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Tang Y, Behrens RT, St Gelais C, Wu S, Vivekanandan S, Razin E, Fang P, Wu L, Sherer N, Musier-Forsyth K. Human lysyl-tRNA synthetase phosphorylation promotes HIV-1 proviral DNA transcription. Nucleic Acids Res 2023; 51:12111-12123. [PMID: 37933844 PMCID: PMC10711549 DOI: 10.1093/nar/gkad941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 09/18/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023] Open
Abstract
Human lysyl-tRNA synthetase (LysRS) was previously shown to be re-localized from its normal cytoplasmic location in a multi-aminoacyl-tRNA synthetase complex (MSC) to the nucleus of HIV-1 infected cells. Nuclear localization depends on S207 phosphorylation but the nuclear function of pS207-LysRS in the HIV-1 lifecycle is unknown. Here, we show that HIV-1 replication was severely reduced in a S207A-LysRS knock-in cell line generated by CRISPR/Cas9; this effect was rescued by S207D-LysRS. LysRS phosphorylation up-regulated HIV-1 transcription, as did direct transfection of Ap4A, an upstream transcription factor 2 (USF2) activator that is synthesized by pS207-LysRS. Overexpressing an MSC-derived peptide known to stabilize LysRS MSC binding inhibited HIV-1 replication. Transcription of HIV-1 proviral DNA and other USF2 target genes was reduced in peptide-expressing cells. We propose that nuclear pS207-LysRS generates Ap4A, leading to activation of HIV-1 transcription. Our results suggest a new role for nuclear LysRS in facilitating HIV-1 replication and new avenues for antiviral therapy.
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Affiliation(s)
- Yingke Tang
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Center for RNA Biology, Ohio State University, Columbus, OH, USA
| | - Ryan T Behrens
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Corine St Gelais
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Center for RNA Biology, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Siqi Wu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, China
| | - Saravanan Vivekanandan
- Cellular and Molecular Mechanisms of Inflammation Program, National University of Singapore and The Hebrew University of Jerusalem (NUS–HUJ), Singapore
| | - Ehud Razin
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Israel
| | - Pengfei Fang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, China
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nathan Sherer
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Center for RNA Biology, Ohio State University, Columbus, OH, USA
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2
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Behrens RT, Sherer NM. Retroviral hijacking of host transport pathways for genome nuclear export. mBio 2023; 14:e0007023. [PMID: 37909783 PMCID: PMC10746203 DOI: 10.1128/mbio.00070-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Recent advances in the study of virus-cell interactions have improved our understanding of how viruses that replicate their genomes in the nucleus (e.g., retroviruses, hepadnaviruses, herpesviruses, and a subset of RNA viruses) hijack cellular pathways to export these genomes to the cytoplasm where they access virion egress pathways. These findings shed light on novel aspects of viral life cycles relevant to the development of new antiviral strategies and can yield new tractable, virus-based tools for exposing additional secrets of the cell. The goal of this review is to summarize defined and emerging modes of virus-host interactions that drive the transit of viral genomes out of the nucleus across the nuclear envelope barrier, with an emphasis on retroviruses that are most extensively studied. In this context, we prioritize discussion of recent progress in understanding the trafficking and function of the human immunodeficiency virus type 1 Rev protein, exemplifying a relatively refined example of stepwise, cooperativity-driven viral subversion of multi-subunit host transport receptor complexes.
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Affiliation(s)
- Ryan T. Behrens
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, USA
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Behrens RT, Rajashekar JK, Bruce JW, Evans EL, Hansen AM, Salazar-Quiroz N, Simons LM, Ahlquist P, Hultquist JF, Kumar P, Sherer NM. Exploiting a rodent cell block for intrinsic resistance to HIV-1 gene expression in human T cells. mBio 2023; 14:e0042023. [PMID: 37676006 PMCID: PMC10653828 DOI: 10.1128/mbio.00420-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/13/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Unlike humans, mice are unable to support HIV-1 infection. This is due, in part, to a constellation of defined minor, species-specific differences in conserved host proteins needed for viral gene expression. Here, we used precision CRISPR/Cas9 gene editing to engineer a "mousified" version of one such host protein, cyclin T1 (CCNT1), in human T cells. CCNT1 is essential for efficient HIV-1 transcription, making it an intriguing target for gene-based inactivation of virus replication. We show that isogenic cell lines engineered to encode CCNT1 bearing a single mouse-informed amino acid change (tyrosine in place of cysteine at position 261) exhibit potent, durable, and broad-spectrum resistance to HIV-1 and other pathogenic lentiviruses, and with no discernible impact on host cell biology. These results provide proof of concept for targeting CCNT1 in the context of one or more functional HIV-1 cure strategies.
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Affiliation(s)
- Ryan T. Behrens
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jyothi Krishnaswamy Rajashekar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James W. Bruce
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Edward L. Evans
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amelia M. Hansen
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Natalia Salazar-Quiroz
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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4
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Evans EL, Pocock GM, Einsdorf G, Behrens RT, Dobson ETA, Wiedenmann M, Birkhold C, Ahlquist P, Eliceiri KW, Sherer NM. HIV RGB: Automated Single-Cell Analysis of HIV-1 Rev-Dependent RNA Nuclear Export and Translation Using Image Processing in KNIME. Viruses 2022; 14:903. [PMID: 35632645 PMCID: PMC9145009 DOI: 10.3390/v14050903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 01/27/2023] Open
Abstract
Single-cell imaging has emerged as a powerful means to study viral replication dynamics and identify sites of virus−host interactions. Multivariate aspects of viral replication cycles yield challenges inherent to handling large, complex imaging datasets. Herein, we describe the design and implementation of an automated, imaging-based strategy, “Human Immunodeficiency Virus Red-Green-Blue” (HIV RGB), for deriving comprehensive single-cell measurements of HIV-1 unspliced (US) RNA nuclear export, translation, and bulk changes to viral RNA and protein (HIV-1 Rev and Gag) subcellular distribution over time. Differentially tagged fluorescent viral RNA and protein species are recorded using multicolor long-term (>24 h) time-lapse video microscopy, followed by image processing using a new open-source computational imaging workflow dubbed “Nuclear Ring Segmentation Analysis and Tracking” (NR-SAT) based on ImageJ plugins that have been integrated into the Konstanz Information Miner (KNIME) analytics platform. We describe a typical HIV RGB experimental setup, detail the image acquisition and NR-SAT workflow accompanied by a step-by-step tutorial, and demonstrate a use case wherein we test the effects of perturbing subcellular localization of the Rev protein, which is essential for viral US RNA nuclear export, on the kinetics of HIV-1 late-stage gene regulation. Collectively, HIV RGB represents a powerful platform for single-cell studies of HIV-1 post-transcriptional RNA regulation. Moreover, we discuss how similar NR-SAT-based design principles and open-source tools might be readily adapted to study a broad range of dynamic viral or cellular processes.
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Affiliation(s)
- Edward L. Evans
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ginger M. Pocock
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Gabriel Einsdorf
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- KNIME GmbH, 78467 Konstanz, Germany;
| | - Ryan T. Behrens
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
| | - Ellen T. A. Dobson
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
| | - Marcel Wiedenmann
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- KNIME GmbH, 78467 Konstanz, Germany;
| | | | - Paul Ahlquist
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Morgridge Institute for Research, Madison, WI 53715, USA
- John and Jeanne Rowe Center for Research in Virology, Madison, WI 53715, USA
| | - Kevin W. Eliceiri
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
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5
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Zhang S, Liu F, Halfmann P, Behrens RT, Liu P, Mcilwain SJ, Ong IM, Donahue K, Wang Y, Kawaoka Y, Sherer N, Xu W. Mediator complex subunit 12 is a gatekeeper of SARS-CoV-2 infection in breast cancer cells. Genes Dis 2021; 9:5-8. [PMID: 34423104 PMCID: PMC8372481 DOI: 10.1016/j.gendis.2021.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 01/27/2023] Open
Affiliation(s)
- Shengjie Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA,Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Fabao Liu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peter Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Ryan T. Behrens
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peng Liu
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA,Department of Biostatistics and Medical Informatics, Carbone Cancer Center, University of Wisconsin, Madison, WI 53706, USA
| | - Sean J. Mcilwain
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Irene M. Ong
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA,Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Kristine Donahue
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yidan Wang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Nathan Sherer
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA,Corresponding author. 7459 WIMR II, 1111 Highland Avenue, University of Wisconsin-Madison, Madison, WI 53705-2275, USA.
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6
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Aligeti M, Behrens RT, Pocock GM, Schindelin J, Dietz C, Eliceiri KW, Swanson CM, Malim MH, Ahlquist P, Sherer NM. Cooperativity among Rev-associated nuclear export signals regulates HIV-1 gene expression and is a determinant of virus species tropism. J Virol 2014; 88:14207-21. [PMID: 25275125 PMCID: PMC4249125 DOI: 10.1128/jvi.01897-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/23/2014] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED Murine cells exhibit a profound block to HIV-1 virion production that was recently mapped to a species-specific structural attribute of the murine version of the chromosomal region maintenance 1 (mCRM1) nuclear export receptor and rescued by the expression of human CRM1 (hCRM1). In human cells, the HIV-1 Rev protein recruits hCRM1 to intron-containing viral mRNAs encoding the Rev response element (RRE), thereby facilitating viral late gene expression. Here we exploited murine 3T3 fibroblasts as a gain-of-function system to study hCRM1's species-specific role in regulating Rev's effector functions. We show that Rev is rapidly exported from the nucleus by mCRM1 despite only weak contributions to HIV-1's posttranscriptional stages. Indeed, Rev preferentially accumulates in the cytoplasm of murine 3T3 cells with or without hCRM1 expression, in contrast to human HeLa cells, where Rev exhibits striking en masse transitions between the nuclear and cytoplasmic compartments. Efforts to bias Rev's trafficking either into or out of the nucleus revealed that Rev encoding a second CRM1 binding domain (Rev-2xNES) or Rev-dependent viral gag-pol mRNAs bearing tandem RREs (GP-2xRRE), rescue virus particle production in murine cells even in the absence of hCRM1. Combined, these results suggest a model wherein Rev-associated nuclear export signals cooperate to regulate the number or quality of CRM1's interactions with viral Rev/RRE ribonucleoprotein complexes in the nucleus. This mechanism regulates CRM1-dependent viral gene expression and is a determinant of HIV-1's capacity to produce virions in nonhuman cell types. IMPORTANCE Cells derived from mice and other nonhuman species exhibit profound blocks to HIV-1 replication. Here we elucidate a block to HIV-1 gene expression attributable to the murine version of the CRM1 (mCRM1) nuclear export receptor. In human cells, hCRM1 regulates the nuclear export of viral intron-containing mRNAs through the activity of the viral Rev adapter protein that forms a multimeric complex on these mRNAs prior to recruiting hCRM1. We demonstrate that Rev-dependent gene expression is poor in murine cells despite the finding that, surprisingly, the bulk of Rev interacts efficiently with mCRM1 and is rapidly exported from the nucleus. Instead, we map the mCRM1 defect to the apparent inability of this factor to engage Rev multimers in the context of large viral Rev/RNA ribonucleoprotein complexes. These findings shed new light on HIV-1 gene regulation and could inform the development of novel antiviral strategies that target viral gene expression.
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Affiliation(s)
- Mounavya Aligeti
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan T Behrens
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ginger M Pocock
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Johannes Schindelin
- Morgridge Institute for Research, Madison, Wisconsin, USA Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christian Dietz
- Department of Computer and Information Science, University of Constance, Constance, Germany
| | - Kevin W Eliceiri
- Morgridge Institute for Research, Madison, Wisconsin, USA Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chad M Swanson
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Michael H Malim
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA Morgridge Institute for Research, Madison, Wisconsin, USA Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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