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Article ; Online: HIV-1 Gag co-localizes with euchromatin histone marks at the nuclear periphery.

Chang, Jordan / Parent, Leslie J

2023 Volume 97, Issue 12, Page(s) e0117923

Abstract: ... with USvRNA within 8 hours of expression. In infected T cells (J-Lat 10.6) reactivated from latency and ...

Abstract	Importance: The traditional view of retrovirus assembly posits that packaging of gRNA by HIV-1 Gag occurs in the cytoplasm or at the plasma membrane. However, our previous studies showing that HIV-1 Gag enters the nucleus and binds to USvRNA at transcription sites suggest that gRNA selection may occur in the nucleus. In the present study, we observed that HIV-1 Gag trafficked to the nucleus and co-localized with USvRNA within 8 hours of expression. In infected T cells (J-Lat 10.6) reactivated from latency and in a HeLa cell line stably expressing an inducible Rev-dependent HIV-1 construct, we found that Gag preferentially localized with euchromatin histone marks associated with enhancer and promoter regions near the nuclear periphery, which is the favored site HIV-1 integration. These observations support the innovative hypothesis that HIV-1 Gag associates with euchromatin-associated histones to localize to active transcription sites, promoting capture of newly synthesized gRNA for packaging.
MeSH term(s)	Humans ; Active Transport, Cell Nucleus ; Cell Nucleus/metabolism ; Enhancer Elements, Genetic/genetics ; Euchromatin/genetics ; Euchromatin/metabolism ; gag Gene Products, Human Immunodeficiency Virus/metabolism ; HeLa Cells ; Histone Code ; Histones/metabolism ; HIV-1/genetics ; HIV-1/growth & development ; HIV-1/metabolism ; Promoter Regions, Genetic/genetics ; T-Lymphocytes/virology ; Transcription, Genetic ; Virus Activation ; Viral Genome Packaging
Chemical Substances	Euchromatin ; gag Gene Products, Human Immunodeficiency Virus ; Histones ; rev protein, Human Immunodeficiency Virus-1
Language	English
Publishing date	2023-11-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.01179-23
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Article: HIV-1 Gag colocalizes with euchromatin histone marks at the nuclear periphery.

Chang, Jordan / Parent, Leslie J

bioRxiv : the preprint server for biology

2023

Abstract: ... fraction compared to the heterochromatin-rich region in a latently-infected CD4+ T cell line (J-Lat 10.6 ... T cells (J-Lat 10.6) treated with latency reversal agents, as well as a HeLa cell line stably expressing ...

Abstract	The retroviral Gag protein of human immunodeficiency virus type 1 (HIV-1) plays a central role in the selection of unspliced viral genomic RNA for packaging into new virions. Previously, we demonstrated that full-length HIV-1 Gag undergoes nuclear trafficking where it associates with unspliced viral RNA (vRNA) at transcription sites. To further explore the kinetics of HIV-1 Gag nuclear localization, we used biochemical and imaging techniques to examine the timing of HIV-1 entry into the nucleus. We also aimed to determine more precisely Gag's subnuclear distribution to test the hypothesis that Gag would be associated with euchromatin, the transcriptionally active region of the nucleus. We observed that HIV-1 Gag localized to the nucleus shortly after its synthesis in the cytoplasm, suggesting that nuclear trafficking was not strictly concentration-dependent. Furthermore, we found that HIV-1 Gag preferentially localized to the transcriptionally active euchromatin fraction compared to the heterochromatin-rich region in a latently-infected CD4+ T cell line (J-Lat 10.6) treated with latency-reversal agents. Interestingly, HIV-1 Gag was more closely associated with transcriptionally-active histone markers near the nuclear periphery, where the HIV-1 provirus was previously shown to integrate. Although the precise function of Gag's association with histones in transcriptionally-active chromatin remains uncertain, together with previous reports, this finding is consistent with a potential role for euchromatin-associated Gag molecules to select newly transcribed unspliced vRNA during the initial stage of virion assembly. Importance: The traditional view of retroviral assembly posits that HIV-1 Gag selection of unspliced vRNA begins in the cytoplasm. However, our previous studies demonstrated that HIV-1 Gag enters the nucleus and binds to unspliced HIV-1 RNA at transcription sites, suggesting that genomic RNA selection may occur in the nucleus. In the present study, we observed nuclear entry of HIV-1 Gag and co-localization with unspliced viral RNA within 8 hours post-expression. In CD4+ T cells (J-Lat 10.6) treated with latency reversal agents, as well as a HeLa cell line stably expressing an inducible Rev-dependent provirus, we found that HIV-1 Gag preferentially localized with histone marks associated with enhancer and promoter regions of transcriptionally active euchromatin near the nuclear periphery, which favors HIV-1 proviral integration sites. These observations support the hypothesis that HIV-1 Gag hijacks euchromatin-associated histones to localize to active transcription sites, promoting capture of newly synthesized genomic RNA for packaging.
Language	English
Publishing date	2023-02-25
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.02.24.529990
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Article ; Online: Virus Induced Membraneless Organelles and Biomolecular Condensates.

Mouland, Andrew J / Parent, Leslie / Weber, Stephanie C / Holehouse, Alex S

Journal of molecular biology

2023 Volume 435, Issue 16, Page(s) 168213

MeSH term(s)	Biomolecular Condensates/virology ; Viruses/metabolism ; Virus Replication
Language	English
Publishing date	2023-07-20
Publishing country	Netherlands
Document type	Editorial
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2023.168213
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Article: Comparative analysis of retroviral Gag-host cell interactions: focus on the nuclear interactome.

Lambert, Gregory S / Rice, Breanna L / Kaddis Maldonado, Rebecca J / Chang, Jordan / Parent, Leslie J

bioRxiv : the preprint server for biology

2024

Abstract: Retroviruses exploit a variety of host proteins to assemble and release virions from infected cells. To date, most studies that examined possible interacting partners of retroviral Gag proteins focused on host proteins that localize primarily to the ... ...

Abstract	Retroviruses exploit a variety of host proteins to assemble and release virions from infected cells. To date, most studies that examined possible interacting partners of retroviral Gag proteins focused on host proteins that localize primarily to the cytoplasm or plasma membrane. Given the recent findings that several full-length Gag proteins localize to the nucleus, identifying the Gag-nuclear interactome has high potential for novel findings that reveal previously unknown host processes. In this study, we systematically compared nuclear factors identified in published HIV-1 proteomic studies which had used a variety of experimental approaches. In addition, to contribute to this body of knowledge, we report results from a mass spectrometry approach using affinity-tagged (His
Language	English
Publishing date	2024-03-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.18.575255
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Article ; Online: Visualizing Rous Sarcoma Virus Genomic RNA Dimerization in the Nucleus, Cytoplasm, and at the Plasma Membrane.

Chen, Eunice C / Maldonado, Rebecca J Kaddis / Parent, Leslie J

Viruses

2021 Volume 13, Issue 5

Abstract: Retroviruses are unique in that they package their RNA genomes as non-covalently linked dimers. Failure to dimerize their genomes results in decreased infectivity and reduced packaging of genomic RNA into virus particles. Two models of retrovirus genome ... ...

Abstract	Retroviruses are unique in that they package their RNA genomes as non-covalently linked dimers. Failure to dimerize their genomes results in decreased infectivity and reduced packaging of genomic RNA into virus particles. Two models of retrovirus genome dimerization have been characterized: in murine leukemia virus (MLV), genomic RNA dimerization occurs co-transcriptionally in the nucleus, resulting in the preferential formation of genome homodimers; whereas in human immunodeficiency virus (HIV-1), genomic RNA dimerization occurs in the cytoplasm and at the plasma membrane, with a random distribution of heterodimers and homodimers. Although in vitro studies have identified the genomic RNA sequences that facilitate dimerization in Rous sarcoma virus (RSV), in vivo characterization of the location and preferences of genome dimerization has not been performed. In this study, we utilized three single molecule RNA imaging approaches to visualize genome dimers of RSV in cultured quail fibroblasts. The formation of genomic RNA heterodimers within cells was dependent on the presence of the dimerization initiation site (DIS) sequence in the L3 stem. Subcellular localization analysis revealed that heterodimers were present the nucleus, cytoplasm, and at the plasma membrane, indicating that genome dimers can form in the nucleus. Furthermore, single virion analysis revealed that RSV preferentially packages genome homodimers into virus particles. Therefore, the mechanism of RSV genomic RNA dimer formation appears more similar to MLV than HIV-1.
MeSH term(s)	Cell Membrane ; Cell Nucleus ; Cells, Cultured ; Cytoplasm ; Dimerization ; Genome, Viral ; Humans ; In Situ Hybridization, Fluorescence/methods ; Molecular Imaging/methods ; RNA, Viral/chemistry ; RNA, Viral/genetics ; Rous sarcoma virus/genetics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-05-13
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13050903
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Article ; Online: Ambient air pollution and prostate cancer risk in a population-based Canadian case-control study.

Youogo, Leslie Michele-Ange Kouam / Parent, Marie-Elise / Hystad, Perry / Villeneuve, Paul J

Environmental epidemiology (Philadelphia, Pa.)

2022 Volume 6, Issue 4, Page(s) e219

Abstract: Ambient air pollution is a human carcinogen and a possible risk factor for prostate cancer.: Methods: We investigated associations between ambient concentrations particulate matter 2.5 (PM: Results: We found positive associations between exposure ... ...

Abstract	Ambient air pollution is a human carcinogen and a possible risk factor for prostate cancer. Methods: We investigated associations between ambient concentrations particulate matter 2.5 (PM Results: We found positive associations between exposure to PM Conclusions: Our findings support the hypothesis that ambient air pollution increases the risk of prostate cancer.
Language	English
Publishing date	2022-07-19
Publishing country	United States
Document type	Journal Article
ISSN	2474-7882
ISSN (online)	2474-7882
DOI	10.1097/EE9.0000000000000219
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Article ; Online: Liquid-liquid phase separation of nucleocapsid proteins during SARS-CoV-2 and HIV-1 replication.

Chau, Bao-An / Chen, Venessa / Cochrane, Alan W / Parent, Leslie J / Mouland, Andrew J

Cell reports

2022 Volume 42, Issue 1, Page(s) 111968

Abstract: The leap of retroviruses and coronaviruses from animal hosts to humans has led to two ongoing pandemics and tens of millions of deaths worldwide. Retrovirus and coronavirus nucleocapsid proteins have been studied extensively as potential drug targets due ...

Abstract	The leap of retroviruses and coronaviruses from animal hosts to humans has led to two ongoing pandemics and tens of millions of deaths worldwide. Retrovirus and coronavirus nucleocapsid proteins have been studied extensively as potential drug targets due to their central roles in virus replication, among which is their capacity to bind their respective genomic RNAs for packaging into nascent virions. This review focuses on fundamental studies of these nucleocapsid proteins and how their intrinsic abilities to condense through liquid-liquid phase separation (LLPS) contribute to viral replication. Therapeutic targeting of these condensates and methodological advances are also described to address future questions on how phase separation contributes to viral replication.
MeSH term(s)	Humans ; Coronavirus Nucleocapsid Proteins ; COVID-19 ; Nucleocapsid Proteins ; SARS-CoV-2/physiology ; Virus Replication ; HIV-1/physiology
Chemical Substances	Coronavirus Nucleocapsid Proteins ; Nucleocapsid Proteins
Language	English
Publishing date	2022-12-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.111968
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Article ; Online: RNA-Binding Domains of Heterologous Viral Proteins Substituted for Basic Residues in the RSV Gag NC Domain Restore Specific Packaging of Genomic RNA.

Rice, Breanna L / Lochmann, Timothy L / Parent, Leslie J

Viruses

2020 Volume 12, Issue 4

Abstract: The Rous sarcoma virus Gag polyprotein transiently traffics through the nucleus, which is required for efficient incorporation of the viral genomic RNA (gRNA) into virus particles. Packaging of gRNA is mediated by two zinc knuckles and basic residues ... ...

Abstract	The Rous sarcoma virus Gag polyprotein transiently traffics through the nucleus, which is required for efficient incorporation of the viral genomic RNA (gRNA) into virus particles. Packaging of gRNA is mediated by two zinc knuckles and basic residues located in the nucleocapsid (NC) domain in Gag. To further examine the role of basic residues located downstream of the zinc knuckles in gRNA encapsidation, we used a gain-of-function approach. We replaced a basic residue cluster essential for gRNA packaging with heterologous basic residue motif (BR) with RNA-binding activity from either the HIV-1 Rev protein (Rev BR) or the HSV ICP27 protein (ICP27 BR). Compared to wild-type Gag, the mutant ICP27 BR and Rev BR Gag proteins were much more strongly localized to the nucleus and released significantly lower levels of virus particles. Surprisingly, both the ICP27 BR and Rev BR mutants packaged normal levels of gRNA per virus particle when examined in the context of a proviral vector, yet both mutants were noninfectious. These results support the hypothesis that basic residues located in the C-terminal region of NC are required for selective gRNA packaging, potentially by binding non-specifically to RNA via electrostatic interactions.
MeSH term(s)	Amino Acid Substitution ; Gene Products, gag/chemistry ; Gene Products, gag/genetics ; Gene Products, gag/metabolism ; Genome, Viral ; Humans ; Protein Binding ; Protein Transport ; RNA-Binding Motifs ; Rous sarcoma virus/physiology ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Virus Assembly ; Virus Release
Chemical Substances	Gene Products, gag ; Viral Proteins
Language	English
Publishing date	2020-03-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v12040370
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Article ; Online: TNPO3-Mediated Nuclear Entry of the Rous Sarcoma Virus Gag Protein Is Independent of the Cargo-Binding Domain.

Rice, Breanna L / Stake, Matthew S / Parent, Leslie J

Journal of virology

2020 Volume 94, Issue 17

Abstract: Retroviral Gag polyproteins orchestrate the assembly and release of nascent virus particles from the plasma membranes of infected cells. Although it was traditionally thought that Gag proteins trafficked directly from the cytosol to the plasma membrane, ... ...

Abstract	Retroviral Gag polyproteins orchestrate the assembly and release of nascent virus particles from the plasma membranes of infected cells. Although it was traditionally thought that Gag proteins trafficked directly from the cytosol to the plasma membrane, we discovered that the oncogenic avian alpharetrovirus Rous sarcoma virus (RSV) Gag protein undergoes transient nucleocytoplasmic transport as an intrinsic step in virus assembly. Using a genetic approach in yeast, we identified three karyopherins that engage the two independent nuclear localization signals (NLSs) in Gag. The primary NLS is in the nucleocapsid (NC) domain of Gag and binds directly to importin-α, which recruits importin-β to mediate nuclear entry. The second NLS (TNPO3), which resides in the matrix (MA) domain, is dependent on importin-11 and transportin-3 (TNPO3), which are known as MTR10p and Kap120p in yeast, although it is not clear whether these import factors are independent or additive. The functions of importin-α/importin-β and importin-11 have been verified in avian cells, whereas the role of TNPO3 has not been studied. In this report, we demonstrate that TNPO3 directly binds to Gag and mediates its nuclear entry. To our surprise, this interaction did not require the cargo-binding domain (CBD) of TNPO3, which typically mediates nuclear entry for other binding partners of TNPO3, including SR domain-containing splicing factors and tRNAs that reenter the nucleus. These results suggest that RSV hijacks this host nuclear import pathway using a unique mechanism, potentially allowing other cargo to simultaneously bind TNPO3.
MeSH term(s)	Active Transport, Cell Nucleus ; Cell Nucleus ; Gene Products, gag/genetics ; Gene Products, gag/metabolism ; Karyopherins/metabolism ; Nuclear Localization Signals/metabolism ; Nucleocapsid/metabolism ; Protein Domains ; Protein Transport ; Rous sarcoma virus/physiology ; Saccharomyces cerevisiae ; Virus Assembly ; Virus Internalization ; alpha Karyopherins/metabolism ; beta Karyopherins/genetics ; beta Karyopherins/metabolism
Chemical Substances	Gene Products, gag ; Karyopherins ; Nuclear Localization Signals ; TNPO3 protein, human ; alpha Karyopherins ; beta Karyopherins
Language	English
Publishing date	2020-08-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00640-20
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Article: The Rous sarcoma virus Gag polyprotein forms biomolecular condensates driven by intrinsically-disordered regions.

Maldonado, Rebecca Kaddis / Rice, Breanna L / Lambert, Gregory S / Sudol, Malgorzata / Flanagan, John M / Parent, Leslie J

bioRxiv : the preprint server for biology

2023

Abstract: Biomolecular condensates (BMCs) play important roles in cellular structures including transcription factories, splicing speckles, and nucleoli. BMCs bring together proteins and other macromolecules, selectively concentrating them so that specific ... ...

Abstract	Biomolecular condensates (BMCs) play important roles in cellular structures including transcription factories, splicing speckles, and nucleoli. BMCs bring together proteins and other macromolecules, selectively concentrating them so that specific reactions can occur without interference from the surrounding environment. BMCs are often made up of proteins that contain intrinsically disordered regions (IDRs), form phase-separated spherical puncta, form liquid-like droplets that undergo fusion and fission, contain molecules that are mobile, and are disrupted with phase-dissolving drugs such as 1,6-hexanediol. In addition to cellular proteins, many viruses, including influenza A, SARS-CoV-2, and human immunodeficiency virus type 1 (HIV-1) encode proteins that undergo phase separation and rely on BMC formation for replication. In prior studies of the retrovirus Rous sarcoma virus (RSV), we observed that the Gag protein forms discrete spherical puncta in the nucleus, cytoplasm, and at the plasma membrane that co-localize with viral RNA and host factors, raising the possibility that RSV Gag forms BMCs that participate in the virion intracellular assembly pathway. In our current studies, we found that Gag contains IDRs in the N-terminal (MAp2p10) and C-terminal (NC) regions of the protein and fulfills many criteria of BMCs. Although the role of BMC formation in RSV assembly requires further study, our results suggest the biophysical properties of condensates are required for the formation of Gag complexes in the nucleus and the cohesion of these complexes as they traffic through the nuclear pore, into the cytoplasm, and to the plasma membrane, where the final assembly and release of virus particles occurs.
Language	English
Publishing date	2023-04-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.04.07.536043
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