1
|
Narasipura SD, Zayas JP, Ash MK, Reyes A, Shull T, Gambut S, Schneider JR, Lorenzo-Redondo R, Al-Harthi L, Mamede JI. HIV-1 infection promotes neuroinflammation and neuron pathogenesis in novel microglia-containing cerebral organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598579. [PMID: 38915632 PMCID: PMC11195220 DOI: 10.1101/2024.06.13.598579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cerebral organoids (COs) are a valuable tool to study the intricate interplay between glial cells and neurons in brain development and disease, including HIV-associated neuroinflammation. We developed a novel approach to generate microglia containing COs (CO-iMs) by co-culturing hematopoietic progenitors and induced pluripotent stem cells. This approach allowed for the differentiation of microglia within the organoids concomitantly to the neuronal progenitors. CO- iMs exhibited higher efficiency in generation of CD45 + /CD11b + /Iba-1 + microglia cells compared to conventional COs with physiologically relevant proportion of microglia (∼7%). CO-iMs exhibited substantially higher expression of microglial homeostatic and sensome markers as well as markers for the complement cascade. CO-iMs showed susceptibility to HIV infection resulting in a significant increase in several pro-inflammatory cytokines/chemokines and compromised neuronal function, which were abrogated by addition of antiretrovirals. Thus, CO-iM is a robust model to decipher neuropathogenesis, neurological disorders, and viral infections of brain cells in a 3D culture system.
Collapse
|
2
|
A novel feature and sample joint transfer learning method with feature selection in semi-supervised scenarios for identifying the sequence of some species with less known genetic data. Soft comput 2023. [DOI: 10.1007/s00500-022-07773-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
3
|
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
|
4
|
Waight E, Zhang C, Mathews S, Kevadiya BD, Lloyd KCK, Gendelman HE, Gorantla S, Poluektova LY, Dash PK. Animal models for studies of HIV-1 brain reservoirs. J Leukoc Biol 2022; 112:1285-1295. [PMID: 36044375 PMCID: PMC9804185 DOI: 10.1002/jlb.5vmr0322-161r] [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: 01/18/2022] [Revised: 05/26/2022] [Indexed: 01/07/2023] Open
Abstract
The HIV-1 often evades a robust antiretroviral-mediated immune response, leading to persistent infection within anatomically privileged sites including the CNS. Continuous low-level infection occurs in the presence of effective antiretroviral therapy (ART) in CD4+ T cells and mononuclear phagocytes (MP; monocytes, macrophages, microglia, and dendritic cells). Within the CNS, productive viral infection is found exclusively in microglia and meningeal, perivascular, and choroidal macrophages. MPs serve as the principal viral CNS reservoir. Animal models have been developed to recapitulate natural human HIV-1 infection. These include nonhuman primates, humanized mice, EcoHIV, and transgenic rodent models. These models have been used to study disease pathobiology, antiretroviral and immune modulatory agents, viral reservoirs, and eradication strategies. However, each of these models are limited to specific component(s) of human disease. Indeed, HIV-1 species specificity must drive therapeutic and cure studies. These have been studied in several model systems reflective of latent infections, specifically in MP (myeloid, monocyte, macrophages, microglia, and histiocyte cell) populations. Therefore, additional small animal models that allow productive viral replication to enable viral carriage into the brain and the virus-susceptible MPs are needed. To this end, this review serves to outline animal models currently available to study myeloid brain reservoirs and highlight areas that are lacking and require future research to more effectively study disease-specific events that could be useful for viral eradication studies both in and outside the CNS.
Collapse
Affiliation(s)
- Emiko Waight
- Department of Pharmacology and Experimental Neuroscience, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Chen Zhang
- Department of Pharmacology and Experimental Neuroscience, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Saumi Mathews
- Department of Pharmacology and Experimental Neuroscience, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Bhavesh D. Kevadiya
- Department of Pharmacology and Experimental Neuroscience, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - K. C. Kent Lloyd
- Department of Surgery, School of Medicine, and Mouse Biology ProgramUniversity of California DavisCaliforniaUSA
| | - Howard E. Gendelman
- Department of Pharmacology and Experimental Neuroscience, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Santhi Gorantla
- Department of Pharmacology and Experimental Neuroscience, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Larisa Y. Poluektova
- Department of Pharmacology and Experimental Neuroscience, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Prasanta K. Dash
- Department of Pharmacology and Experimental Neuroscience, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| |
Collapse
|
5
|
How HIV-1 Gag Manipulates Its Host Cell Proteins: A Focus on Interactors of the Nucleocapsid Domain. Viruses 2020; 12:v12080888. [PMID: 32823718 PMCID: PMC7471995 DOI: 10.3390/v12080888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/27/2022] Open
Abstract
The human immunodeficiency virus (HIV-1) polyprotein Gag (Group-specific antigen) plays a central role in controlling the late phase of the viral lifecycle. Considered to be only a scaffolding protein for a long time, the structural protein Gag plays determinate and specific roles in HIV-1 replication. Indeed, via its different domains, Gag orchestrates the specific encapsidation of the genomic RNA, drives the formation of the viral particle by its auto-assembly (multimerization), binds multiple viral proteins, and interacts with a large number of cellular proteins that are needed for its functions from its translation location to the plasma membrane, where newly formed virions are released. Here, we review the interactions between HIV-1 Gag and 66 cellular proteins. Notably, we describe the techniques used to evidence these interactions, the different domains of Gag involved, and the implications of these interactions in the HIV-1 replication cycle. In the final part, we focus on the interactions involving the highly conserved nucleocapsid (NC) domain of Gag and detail the functions of the NC interactants along the viral lifecycle.
Collapse
|
6
|
Tuske S, Zheng J, Olson ED, Ruiz FX, Pascal BD, Hoang A, Bauman JD, Das K, DeStefano JJ, Musier-Forsyth K, Griffin PR, Arnold E. Integrative structural biology studies of HIV-1 reverse transcriptase binding to a high-affinity DNA aptamer. Curr Res Struct Biol 2020; 2:116-129. [PMID: 33870216 PMCID: PMC8052095 DOI: 10.1016/j.crstbi.2020.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/03/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
The high-resolution crystal structure of HIV-1 reverse transcriptase (RT) bound to a 38-mer DNA hairpin aptamer with low pM affinity was previously described. The high-affinity binding aptamer contained 2'-O-methyl modifications and a seven base-pair GC-rich tract and the structure of the RT-aptamer complex revealed specific contacts between RT and the template strand of the aptamer. Similar to all crystal structures of RT bound to nucleic acid template-primers, the aptamer bound RT with a bend in the duplex DNA. To understand the structural basis for the ultra-high-affinity aptamer binding, an integrative structural biology approach was used. Hydrogen-deuterium exchange coupled to liquid chromatography-mass spectrometry (HDX-MS) was used to examine the structural dynamics of RT alone and in the presence of the DNA aptamer. RT was selectively labeled with 15N to unambiguously identify peptides from each subunit. HDX of unliganded RT shows a mostly stable core. The p66 fingers and thumb subdomains, and the RNase H domain are relatively dynamic. HDX indicates that both the aptamer and a scrambled version significantly stabilize regions of RT that are dynamic in the absence of DNA. No substantial differences in RT dynamics are observed between aptamer and scrambled aptamer binding, despite a large difference in binding affinity. Small-angle X-ray scattering and circular dichroism spectroscopy were used to investigate the aptamer conformation in solution and revealed a pre-bent DNA that possesses both A- and B-form helical character. Both the 2'-O-methyl modifications and the GC tract appear to contribute to an energetically favorable conformation for binding to RT that contributes to the aptamer's ultra-high affinity for RT. The X-ray structure of RT with an RNA/DNA version of the aptamer at 2.8 Å resolution revealed a potential role of the hairpin positioning in affinity. Together, the data suggest that both the 2'-O-methyl modifications and the GC tract contribute to an energetically favorable conformation for high-affinity binding to RT.
Collapse
Affiliation(s)
- Steve Tuske
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Erik D. Olson
- Department of Chemistry and Biochemistry, Center for RNA Biology, And Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Bruce D. Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Anthony Hoang
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD, 20740, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, And Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| |
Collapse
|
7
|
Monette A, Niu M, Chen L, Rao S, Gorelick RJ, Mouland AJ. Pan-retroviral Nucleocapsid-Mediated Phase Separation Regulates Genomic RNA Positioning and Trafficking. Cell Rep 2020; 31:107520. [PMID: 32320662 PMCID: PMC8965748 DOI: 10.1016/j.celrep.2020.03.084] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/12/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023] Open
Abstract
The duality of liquid-liquid phase separation (LLPS) of cellular components into membraneless organelles defines the nucleation of both normal and disease processes including stress granule (SG) assembly. From mounting evidence of LLPS utility by viruses, we discover that HIV-1 nucleocapsid (NC) protein condenses into zinc-finger (ZnF)-dependent LLPSs that are dynamically influenced by cytosolic factors. ZnF-dependent and Zinc (Zn2+)-chelation-sensitive NC-LLPS are formed in live cells. NC-Zn2+ ejection reverses the HIV-1 blockade on SG assembly, inhibits NC-SG assembly, disrupts NC/Gag-genomic RNA (vRNA) ribonucleoprotein complexes, and causes nuclear sequestration of NC and the vRNA, inhibiting Gag expression and virus release. NC ZnF mutagenesis eliminates the HIV-1 blockade of SG assembly and repositions vRNA to SGs. We find that NC-mediated, Zn2+-coordinated phase separation is conserved among diverse retrovirus subfamilies, illustrating that this exquisitely evolved Zn2+-dependent feature of virus replication represents a critical target for pan-antiretroviral therapies.
Collapse
Affiliation(s)
- Anne Monette
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada.
| | - Meijuan Niu
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Lois Chen
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Shringar Rao
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Biochemistry, Erasmus University Medical Center, Ee634, PO Box 2040, 3000CA Rotterdam, the Netherlands
| | - Robert James Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Andrew John Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada; Department of Medicine, McGill University, Montréal, QC H3G 2M1, Canada.
| |
Collapse
|
8
|
Kinetics of Early Innate Immune Activation during HIV-1 Infection of Humanized Mice. J Virol 2019; 93:JVI.02123-18. [PMID: 30867315 PMCID: PMC6532090 DOI: 10.1128/jvi.02123-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 03/01/2019] [Indexed: 02/07/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is associated with aberrant immune activation; however, most model systems for HIV-1 have been used during established infection. Here, we utilize ultrasensitive HIV-1 quantification to delineate early events during the eclipse, burst, and chronic phases of HIV-1 infection in humanized mice. We show that very early in infection, HIV-1 suppresses peripheral type I interferon (IFN) and interferon-stimulated gene (ISG) responses, including the HIV-1 restriction factor IFI44. At the peak of innate immune activation, prior to CD4 T cell loss, HIV-1 infection differentially affects peripheral and lymphoid Toll-like receptor (TLR) expression profiles in T cells and macrophages. This results in a trend toward an altered activation of nuclear factor κB (NF-κB), TANK-binding kinase 1 (TBK1), and interferon regulatory factor 3 (IRF3). The subsequent type I and III IFN responses result in preferential induction of peripheral ISG responses. Following this initial innate immune activation, peripheral expression of the HIV-1 restriction factor SAM domain- and HD domain-containing protein 1 (SAMHD1) returns to levels below those observed in uninfected mice, suggesting that HIV-1 interferes with their basal expression. However, peripheral cells still retain their responsiveness to exogenous type I IFN, whereas splenic cells show a reduction in select ISGs in response to IFN. This demonstrates the highly dynamic nature of very early HIV-1 infection and suggests that blocks to the induction of HIV-1 restriction factors contribute to the establishment of viral persistence.IMPORTANCE Human immunodeficiency virus type 1 (HIV-1) infection is restricted to humans and some nonhuman primates (e.g., chimpanzee and gorilla). Alternative model systems based on simian immunodeficiency virus (SIV) infection of macaques are available but do not recapitulate all aspects of HIV-1 infection and disease. Humanized mice, which contain a human immune system, can be used to study HIV-1, but only limited information on early events and immune responses is available to date. Here, we describe very early immune responses to HIV-1 and demonstrate a suppression of cell-intrinsic innate immunity. Furthermore, we show that HIV-1 infection interacts differently with innate immune responses in blood and lymphoid organs.
Collapse
|
9
|
René B, Mauffret O, Fossé P. Retroviral nucleocapsid proteins and DNA strand transfers. BIOCHIMIE OPEN 2018; 7:10-25. [PMID: 30109196 PMCID: PMC6088434 DOI: 10.1016/j.biopen.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/08/2018] [Indexed: 12/12/2022]
Abstract
An infectious retroviral particle contains 1000-1500 molecules of the nucleocapsid protein (NC) that cover the diploid RNA genome. NC is a small zinc finger protein that possesses nucleic acid chaperone activity that enables NC to rearrange DNA and RNA molecules into the most thermodynamically stable structures usually those containing the maximum number of base pairs. Thanks to the chaperone activity, NC plays an essential role in reverse transcription of the retroviral genome by facilitating the strand transfer reactions of this process. In addition, these reactions are involved in recombination events that can generate multiple drug resistance mutations in the presence of anti-HIV-1 drugs. The strand transfer reactions rely on base pairing of folded DNA/RNA structures. The molecular mechanisms responsible for NC-mediated strand transfer reactions are presented and discussed in this review. Antiretroviral strategies targeting the NC-mediated strand transfer events are also discussed.
Collapse
Affiliation(s)
- Brigitte René
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Olivier Mauffret
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Philippe Fossé
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| |
Collapse
|
10
|
Olson ED, Musier-Forsyth K. Retroviral Gag protein-RNA interactions: Implications for specific genomic RNA packaging and virion assembly. Semin Cell Dev Biol 2018; 86:129-139. [PMID: 29580971 DOI: 10.1016/j.semcdb.2018.03.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/09/2018] [Accepted: 03/22/2018] [Indexed: 02/04/2023]
Abstract
Retroviral Gag proteins are responsible for coordinating many aspects of virion assembly. Gag possesses two distinct nucleic acid binding domains, matrix (MA) and nucleocapsid (NC). One of the critical functions of Gag is to specifically recognize, bind, and package the retroviral genomic RNA (gRNA) into assembling virions. Gag interactions with cellular RNAs have also been shown to regulate aspects of assembly. Recent results have shed light on the role of MA and NC domain interactions with nucleic acids, and how they jointly function to ensure packaging of the retroviral gRNA. Here, we will review the literature regarding RNA interactions with NC, MA, as well as overall mechanisms employed by Gag to interact with RNA. The discussion focuses on human immunodeficiency virus type-1, but other retroviruses will also be discussed. A model is presented combining all of the available data summarizing the various factors and layers of selection Gag employs to ensure specific gRNA packaging and correct virion assembly.
Collapse
Affiliation(s)
- Erik D Olson
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, Ohio State University, Columbus, OH, 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
11
|
Naufer MN, Furano AV, Williams MC. Protein-nucleic acid interactions of LINE-1 ORF1p. Semin Cell Dev Biol 2018; 86:140-149. [PMID: 29596909 PMCID: PMC6428221 DOI: 10.1016/j.semcdb.2018.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/19/2018] [Accepted: 03/23/2018] [Indexed: 11/03/2022]
Abstract
Long interspersed nuclear element 1 (LINE-1 or L1) is the dominant retrotransposon in mammalian genomes. L1 encodes two proteins ORF1p and ORF2p that are required for retrotransposition. ORF2p functions as the replicase. ORF1p is a coiled coil-mediated trimeric, high affinity RNA binding protein that packages its full- length coding transcript into an ORF2p-containing ribonucleoprotein (RNP) complex, the retrotransposition intermediate. ORF1p also is a nucleic acid chaperone that presumably facilitates the proposed nucleic acid remodeling steps involved in retrotransposition. Although detailed mechanistic understanding of ORF1p function in this process is lacking, recent studies showed that the rate at which ORF1p can form stable nucleic acid-bound oligomers in vitro is positively correlated with formation of an active L1 RNP as assayed in vivo using a cell culture-based retrotransposition assay. This rate was sensitive to minor amino acid changes in the coiled coil domain, which had no effect on nucleic acid chaperone activity. Additional studies linking the complex nucleic acid binding properties to the conformational changes of the protein are needed to understand how ORF1p facilitates retrotransposition.
Collapse
Affiliation(s)
- M Nabuan Naufer
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Anthony V Furano
- The Laboratory of Molecular and Cellular Biology, NIDDK, NIH, Bethesda, MD 20892, USA
| | - Mark C Williams
- Northeastern University, Department of Physics, Boston, MA 02115, USA.
| |
Collapse
|
12
|
Ingemarsdotter CK, Zeng J, Long Z, Lever AML, Kenyon JC. An RNA-binding compound that stabilizes the HIV-1 gRNA packaging signal structure and specifically blocks HIV-1 RNA encapsidation. Retrovirology 2018. [PMID: 29540207 PMCID: PMC5853050 DOI: 10.1186/s12977-018-0407-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background NSC260594, a quinolinium derivative from the NCI diversity set II compound library, was previously identified in a target-based assay as an inhibitor of the interaction between the HIV-1 (ψ) stem-loop 3 (SL3) RNA and Gag. This compound was shown to exhibit potent antiviral activity. Here, the effects of this compound on individual stages of the viral lifecycle were examined by qRT-PCR, ELISA and Western blot, to see if its actions were specific to the viral packaging stage. The structural effects of NSC260594 binding to the HIV-1 gRNA were also examined by SHAPE and dimerization assays. Results Treatment of cells with NSC260594 did not reduce the number of integration events of incoming virus, and treatment of virus producing cells did not affect the level of intracellular Gag protein or viral particle release as determined by immunoblot. However, NSC260594 reduced the incorporation of gRNA into virions by up to 82%, without affecting levels of gRNA inside the cell. This reduction in packaging correlated closely with the reduction in infectivity of the released viral particles. To establish the structural effects of NSC260594 on the HIV-1 gRNA, we performed SHAPE analyses to pinpoint RNA structural changes. NSC260594 had a stabilizing effect on the wild type RNA that was not confined to SL3, but that was propagated across the structure. A packaging mutant lacking SL3 did not show this effect. Conclusions NSC260594 acts as a specific inhibitor of HIV-1 RNA packaging. No other viral functions are affected. Its action involves preventing the interaction of Gag with SL3 by stabilizing this small RNA stem-loop which then leads to stabilization of the global packaging signal region (psi or ψ). This confirms data, previously only shown in analyses of isolated SL3 oligonucleotides, that SL3 is structurally labile in the presence of Gag and that this is critical for the complete psi region to be able to adopt different conformations. Since replication is otherwise unaffected by NSC260594 the flexibility of SL3 appears to be a unique requirement for genome encapsidation and identifies this process as a highly specific drug target. This study is proof of principle that development of a new class of antiretroviral drugs that specifically target viral packaging by binding to the viral genomic RNA is achievable. Electronic supplementary material The online version of this article (10.1186/s12977-018-0407-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Carin K Ingemarsdotter
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Level 5, Hills Rd, Cambridge, CB2 0QQ, UK
| | - Jingwei Zeng
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Level 5, Hills Rd, Cambridge, CB2 0QQ, UK
| | - Ziqi Long
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Level 5, Hills Rd, Cambridge, CB2 0QQ, UK
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Level 5, Hills Rd, Cambridge, CB2 0QQ, UK.,Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Julia C Kenyon
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Level 5, Hills Rd, Cambridge, CB2 0QQ, UK. .,Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore. .,Homerton College, University of Cambridge, Cambridge, UK.
| |
Collapse
|