs by binding with high-affinity to the viral Gag protein during virus assembly. However, the molecular intricacies involved during selective gRNA packaging are poorly understood. Binding and footprinting assays on mouse mammary tumor virus (MMTV) gRNA with purified Pr77Gag along with in cell gRNA packaging study identified two Pr77Gag binding sites constituting critical, non-redundant packaging signals. These included: a purine loop in a bifurcated stem-loop containing the gRNA dimerization initiation site, and the primer binding site (PBS). Despite these sites being present on both unspliced and spliced RNAs, Pr77Gag specifically bound to unspliced RNA, since only that could adopt the native bifurcated stem-loop structure containing looped purines. These results map minimum structural elements required to initiate MMTV gRNA packaging, distinguishing features that are conserved amongst divergent retroviruses from those perhaps unique to MMTV. Unlike purine-rich motifs frequently associated with packaging signals, direct involvement of PBS in gRNA packaging has not been documented in retroviruses. These results enhance our understanding of retroviral gRNA packaging/assembly, making it not only a target for novel therapeutic interventions, but also development of safer gene therapy vectors.
Collapse
Affiliation(s)
- Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Fathima Nuzra Nagoor Pitchai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Vineeta N Pillai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Lizna Mohamed Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Anjana Krishnan
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, United Arab Emirates
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, United Arab Emirates
| |
Collapse
|
8
|
Ali LM, Pitchai FNN, Vivet-Boudou V, Chameettachal A, Jabeen A, Pillai VN, Mustafa F, Marquet R, Rizvi TA. Role of Purine-Rich Regions in Mason-Pfizer Monkey Virus (MPMV) Genomic RNA Packaging and Propagation. Front Microbiol 2020; 11:595410. [PMID: 33250884 PMCID: PMC7674771 DOI: 10.3389/fmicb.2020.595410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
A distinguishing feature of the Mason-Pfizer monkey virus (MPMV) packaging signal RNA secondary structure is a single-stranded purine-rich sequence (ssPurines) in close vicinity to a palindromic stem loop (Pal SL) that functions as MPMV dimerization initiation site (DIS). However, unlike other retroviruses, MPMV contains a partially base-paired repeat sequence of ssPurines (bpPurines) in the adjacent region. Both purine-rich sequences have earlier been proposed to act as potentially redundant Gag binding sites to initiate the process of MPMV genomic RNA (gRNA) packaging. The objective of this study was to investigate the biological significance of ssPurines and bpPurines in MPMV gRNA packaging by systematic mutational and biochemical probing analyses. Deletion of either ssPurines or bpPurines individually had no significant effect on MPMV gRNA packaging, but it was severely compromised when both sequences were deleted simultaneously. Selective 2′ hydroxyl acylation analyzed by primer extension (SHAPE) analysis of the mutant RNAs revealed only mild effects on structure by deletion of either ssPurines or bpPurines, while the structure was dramatically affected by the two simultaneous deletions. This suggests that ssPurines and bpPurines play a redundant role in MPMV gRNA packaging, probably as Gag binding sites to facilitate gRNA capture and encapsidation. Interestingly, the deletion of bpPurines revealed an additional severe defect on RNA propagation that was independent of the presence or absence of ssPurines or the gRNA structure of the region. These findings further suggest that the bpPurines play an additional role in the early steps of MPMV replication cycle that is yet to be identified.
Collapse
Affiliation(s)
- Lizna Mohamed Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Fathima Nuzra Nagoor Pitchai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Valérie Vivet-Boudou
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ayesha Jabeen
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Vineeta N Pillai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Roland Marquet
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| |
Collapse
|
9
|
Purification and Functional Characterization of a Biologically Active Full-Length Feline Immunodeficiency Virus (FIV) Pr50 Gag. Viruses 2019; 11:v11080689. [PMID: 31357656 PMCID: PMC6723490 DOI: 10.3390/v11080689] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 01/01/2023] Open
Abstract
The feline immunodeficiency virus (FIV) full-length Pr50Gag precursor is a key player in the assembly of new viral particles. It is also a critical component of the efficient selection and packaging of two copies of genomic RNA (gRNA) into the newly formed virus particles from a wide pool of cellular and spliced viral RNA. To understand the molecular mechanisms involved during FIV gRNA packaging, we expressed the His6-tagged and untagged recombinant FIV Pr50Gag protein both in eukaryotic and prokaryotic cells. The recombinant Pr50Gag-His6-tag fusion protein was purified from soluble fractions of prokaryotic cultures using immobilized metal affinity chromatography (IMAC). This purified protein was able to assemble in vitro into virus-like particles (VLPs), indicating that it preserved its ability to oligomerize/multimerize. Furthermore, VLPs formed in eukaryotic cells by the FIV full-length Pr50Gag both in the presence and absence of His6-tag could package FIV sub-genomic RNA to similar levels, suggesting that the biological activity of the recombinant full-length Pr50Gag fusion protein was retained in the presence of His6-tag at the carboxy terminus. Successful expression and purification of a biologically active, recombinant full-length Pr50Gag-His6-tag fusion protein will allow study of the intricate RNA-protein interactions involved during FIV gRNA encapsidation.
Collapse
|