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Klemm C, Wood H, Thomas GH, Ólafsson G, Torres MT, Thorpe PH. Forced association of SARS-CoV-2 proteins with the yeast proteome perturb vesicle trafficking. MICROBIAL CELL (GRAZ, AUSTRIA) 2021; 8:280-296. [PMID: 34909432 PMCID: PMC8642885 DOI: 10.15698/mic2021.12.766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the highly infectious coronavirus disease COVID-19. Extensive research has been performed in recent months to better understand how SARS-CoV-2 infects and manipulates its host to identify potential drug targets and support patient recovery from COVID-19. However, the function of many SARS-CoV-2 proteins remains uncharacterised. Here we used the Synthetic Physical Interactions (SPI) method to recruit SARS-CoV-2 proteins to most of the budding yeast proteome to identify conserved pathways which are affected by SARS-CoV-2 proteins. The set of yeast proteins that result in growth defects when associated with the viral proteins have homologous functions that overlap those identified in studies performed in mammalian cells. Specifically, we were able to show that recruiting the SARS-CoV-2 NSP1 protein to HOPS, a vesicle-docking complex, is sufficient to perturb membrane trafficking in yeast consistent with the hijacking of the endoplasmic-reticulum-Golgi intermediate compartment trafficking pathway during viral infection of mammalian cells. These data demonstrate that the yeast SPI method is a rapid way to identify potential functions of ectopic viral proteins.
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Affiliation(s)
- Cinzia Klemm
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Henry Wood
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Grace Heredge Thomas
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Guðjón Ólafsson
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Mara Teixeira Torres
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
| | - Peter H. Thorpe
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS, UK
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Contribution of yeast models to virus research. Appl Microbiol Biotechnol 2021; 105:4855-4878. [PMID: 34086116 PMCID: PMC8175935 DOI: 10.1007/s00253-021-11331-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Abstract Time and again, yeast has proven to be a vital model system to understand various crucial basic biology questions. Studies related to viruses are no exception to this. This simple eukaryotic organism is an invaluable model for studying fundamental cellular processes altered in the host cell due to viral infection or expression of viral proteins. Mechanisms of infection of several RNA and relatively few DNA viruses have been studied in yeast to date. Yeast is used for studying several aspects related to the replication of a virus, such as localization of viral proteins, interaction with host proteins, cellular effects on the host, etc. The development of novel techniques based on high-throughput analysis of libraries, availability of toolboxes for genetic manipulation, and a compact genome makes yeast a good choice for such studies. In this review, we provide an overview of the studies that have used yeast as a model system and have advanced our understanding of several important viruses. Key points • Yeast, a simple eukaryote, is an important model organism for studies related to viruses. • Several aspects of both DNA and RNA viruses of plants and animals are investigated using the yeast model. • Apart from the insights obtained on virus biology, yeast is also extensively used for antiviral development.
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Nkeze J, Li L, Benko Z, Li G, Zhao RY. Molecular characterization of HIV-1 genome in fission yeast Schizosaccharomyces pombe. Cell Biosci 2015; 5:47. [PMID: 26309721 PMCID: PMC4549081 DOI: 10.1186/s13578-015-0037-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/27/2015] [Indexed: 11/25/2022] Open
Abstract
Background The human immunodeficiency virus type 1 (HIV-1) genome (~9 kb RNA) is flanked by two long terminal repeats (LTR) promoter regions with nine open reading frames, which encode Gag, Pol and Env polyproteins, four accessory proteins (Vpu, Vif, Vpr, Nef) and two regulatory proteins (Rev, Tat). In this study, we carried out a genome-wide and functional analysis of the HIV-1 genome in fission yeast (Schizosaccharomyces pombe). Results Each one of the HIV-1 genes was cloned and expressed individually in fission yeast. Subcellular localization of each viral protein was first examined. The effect of protein expression on cellular proliferation and colony formations, an indication of cytotoxicity, were observed. Overall, there is a general correlation of subcellular localization of each viral protein between fission yeast and mammalian cells. Three viral proteins, viral protein R (Vpr), protease (PR) and regulator of expression of viral protein (Rev), were found to inhibit cellular proliferation. Rev was chosen for further analysis in fission yeast and mammalian cells. Consistent with the observation in fission yeast, expression of HIV-1 rev gene also caused growth retardation in mammalian cells. However, the observed growth delay was neither due to the cytotoxic effect nor due to alterations in cell cycling. Mechanistic testing of the Rev effect suggests it triggers transient induction of cellular oxidative stress. Conclusions Some of the behavioral and functional similarities of Rev between fission yeast and mammalian cells suggest fission yeast might be a useful model system for further studies of molecular functions of Rev and other HIV-1 viral proteins.
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Affiliation(s)
- Joseph Nkeze
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA
| | - Lin Li
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,AIDS Research Department, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Zsigmond Benko
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Ge Li
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA
| | - Richard Y Zhao
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA
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Yeast and the AIDS virus: the odd couple. J Biomed Biotechnol 2012; 2012:549020. [PMID: 22778552 PMCID: PMC3385842 DOI: 10.1155/2012/549020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 04/14/2012] [Accepted: 04/16/2012] [Indexed: 12/13/2022] Open
Abstract
Despite being simple eukaryotic organisms, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have been widely used as a model to study human pathologies and the replication of human, animal, and plant viruses, as well as the function of individual viral proteins. The complete genome of S. cerevisiae was the first of eukaryotic origin to be sequenced and contains about 6,000 genes. More than 75% of the genes have an assigned function, while more than 40% share conserved sequences with known or predicted human genes. This strong homology has allowed the function of human orthologs to be unveiled starting from the data obtained in yeast. RNA plant viruses were the first to be studied in yeast. In this paper, we focus on the use of the yeast model to study the function of the proteins of human immunodeficiency virus type 1 (HIV-1) and the search for its cellular partners. This human retrovirus is the cause of AIDS. The WHO estimates that there are 33.4 million people worldwide living with HIV/AIDS, with 2.7 million new HIV infections per year and 2.0 million annual deaths due to AIDS. Current therapy is able to control the disease but there is no permanent cure or a vaccine. By using yeast, it is possible to dissect the function of some HIV-1 proteins and discover new cellular factors common to this simple cell and humans that may become potential therapeutic targets, leading to a long-lasting treatment for AIDS.
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Retrotransposition is associated with genome instability during chronological aging. Proc Natl Acad Sci U S A 2011; 108:20376-81. [PMID: 22021441 DOI: 10.1073/pnas.1100271108] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Genetic damage through mutations and genome rearrangements has been hypothesized to contribute to aging. The specific mechanisms responsible for age-induced increases in mutation and chromosome rearrangement frequencies and a potential causative role for DNA damage in aging are under active investigation. Retrotransposons are mobile genetic elements that cause insertion mutations and contribute to genome rearrangements through nonallelic recombination events in humans and other organisms. We have investigated the role of endogenous Ty1 retrotransposons in aging-associated increases in genome instability using the Saccharomyces cerevisiae chronological aging model. We show that age-induced increases in loss of heterozygosity and chromosome loss events are consistently diminished by mutations or treatments that reduce Ty1 retrotransposition. Ty1 mobility is elevated in very old yeast populations, and new retromobility events are often associated with chromosome rearrangements. These results reveal a correlation between retrotransposition and genome instability during yeast aging. Retrotransposition may contribute to genetic damage during aging in diverse organisms and provides a useful tool for studying whether genetic damage is a causative factor for aging.
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Structure-analysis of the HIV-1 integrase Y143C/R raltegravir resistance mutation in association with the secondary mutation T97A. Antimicrob Agents Chemother 2011; 55:3187-94. [PMID: 21576445 DOI: 10.1128/aac.00071-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The HIV-1 integrase (IN) mutations Y143C/R are known as raltegravir (RAL) primary resistance mutations. In a previous study (S. Reigadas et al., PLoS One 5:e10311, 2010), we investigated the genetic pathway and the dynamics of emergence of the Y143C/R mutations in three patients failing RAL-containing regimens. In these patients, the Y143C/R mutation was associated with the T97A mutation. The aim of the present biochemical and molecular studies in vitro was to evaluate whether the secondary mutation, T97A, associated with the Y143C/R mutation could increase the level of resistance to RAL and impact IN activities. Site-directed mutagenesis experiments were performed with expression vectors harboring the region of the pol gene coding for IN. With a 3'-end processing assay, the 50% inhibitory concentrations (IC(50)) were 1.2 μM, 1.2 μM, 2.4 μM (fold change [FC], 2), and 20 μM (FC, 16.7) for IN wild type (WT), the IN T97A mutation, the IN Y143C/T97A mutation, and the IN Y143R/T97A mutation, respectively. FCs of 18 and 100 were observed with the strand transfer assay for IN Y143C/T97A and Y143R/T97A mutations, with IC(50) of 0.625 μM and 2.5 μM, respectively. In the strand transfer assay, the IN Y143C or R mutation combined with the secondary mutation T97A severely impaired susceptibility to RAL compared to results with the IN Y143C or R mutation alone. Assays without RAL suggested that the T97A mutation could rescue the catalytic activity which was impaired by the presence of the Y143C/R mutation. The combination of the T97A mutation with the primary RAL resistance mutations Y143C/R strongly reduces the susceptibility to RAL and rescues the catalytic defect due to the Y143C/R mutation. This result indicates that the emergence of the Y143C/R/T97A double-mutation pattern in patients is a signature of a high resistance level.
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Ty1 integrase overexpression leads to integration of non-Ty1 DNA fragments into the genome of Saccharomyces cerevisiae. Mol Genet Genomics 2010; 284:231-42. [PMID: 20677012 PMCID: PMC2939329 DOI: 10.1007/s00438-010-0561-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 07/08/2010] [Indexed: 10/25/2022]
Abstract
The integrase of the Saccharomyces cerevisiae retrotransposon Ty1 integrates Ty1 cDNA into genomic DNA likely via a transesterification reaction. Little is known about the mechanisms ensuring that integrase does not integrate non-Ty DNA fragments. In an effort to elucidate the conditions under which Ty1 integrase accepts non-Ty DNA as substrate, PCR fragments encompassing a selectable marker gene were transformed into yeast strains overexpressing Ty1 integrase. These fragments do not exhibit similarity to Ty1 cDNA except for the presence of the conserved terminal dinucleotide 5'-TG-CA-3'. The frequency of fragment insertion events increased upon integrase overexpression. Characterization of insertion events by genomic sequencing revealed that most insertion events exhibited clear hallmarks of integrase-mediated reactions, such as 5 bp target site duplication and target site preferences. Alteration of the terminal dinucleotide abolished the suitability of the PCR fragments to serve as substrates. We hypothesize that substrate specificity under normal conditions is mainly due to compartmentalization of integrase and Ty cDNA, which meet in virus-like particles. In contrast, recombinant integrase, which is not confined to virus-like particles, is able to accept non-Ty DNA, provided that it terminates in the proper dinucleotide sequence.
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Reigadas S, Anies G, Masquelier B, Calmels C, Stuyver LJ, Parissi V, Fleury H, Andreola ML. The HIV-1 integrase mutations Y143C/R are an alternative pathway for resistance to Raltegravir and impact the enzyme functions. PLoS One 2010; 5:e10311. [PMID: 20436677 PMCID: PMC2859942 DOI: 10.1371/journal.pone.0010311] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 03/28/2010] [Indexed: 11/21/2022] Open
Abstract
Resistance to HIV-1 integrase (IN) inhibitor raltegravir (RAL), is encoded by mutations in the IN region of the pol gene. The emergence of the N155H mutation was replaced by a pattern including the Y143R/C/H mutations in three patients with anti-HIV treatment failure. Cloning analysis of the IN gene showed an independent selection of the mutations at loci 155 and 143. Characterization of the phenotypic evolution showed that the switch from N155H to Y143C/R was linked to an increase in resistance to RAL. Wild-type (WT) IN and IN with mutations Y143C or Y143R were assayed in vitro in 3′end-processing, strand transfer and concerted integration assays. Activities of mutants were moderately impaired for 3′end-processing and severely affected for strand transfer. Concerted integration assay demonstrated a decrease in mutant activities using an uncleaved substrate. With 3′end-processing assay, IC50 were 0.4 µM, 0.9 µM (FC = 2.25) and 1.2 µM (FC = 3) for WT, IN Y143C and IN Y143R, respectively. An FC of 2 was observed only for IN Y143R in the strand transfer assay. In concerted integration, integrases were less sensitive to RAL than in ST or 3′P but mutants were more resistant to RAL than WT.
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Affiliation(s)
- Sandrine Reigadas
- Laboratoire de Virologie, CHU de Bordeaux, EA 2968, Université Victor Segalen, Bordeaux, France
| | - Guerric Anies
- Laboratoire de Virologie, CHU de Bordeaux, EA 2968, Université Victor Segalen, Bordeaux, France
| | - Bernard Masquelier
- Laboratoire de Virologie, CHU de Bordeaux, EA 2968, Université Victor Segalen, Bordeaux, France
| | | | | | | | - Herve Fleury
- Laboratoire de Virologie, CHU de Bordeaux, EA 2968, Université Victor Segalen, Bordeaux, France
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Coombs JM. Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface. Methods Mol Biol 2009; 532:413-33. [PMID: 19271199 DOI: 10.1007/978-1-60327-853-9_24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The deep terrestrial subsurface is a vast, largely unexplored environment that is oligotrophic, highly heterogeneous, and may contain extremes of both physical and chemical factors. In spite of harsh conditions, subsurface studies at several widely distributed geographic sites have revealed diverse communities of viable organisms, which have provided evidence of low but detectable metabolic activity. Although much of the terrestrial subsurface may be considered to be distant and isolated, the concept of horizontal gene transfer (HGT) in this environment has far-reaching implications for bioremediation efforts and groundwater quality, industrial harvesting of subsurface natural resources such as petroleum, and accurate assessment of the risks associated with DNA release and transport from genetically modified organisms. This chapter will explore what is known about some of the major mechanisms of HGT, and how the information gained from surface organisms might apply to conditions in the terrestrial subsurface. Evidence for the presence of mobile elements in subsurface bacteria and limited retrospective studies examining genetic signatures of potential past gene transfer events will be discussed.
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Affiliation(s)
- Jonna M Coombs
- Department of Biology, Adelphi University, Garden City, NY, USA
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10
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Desfarges S, Salin B, Calmels C, Andreola ML, Parissi V, Fournier M. HIV-1 integrase trafficking in S. cerevisiae: a useful model to dissect the microtubule network involvement of viral protein nuclear import. Yeast 2009; 26:39-54. [PMID: 19180639 DOI: 10.1002/yea.1651] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Intracellular transport of karyophilic cargos comprises translocation to the nuclear envelope and subsequent nuclear import. Small cargos such as isolated proteins can reach the nuclear envelope by diffusion but movement of larger structures depends on active translocation, typically using microtubules. Centripetal transport ends at the perinuclear microtubule organizing centre called the spindle pole body (SPB) in yeast. Previously, we found by two hybrids that the karyophilic lentiviral-encoded integrase (IN) interacts with two yeast microtubule-associated proteins, Dyn2p (dynein light chain protein) and Stu2p, a centrosomal protein (de Soultrait et al., 2002). Thus, to investigate the hinge between cytoplasmic retrograde transport and nuclear import, we decided to analyse HIV-1 IN trafficking in yeast as the model, since each of these biological mechanisms is evolutionarily conserved in eukaryotic cells. Here, we found an accumulation of IN at the SPB in yeast via Stu2p colocalization. Disruption of the microtubule network by nocodazole or IN expression in a dynein 2-deficient yeast strain prevented IN accumulation in the nuclear periphery and additionally inhibited IN transport into the nucleus. By mutagenesis, we showed that trafficking of IN towards the SPB requires the C-terminus of the molecule. Taking our findings together, we proposed a model in which IN nuclear import seems to depend on an essential intermediate step in the SPB. We found that Dyn2p and Stu2p play an important role in driving IN toward MTOC and could optimize nuclear entry of the retroviral enzyme. Our results suggest a new hypothesis in keeping with the current HIV-1 intracellular trafficking model.
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Affiliation(s)
- S Desfarges
- Laboratoire Microbiologie Cellulaire et Moléculaire et Pathogénicité, Département 1, UMR 5234-CNRS, Bordeaux, France
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Xu Z, Zheng Y, Ao Z, Clement M, Mouland AJ, Kalpana GV, Belhumeur P, Cohen EA, Yao X. Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication. Retrovirology 2008; 5:102. [PMID: 19014595 PMCID: PMC2615443 DOI: 10.1186/1742-4690-5-102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 11/14/2008] [Indexed: 11/29/2022] Open
Abstract
Background HIV-1 integrase (IN) is a key viral enzymatic molecule required for the integration of the viral cDNA into the genome. Additionally, HIV-1 IN has been shown to play important roles in several other steps during the viral life cycle, including reverse transcription, nuclear import and chromatin targeting. Interestingly, previous studies have demonstrated that the expression of HIV-1 IN induces the lethal phenotype in some strains of Saccharomyces cerevisiae. In this study, we performed mutagenic analyses of the C-terminal region of the catalytic core domain of HIV-1 IN in order to delineate the critical amino acid(s) and/or motif(s) required for the induction of the lethal phenotype in the yeast strain HP16, and to further elucidate the molecular mechanism which causes this phenotype. Results Our study identified three HIV-1 IN mutants, V165A, A179P and KR186,7AA, located in the C-terminal region of the catalytic core domain of IN that do not induce the lethal phenotype in yeast. Chromatin binding assays in yeast and mammalian cells demonstrated that these IN mutants were impaired for the ability to bind chromatin. Additionally, we determined that while these IN mutants failed to interact with LEDGF/p75, they retained the ability to bind Integrase interactor 1. Furthermore, we observed that VSV-G-pseudotyped HIV-1 containing these IN mutants was unable to replicate in the C8166 T cell line and this defect was partially rescued by complementation with the catalytically inactive D64E IN mutant. Conclusion Overall, this study demonstrates that three mutations located in the C-terminal region of the catalytic core domain of HIV-1 IN inhibit the IN-induced lethal phenotype in yeast by inhibiting the binding of IN to the host chromatin. These results demonstrate that the C-terminal region of the catalytic core domain of HIV-1 IN is important for binding to host chromatin and is crucial for both viral replication and the promotion of the IN-induced lethal phenotype in yeast.
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Affiliation(s)
- Zaikun Xu
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, University of Manitoba, 508-730 William Avenue, Winnipeg, R3E 0W3, Canada.
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Desfarges S, San Filippo J, Fournier M, Calmels C, Caumont-Sarcos A, Litvak S, Sung P, Parissi V. Chromosomal integration of LTR-flanked DNA in yeast expressing HIV-1 integrase: down regulation by RAD51. Nucleic Acids Res 2006; 34:6215-24. [PMID: 17090598 PMCID: PMC1693895 DOI: 10.1093/nar/gkl843] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
HIV-1 integrase (IN) is the key enzyme catalyzing the proviral DNA integration step. Although the enzyme catalyzes the integration step accurately in vitro, whether IN is sufficient for in vivo integration and how it interacts with the cellular machinery remains unclear. We set up a yeast cellular integration system where integrase was expressed as the sole HIV-1 protein and targeted the chromosomes. In this simple eukaryotic model, integrase is necessary and sufficient for the insertion of a DNA containing viral LTRs into the genome, thereby allowing the study of the isolated integration step independently of other viral mechanisms. Furthermore, the yeast system was used to identify cellular mechanisms involved in the integration step and allowed us to show the role of homologous recombination systems. We demonstrated physical interactions between HIV-1 IN and RAD51 protein and showed that HIV-1 integrase activity could be inhibited both in the cell and in vitro by RAD51 protein. Our data allowed the identification of RAD51 as a novel in vitro IN cofactor able to down regulate the activity of this retroviral enzyme, thereby acting as a potential cellular restriction factor to HIV infection.
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Affiliation(s)
- S. Desfarges
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
| | - J. San Filippo
- Deptartment of Molecular Biophysics and Biochemistry, Yale University School of Medicine333 Cedar Street, SHM C130, New Haven, CT 06520, USA
| | - M. Fournier
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
| | - C. Calmels
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
| | - A. Caumont-Sarcos
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
| | - S. Litvak
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
| | - P. Sung
- Deptartment of Molecular Biophysics and Biochemistry, Yale University School of Medicine333 Cedar Street, SHM C130, New Haven, CT 06520, USA
| | - V. Parissi
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
- To whom correspondence should be addressed. Tel: +33 5 57 57 1740; Fax: +33 5 57 57 1766;
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Vera J, Parissi V, García A, Zúñiga R, Andreola ML, Caumont-Sarcos A, Tarrago-Litvak L, Leon O. Yeast system as a model to study Moloney murine leukemia virus integrase: expression, mutagenesis and search for eukaryotic partners. J Gen Virol 2005; 86:2481-2488. [PMID: 16099906 DOI: 10.1099/vir.0.81006-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Moloney murine leukemia virus (M-MuLV) integrase (IN) catalyses the insertion of the viral genome into the host chromosomal DNA. The limited solubility of the recombinant protein produced in Escherichia coli led the authors to explore the use of Saccharomyces cerevisiae for expression of M-MuLV IN. IN was expressed in yeast and purified by chromatography on nickel-NTA agarose. IN migrated as a single band in SDS-PAGE and did not contain IN degradation products. The enzyme was about twofold more active than the enzyme purified from E. coli and was free of nucleases. Using the yeast system, the substitution of the putative catalytic amino acid Asp184 by alanine was also analysed. The mutated enzyme was inactive in the in vitro assays. This is the first direct demonstration that mutation of Asp184 inactivates M-MuLV IN. Finally, S. cerevisiae was used as a model to assess the ability of M-MuLV IN to interact with eukaryotic protein partners. The expression of an active M-MuLV IN in yeast strains deficient in RAD52 induced a lethal effect. This phenotype could be attributed to cellular damage, as suggested by the viability of cells expressing inactive D184A IN. Furthermore, when active IN was expressed in a yeast strain lacking the ySNF5 transcription factor, the lethal effect was abolished, suggesting the involvement of ySNF5 in the cellular damage induced by IN. These results indicate that S. cerevisiae could be a useful model to study the interaction of IN with cellular components in order to identify potential counterparts of the natural host.
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Affiliation(s)
- Jorge Vera
- Programa de Virologia, ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Vincent Parissi
- Bordeaux, F-33000 France; IFR 66 'Pathologies Infectieuses et Cancers', Bordeaux, F-33000 France. 146 rue Léo Saignat, 33076 Bordeaux cedex, France
- CNRS UMR 5097, Bordeaux, F-33000 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33000 France. 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Andrea García
- Programa de Virologia, ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Roberto Zúñiga
- Programa de Virologia, ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Marie-Line Andreola
- Bordeaux, F-33000 France; IFR 66 'Pathologies Infectieuses et Cancers', Bordeaux, F-33000 France. 146 rue Léo Saignat, 33076 Bordeaux cedex, France
- CNRS UMR 5097, Bordeaux, F-33000 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33000 France. 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Anne Caumont-Sarcos
- Bordeaux, F-33000 France; IFR 66 'Pathologies Infectieuses et Cancers', Bordeaux, F-33000 France. 146 rue Léo Saignat, 33076 Bordeaux cedex, France
- CNRS UMR 5097, Bordeaux, F-33000 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33000 France. 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Laura Tarrago-Litvak
- Bordeaux, F-33000 France; IFR 66 'Pathologies Infectieuses et Cancers', Bordeaux, F-33000 France. 146 rue Léo Saignat, 33076 Bordeaux cedex, France
- CNRS UMR 5097, Bordeaux, F-33000 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33000 France. 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Oscar Leon
- Programa de Virologia, ICBM, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
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14
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Bessong PO, Obi CL, Andréola ML, Rojas LB, Pouységu L, Igumbor E, Meyer JJM, Quideau S, Litvak S. Evaluation of selected South African medicinal plants for inhibitory properties against human immunodeficiency virus type 1 reverse transcriptase and integrase. JOURNAL OF ETHNOPHARMACOLOGY 2005; 99:83-91. [PMID: 15848024 DOI: 10.1016/j.jep.2005.01.056] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Revised: 01/05/2005] [Accepted: 01/28/2005] [Indexed: 05/24/2023]
Abstract
Seventeen aqueous and methanol extracts from nine South African medicinal plants, ethnobotanically selected, were screened for inhibitory properties against HIV-1 reverse transcriptase (RT). Isolated compounds were additionally evaluated on HIV-1 integrase (IN). The strongest inhibition against the RNA-dependent-DNA polymerase (RDDP) activity of RT was observed with the methanol extract of the stem-bark of Peltophorum africanum Sond. (Fabaceae) (IC(50) 3.5 microg/ml), while the methanol extract of the roots of Combretum molle R.Br. ex G. Don (Combretaceae) was the most inhibitory on the ribonuclease H (RNase H) activity (IC(50) 9.7 microg/ml). The known compounds bergenin and catechin, and a red coloured gallotannin composed of meta-depside chains of gallic and protocatechuic acids esterified to a 1-O-isobutyroly-beta-D-glucopyranose core, were isolated from the methanol extract of the roots and stem-bark of Peltophorum africanum. The gallotannin inhibited the RDDP and RNase H functions of RT with IC(50) values of 6.0 and 5.0 microM, respectively, and abolished the 3'-end processing activity of IN at 100 microM. Catechin showed no effect on RT but had a moderate activity on HIV-1 IN. Bergenin was inactive on both enzymes. The aqueous and methanol extracts were non-toxic in a HeLaP4 cell line at a concentration of 400 microg/ml.
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Affiliation(s)
- Pascal Obong Bessong
- Department of Microbiology, University of Venda for Science and Technology, PMB X5050, Thohoyandou 0950, South Africa.
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15
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Faure A, Calmels C, Desjobert C, Castroviejo M, Caumont-Sarcos A, Tarrago-Litvak L, Litvak S, Parissi V. HIV-1 integrase crosslinked oligomers are active in vitro. Nucleic Acids Res 2005; 33:977-86. [PMID: 15718297 PMCID: PMC549407 DOI: 10.1093/nar/gki241] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The oligomeric state of active human immunodeficiency virus type 1 (HIV-1) integrase (IN) has not been clearly elucidated. We analyzed the activity of the different purified oligomeric forms of recombinant IN obtained after stabilization by platinum crosslinking. The crosslinked tetramer isolated by gel chromatography was able to catalyze the full-site integration of the two viral LTR ends into a target DNA in vitro, whereas the isolated dimeric form of the enzyme was involved in the processing and integration of only one viral end. Accurate concerted integration by IN tetramers was confirmed by cloning and sequencing. Kinetic studies of DNA-integrase complexes led us to propose a model explaining the formation of an active complex. Our data suggest that the tetrameric IN bound to the viral DNA ends is the minimal complex involved in the concerted integration of both LTRs and should be the oligomeric form targeted by future inhibitors.
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Affiliation(s)
| | | | | | | | | | | | | | - Vincent Parissi
- To whom correspondence should be addressed at UMR 5097, CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France. Tel: +33 0 5 57 57 17 40; Fax: +33 0 5 57 57 17 66;
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16
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Balan A, Schenberg ACG. A conditional suicide system forSaccharomyces cerevisiae relying on the intracellular production of theSerratia marcescens nuclease. Yeast 2005; 22:203-12. [PMID: 15704225 DOI: 10.1002/yea.1203] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A conditional lethal system for biological containment of genetically modified strains of Saccharomyces cerevisiae is described. This suicide system is based on the intracellular production of the Serratia marcescens nuclease in the yeast cell, aiming at the destruction of the host genetic material. The S. marcescens nuclease, encoded by the nucA gene, is normally secreted by the bacterium into the medium. In the present work, the nucA gene, devoid of its signal peptide coding sequence, was cloned in a yeast expression vector, under control of the glucose-repressed S. cerevisiae alcohol dehydrogenase 2 gene (ADH2) promoter. When transformed into S. cerevisiae, the recombinant plasmid proved to be effective in killing the host cells upon glucose depletion from the medium, and the nuclease activity was found in lysates prepared from the transformants. In addition, the nuclease degrading effect was shown to reach chromosomal DNA in the yeast host. The killing effect of the nucA plasmid was also demonstrated in soil microcosm assays, indicating that whenever the GMM escapes into the environment where glucose is scarce, the nucA gene will be expressed and the resulting nuclease will destroy the genetic material and kill the cells. In contrast to other suicide systems that target the cell envelope, the advantage of the one described here is that it disfavours horizontal gene transfer from recombinant yeast cells to other microorganisms found in the environment.
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Affiliation(s)
- Andrea Balan
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, Avenida Professor Lineu Prestes 1374, São Paulo 05508-900, SP, Brasil
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17
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Calmels C, de Soultrait VR, Caumont A, Desjobert C, Faure A, Fournier M, Tarrago-Litvak L, Parissi V. Biochemical and random mutagenesis analysis of the region carrying the catalytic E152 amino acid of HIV-1 integrase. Nucleic Acids Res 2004; 32:1527-38. [PMID: 14999095 PMCID: PMC390286 DOI: 10.1093/nar/gkh298] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
HIV-1 integrase (IN) catalyzes the integration of the proviral DNA into the cellular genome. The catalytic triad D64, D116 and E152 of HIV-1 IN is involved in the reaction mechanism and the DNA binding. Since the integration and substrate binding processes are not yet exactly known, we studied the role of amino acids localized in the catalytic site. We focused our interest on the V151E152S153 region. We generated random mutations inside this domain and selected mutated active INs by using the IN-induced yeast lethality assay. In vitro analysis of the selected enzymes showed that the IN nuclease activities (specific 3'-processing and non-sequence-specific endonuclease), the integration and disintegration reactions and the binding of the various DNA substrates were affected differently. Our results support the hypothesis that the three reactions may involve different DNA binding sites, enzyme conformations or mechanisms. We also show that the V151E152S153 region involvement in the integration reaction is more important than for the 3'-processing activity and can be involved in the recognition of DNA. The IN mutants may lead to the development of new tools for studying the integration reaction, and could serve as the basis for the discovery of integration-specific inhibitors.
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Affiliation(s)
- C Calmels
- UMR-5097, CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, and IFR 66 Pathologies Infectieuses et Cancers, Bordeaux, France
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18
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Parissi V, Caumont A, de Soultrait VR, Desjobert C, Calmels C, Fournier M, Gourgue G, Bonneu M, Tarrago-Litvak L, Litvak S. The lethal phenotype observed after HIV-1 integrase expression in yeast cells is related to DNA repair and recombination events. Gene 2004; 322:157-68. [PMID: 14644507 DOI: 10.1016/j.gene.2003.08.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) integrase (IN) catalyzes the insertion of the viral genome into the host cell DNA, an essential reaction during the retroviral cycle. We described previously that expression of HIV-1 IN in some yeast strains may lead to the emergence of a lethal phenotype which was not observed when the catalytically crucial residues D, D, (35)E were mutated. The lethal effect in yeast seems to be related to the mutagenic effect of the recombinant HIV-1 IN, most probably via the non-sequence-specific endonucleolytic activity carried by this enzyme. This non-sequence-specific endonuclease activity was further characterized. Although the enzyme was active on DNA substrates devoid of viral long terminal repeat (LTR) sequences, the presence of LTR regions stimulated significantly this activity. Genetic experiments were designed to show that both the mutagenic effect and the level of recombination events were affected in cells expressing the active retroviral enzyme, while expression of the mutated inactive IN D116A has no significant effect. A close interaction was demonstrated between integrase activity and in vivo/in vitro recombination process, suggesting that retroviral integration and recombination mechanism are linked in the infected cell. Our results show that the yeast system is a powerful cellular model to study the non-sequence-specific endonucleolytic activity of IN. Its characterization is essential since this activity might represent a very important step in the retroviral infectious cycle and would provide further insights into the function of IN. Indeed, effectors of this activity should be sought as potential antiviral agents since stimulation of this enzymatic activity would induce the destruction of early synthesized proviral DNA.
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Affiliation(s)
- Vincent Parissi
- UMR-5097 REGER, CNRS-Université Victor Segalen Bordeaux 2, IFR 66 "Pathologies Infectieuses", 146 rue Léo Saignat, 33076 cedex Bordeaux, France.
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19
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Andréola ML, De Soultrait VR, Fournier M, Parissi V, Desjobert C, Litvak S. HIV-1 integrase and RNase H activities as therapeutic targets. Expert Opin Ther Targets 2002; 6:433-46. [PMID: 12223059 DOI: 10.1517/14728222.6.4.433] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The retroviruses are a large, diverse family of enveloped RNA viruses defined by their structure, composition and replicative properties. The hallmark of the family is its replicative strategy, essential steps of which include reverse transcription of the viral RNA and the subsequent integration of this DNA into the genome of the cell. These steps are performed by two viral-encoded enzymes, reverse transcriptase (RT), which possesses DNA polymerase and ribonuclease H (RNase H) activities, and integrase (IN). These enzymes are excellent targets for retroviral therapy since they are essential for viral replication. Numerous substances capable of inhibiting the DNA polymerase activity of HIV-1 RT are available, while few specific inhibitors of RNase H activity have been described. IN is absolutely necessary for stable and productive infection of cells. Some IN inhibitors have been recently reported and are available demonstrating the potential of IN as an antiviral target. This paper is an overview of the inhibitors of RNase H and IN and describes the most promising inhibitors.
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Affiliation(s)
- M L Andréola
- Laboratory of Replication and Expression of Eukaryotic and Retroviral Genomes, UMR 5097, CNRS-Université Victor Segalen Bordeaux 2, France.
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20
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de Soultrait VR, Caumont A, Durrens P, Calmels C, Parissi V, Recordon P, Bon E, Desjobert C, Tarrago-Litvak L, Fournier M. HIV-1 integrase interacts with yeast microtubule-associated proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1575:40-8. [PMID: 12020817 DOI: 10.1016/s0167-4781(02)00241-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) integrase (IN) mediates the insertion of viral DNA into the human genome. In addition to IN, cellular and viral proteins are associated to proviral DNA in the so-called preintegration complex (PIC). We previously reported that the expression of HIV-1 IN in yeast leads to the emergence of a lethal phenotype. This effect may be linked to the IN activity on infected human cells where integration requires the cleavage of genomic DNA. To isolate and characterize potential cellular partners of HIV-1 IN, we used it as a bait in a two-hybrid system with a yeast genomic library. IN interacted with proteins belonging to the microtubule network, or involved in the protein synthesis apparatus. We focused our interest on one of the selected inserts, L2, which corresponds to the C-end half of the yeast STU2p, a microtubule-associated protein (MAP). STU2p is an essential component of the yeast spindle pole body (SPB), which is able to bind microtubules in vitro. After expressing and purifying L2 as a recombinant protein, we showed its binding to IN by ELISA immunodetection. L2 was also able to inhibit IN activity in vitro. In addition, the effect of L2 was tested using the "lethal yeast phenotype". The coexpression of IN and the L2 peptide abolished the lethal phenotype, thus showing important in vivo interactions between IN and L2. The identification of components of the microtubule network associated with IN suggest a role of this complex in the transport of HIV-1 IN present in the PIC to the nucleus, as already described for other human viruses.
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Affiliation(s)
- Vaea Richard de Soultrait
- UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, BP 103, Bat. 3A-3 Etage, 146 rue Léo Saignat, 33076 Bordeaux X Cedex, France
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21
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de Soultrait VR, Caumont A, Parissi V, Morellet N, Ventura M, Lenoir C, Litvak S, Fournier M, Roques B. A novel short peptide is a specific inhibitor of the human immunodeficiency virus type 1 integrase. J Mol Biol 2002; 318:45-58. [PMID: 12054767 DOI: 10.1016/s0022-2836(02)00033-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The retroviral encoded protein integrase (IN) is required for the insertion of the human immunodeficiency virus type 1 (HIV-1) proviral DNA into the host genome. In spite of the crucial role played by IN in the retroviral life cycle, which makes this enzyme an attractive target for the development of new anti-AIDS agents, very few inhibitors have been described and none seems to have a potential use in anti-HIV therapy. To obtain potent and specific IN inhibitors, we used the two-hybrid system to isolate short peptides. Using HIV-1 IN as a bait and a yeast genomic library as the source of inhibitory peptides (prey), we isolated a 33-mer peptide (I33) that bound tightly to the enzyme. I33 inhibited both in vitro IN activities, i.e. 3' end processing and strand transfer. Further analysis led us to select a shorter peptide, EBR28, corresponding to the N-terminal region of I33. Truncated variants showed that EBR28 interacted with the catalytic domain of IN interfering with the binding of the DNA substrate. Alanine single substitution of each EBR28 residue (alanine scanning) allowed the identification of essential amino acids involved in the inhibition. The EBR28 NMR structure shows that this peptide adopts an alpha-helical conformation with amphipathic properties. Additionally, EBR28 showed a significant antiviral effect when assayed on HIV-1 infected human cells. Thus, this potentially important short lead peptide may not only be helpful to design new anti-HIV agents, but also could prove very useful in further studies of the structural and functional characteristics of HIV-1 IN.
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22
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Abstract
Ku proteins are associated with a variety of cellular processes such as repair of DNA-double-strand breaks, telomere maintenance and retrotransposition. In recent years, we have learned a lot about their cellular and molecular functions and it has turned out that Ku-dependent processes affect the stability of the genome, both positively and negatively, in several ways. This article gives an overview on the role of Ku in determining the shape of the genome.
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Affiliation(s)
- Anna A. Friedl
- Strahlenbiologisches Institut der Universität München, Schiller Straße 42, 80336 München, Germany
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23
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Parissi V, Calmels C, De Soultrait VR, Caumont A, Fournier M, Chaignepain S, Litvak S. Functional interactions of human immunodeficiency virus type 1 integrase with human and yeast HSP60. J Virol 2001; 75:11344-53. [PMID: 11689615 PMCID: PMC114720 DOI: 10.1128/jvi.75.23.11344-11353.2001] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integration of human immunodeficiency virus type 1 (HIV-1) proviral DNA in the nuclear genome is catalyzed by the retroviral integrase (IN). In addition to IN, viral and cellular proteins associated in the high-molecular-weight preintegration complex have been suggested to be involved in this process. In an attempt to define host factors interacting with IN, we used an in vitro system to identify cellular proteins in interaction with HIV-1 IN. The yeast Saccharomyces cerevisiae was chosen since (i) its complete sequence has been established and the primary structure of all the putative proteins from this eucaryote has been deduced, (ii) there is a significant degree of homology between human and yeast proteins, and (iii) we have previously shown that the expression of HIV-1 IN in yeast induces a lethal phenotype. Strong evidences suggest that this lethality is linked to IN activity in infected human cells where integration requires the cleavage of genomic DNA. Using IN-affinity chromatography we identified four yeast proteins interacting with HIV-1 IN, including the yeast chaperonin yHSP60, which is the counterpart of human hHSP60. Yeast lethality induced by HIV-1 IN was abolished when a mutated HSP60 was coexpressed, therefore suggesting that both proteins interact in vivo. Besides interacting with HIV-1 IN, the hHSP60 was able to stimulate the in vitro processing and joining activities of IN and protected this enzyme from thermal denaturation. In addition, the functional human HSP60-HSP10 complex in the presence of ATP was able to recognize the HIV-1 IN as a substrate.
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Affiliation(s)
- V Parissi
- REGER, UMR-5097 Centre National de la Recherche Scientifique (CNRS)-Université Victor Segalen Bordeaux 2, Bordeaux, France.
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24
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Abstract
Human immunodeficiency virus type-1 (HIV-1) integrase catalyzes the irreversible insertion of the viral genome into host chromosomal DNA. We have developed a mammalian expression system for the synthesis of authentic HIV-1 integrase in the absence of other viral proteins. Integrase, which bears a N-terminal phenylalanine, was found to be a short-lived protein in human embryo kidney 293T cells. The degradation of integrase could be suppressed by proteasome inhibitors. N-terminal phenylalanine is recognized as a degradation signal by a ubiquitin-proteasome proteolytic system known as the N-end rule pathway. The replacement of N-terminal phenylalanine with methionine, valine, or glycine, which are stabilizing residues in the N-end rule, resulted in metabolically stabilized integrase proteins (half-life of N-terminal Met-integrase was at least 3 h). Conversely, the substitution of N-terminal phenylalanine with other destabilizing residues retained the metabolic instability of integrase. These findings indicate that the HIV-1 integrase is a physiological substrate of the N-end rule. We discuss a possible functional similarity to the better understood turnover of the bacteriophage Mu transposase and functions of integrase instability to the maintenance and integrity of the host cell genome.
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Affiliation(s)
- L C Mulder
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 10016, USA
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25
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Cherepanov P, Pluymers W, Claeys A, Proost P, Clercq E, Debyser Z. High‐level expression of active HIV‐1 integrase from a synthetic gene in human cells. FASEB J 2000. [DOI: 10.1096/fasebj.14.10.1389] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Peter Cherepanov
- Rega Institute for Medical Research K.U. Leuven B‐3000 Leuven Belgium
| | - Wim Pluymers
- Rega Institute for Medical Research K.U. Leuven B‐3000 Leuven Belgium
| | - Anje Claeys
- Rega Institute for Medical Research K.U. Leuven B‐3000 Leuven Belgium
| | - Paul Proost
- Rega Institute for Medical Research K.U. Leuven B‐3000 Leuven Belgium
| | - Erik Clercq
- Rega Institute for Medical Research K.U. Leuven B‐3000 Leuven Belgium
| | - Zeger Debyser
- Rega Institute for Medical Research K.U. Leuven B‐3000 Leuven Belgium
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26
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Parissi V, Caumont A, Richard de Soultrait V, Dupont CH, Pichuantes S, Litvak S. Inactivation of the SNF5 transcription factor gene abolishes the lethal phenotype induced by the expression of HIV-1 integrase in yeast. Gene 2000; 247:129-36. [PMID: 10773452 DOI: 10.1016/s0378-1119(00)00108-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The ubiquitous human transcription factor Ini1 has been shown to interact with HIV-1 integrase (IN) and to stimulate in vitro the reactions catalyzed by this enzyme. We have previously used a yeast model to study the effect of HIV-1 IN expression (Caumont, A.B., Jamieson, G.A., Pichuantes, S., Nguyen, A.T., Litvak, S., Dupont, C. -H., 1996. Expression of functional HIV-1 integrase in the yeast Saccharomyces cerevisiae leads to the emergence of a lethal phenotype: potential use for inhibitor screening. Curr. Genet. 29, 503-510). Here, we describe the effect of the inactivation of the gene encoding for SNF5, a yeast transcription factor homologous to Ini1, on the lethality induced by the expression of HIV-1 IN in yeast. We observed that the retroviral IN was unable to perform its lethal activity in cells where the SNF5 gene has been disrupted, suggesting that SNF5 may play a role in the lethal effect induced by IN in yeast. SNF5 inactivation affects neither yeast viability nor expression of HIV-1 IN. Given the homology between SNF5 and its human counterpart Ini1, our results suggest that this factor may be important for IN activity in infected cells. Moreover, given the important role proposed for this transcription factor in the integration step and the fact that it is dispensable for cell viability, the interaction between Ini1/ySNF5 and HIV-1 IN should become a potential target in the search for new antiretroviral agents.
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Affiliation(s)
- V Parissi
- CNRS UMR-5097. IFR 66 'Pathologies Infectieuses', Université Victor Segalen Bordeaux 2. 146 rue Leo Saignat, 33076, Bordeaux, France.
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27
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Parissi V, Caumont AB, de Soultrait VR, Calmels C, Pichuantes S, Litvak S, Dupont CH. Selection of amino acid substitutions restoring activity of HIV-1 integrase mutated in its catalytic site using the yeast Saccharomyces cerevisiae. J Mol Biol 2000; 295:755-65. [PMID: 10656788 DOI: 10.1006/jmbi.1999.3416] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The integration of proviral DNA into the genome of the host cell is an essential step in the replication of retroviruses. This reaction is catalyzed by a viral-encoded enzyme, the integrase (IN). We have previously shown that human immunodeficiency virus type 1 (HIV-1) IN causes a lethal effect when expressed in yeast cells. This system, called yeast lethal assay, was used as a tool to study IN activity in a cellular context. The yeast lethal assay allowed the selection and characterization of mutations affecting both the lethal phenotype and the in vitro IN activities. IN mutants were produced by random PCR mutagenesis in an IN gene bearing the inactivating D116A mutation in the catalytic site. The corresponding D116A substituted IN does not lead to lethality in yeast. Subsequent selection of mutants able to restore the lethal effect of IN was carried out using the yeast lethal assay. We isolated three mutants presenting a restored phenotype. The mutated IN genes were sequenced and the corresponding proteins were purified to characterize their in vitro activities. The three mutants presented restoration of the in vitro strand transfer activity, while 3' processing was only partially restored.The three mutants differ from D116A IN by at least one amino acid substitution located in the N-terminal domain of the protein, outside of the active site. These new mutated HIV-1 INs may therefore allow a better understanding of the N-terminal domain function in the integration reaction. In addition, these results support our hypothesis that explains the lethal effect as a consequence of the nuclear damage caused by wild-type IN in yeast cells. These data also indicate that the yeast lethal assay can be used as a tool to study the retroviral integration mechanism in a cellular context and to select specific inhibitors.
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Affiliation(s)
- V Parissi
- Laboratoire REGER, UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, IFR 66 Pathologies Infectieuses. 1, rue Camille Saint Saëns, Bordeaux cedex, 33077, France.
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28
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Caumont A, Jamieson G, de Soultrait VR, Parissi V, Fournier M, Zakharova OD, Bayandin R, Litvak S, Tarrago-Litvak L, Nevinsky GA. High affinity interaction of HIV-1 integrase with specific and non-specific single-stranded short oligonucleotides. FEBS Lett 1999; 455:154-8. [PMID: 10428491 DOI: 10.1016/s0014-5793(99)00859-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Retroviral integrase (IN) catalyzes the integration of double-stranded viral DNA into the host cell genome. The reaction can be divided in two steps: 3'-end processing and DNA strand transfer. Here we studied the effect of short oligonucleotides (ODNs) on human immunodeficiency virus type 1 (HIV-1) IN. ODNs were either specific, with sequences representing the extreme termini of the viral long terminal repeats, or nonspecific. All ODNs were found to competitively inhibit the processing reaction with Ki values in the nM range for the best inhibitors. Our studies on the interaction of IN with ODNs also showed that: (i) besides the 3'-terminal GT, the interaction of IN with the remaining nucleotides of the 21-mer specific sequence was also important for an effective interaction of the enzyme with the substrate; (ii) in the presence of specific ODNs the activity of the enzyme was enhanced, a result which suggests an ODN-induced conformational change of HIV-1 IN.
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Affiliation(s)
- A Caumont
- EP 630 CNRS-Université Victor Segalen Bordeaux 2, France
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29
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Pynka M, Wnuk A, Bander D, Syczewska M, Boroń A, Prost B, Wrzecion S. Disseminated infection with Saccharomyces kluyveri in a patient with AIDS. Infection 1998; 26:184-6. [PMID: 9646114 DOI: 10.1007/bf02771850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A 47-year-old man with acquired immune deficiency syndrome was found to have disseminated Saccharomyces kluyveri infection. The yeast was isolated from blood and cerebro-spinal fluid. An autopsy revealed the presence of the microorganism in many organs including liver, kidneys, pancreas, spleen, lung, and brain. The case confirms a potential pathogenicity of yeasts of the genus Saccharomyces in patients with profound immune deficiency, especially in advanced HIV infection.
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Affiliation(s)
- M Pynka
- Dept. of Infectious Diseases, Pomeranian Medical Academy, Szczecin, Poland
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