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Gwak M, Choi YJ, Yoo NJ, Lee S. Expression of DNA Cytosine Deaminase APOBEC3 Proteins, a Potential Source for Producing Mutations, in Gastric, Colorectal and Prostate Cancers. TUMORI JOURNAL 2018. [DOI: 10.1177/1636.17922] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Min Gwak
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Youn Jin Choi
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Nam Jin Yoo
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - SugHyung Lee
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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2
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Human-APOBEC3G-dependent restriction of porcine endogenous retrovirus replication is mediated by cytidine deamination and inhibition of DNA strand transfer during reverse transcription. Arch Virol 2018; 163:1907-1914. [PMID: 29610985 DOI: 10.1007/s00705-018-3822-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/18/2018] [Indexed: 10/17/2022]
Abstract
Although human apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G, hA3G)-mediated deamination is the major mechanism used to restrict the infectivity of a broad range of retroviruses, it is unclear whether porcine endogenous retrovirus (PERV) is affected by hA3G or porcine A3F (poA3F). To determine whether DNA deamination is required for hA3G- and poA3F-dependent inhibition of PERV transmission, we developed VSV-pseudotype PERV-B expressing hA3G, mutant hA3G-E67Q (encapsidation and RNA binding activity-deficient), mutant hA3G-E259Q (deaminase-deficient), or poA3F. hA3G-E67Q decreased virus infectivity by ~ 93% compared to the ~ 99% decrease of viral infectivity by wild-type hA3G, while hA3G-E259Q decreased the infectivity of PERV-B by ~ 35%. These data suggest that cytidine deamination activity is crucial for efficient restriction of PERV by hA3G, but cytidine deamination cannot fully explain the inactivation of PERV by hA3G. Furthermore, differential DNA denaturation PCR (3D-PCR) products from 293T cells infected with PERV-B expressing hA3G mutants were sequenced. G-to-A hypermutation was detected at a frequency of 4.1% for hA3G, 3.4% for hA3G-E67Q, and 4.7% for poA3F. These results also suggest that hA3G and poA3F inhibit PERV by a deamination-dependent mechanism. To examine the effect of hA3G on the production of PERV DNA, genomic DNA was extracted from 293T cells 12 h after infection with PERV expressing hA3G, and this DNA was used as template for real-time PCR. A 50% decrease in minus strand strong stop (-sss) DNA synthesis/transfer was observed in the presence of hA3G. Based on these results, we conclude that hA3G may restrict PERV by both deamination-dependent mechanisms and inhibition of DNA strand transfer during PERV reverse transcription.
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3
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Konstantoulas CJ, Hagen B, Indik S. Moderate sensitivity of mouse mammary tumour virus to inhibition by human APOBEC3G. J Gen Virol 2017; 98:2362-2367. [PMID: 28809145 DOI: 10.1099/jgv.0.000897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Infectivity of the mouse mammary tumour virus (MMTV) is inhibited by mouse APOBEC3 (mA3) which is efficiently packaged into virions. As the inhibition is only partial, the virus can replicate in tissues expressing mA3 and complete its replication cycle. Here, we have examined the sensitivity of MMTV to inhibition by a human orthologue of mA3, A3G. We report that the virus containing A3G is only moderately susceptible to inhibition by the human factor. Whereas the vif-deficient HIV-1 vector produced in human epithelial cells expressing endogenous levels of A3G was efficiently inhibited, an MMTV vector remained fully infectious. Greater A3G expression levels were necessary to restrict infectivity of MMTV, but only when the factor retained its deaminase activity. Furthermore, the spreading kinetic of a replication competent MMTV was only moderately accelerated in cells with downmodulated A3G expression. These data suggest that MMTV has evolved a mechanism to neutralize antiviral activity of APOBEC3 proteins.
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Affiliation(s)
| | - Benedikt Hagen
- Institute of Virology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Stanislav Indik
- Institute of Virology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
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4
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Zeng Y, Li H, Zhang X, Shang J, Kang Y. Basal transcription of APOBEC3G is regulated by USF1 gene in hepatocyte. Biochem Biophys Res Commun 2016; 470:54-60. [PMID: 26772882 DOI: 10.1016/j.bbrc.2015.12.108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 12/23/2015] [Indexed: 11/13/2022]
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G, A3G) exert antiviral defense as an important factor of innate immunity. A variety of cytokines such as IFN-γ、IL2、IL15、IL7 could induce the transcription of A3G. However, the regulation of other nuclear factor on the transcription of A3G have not been reported at the present. To gain new insights into the transcriptional regulation of this restriction factor, we cloned and characterized the promoter region of A3G and investigate the modulation of USF1 gene on the transcription of A3G. We identified a 232 bp region that was sufficient to regulate the activity of full promoter. Transcriptional start sites (TSS) were identified by the luciferase reporter assays of plasmids containing full or shorter fragments of the A3G promoter. The results demonstrated that the core promoter of A3G is located within the region -159/-84 relative to the TSS. Transcriptional activity of A3G core promoter regulated by USF1 was dependent on an E-box (located at position -91/-86 relative to the major TSS) and was abolished after mutation of this DNA element. USF1 gene can take part in basal transcription regulation of the human A3G gene in hepatocyte, and the identified E-box represented a binding site for the USF1.
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Affiliation(s)
- Yanli Zeng
- Department of Infectious Diseases, Zhengzhou University People's Hospital (Henan Provincial People's Hospital), Zhengzhou, 450003, China
| | - Hui Li
- The Central Hospital of Wuhan, Tongji Medical College Huazhong University of Science Technology, Wuhan, 430000, China
| | - Xiaoju Zhang
- Department of Respiratory Medicine, Zhengzhou University People's Hospital (Henan Provincial People's Hospital), Zhengzhou, 450003, China
| | - Jia Shang
- Department of Infectious Diseases, Zhengzhou University People's Hospital (Henan Provincial People's Hospital), Zhengzhou, 450003, China
| | - Yi Kang
- Department of Infectious Diseases, Zhengzhou University People's Hospital (Henan Provincial People's Hospital), Zhengzhou, 450003, China.
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5
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Lardenoije R, Iatrou A, Kenis G, Kompotis K, Steinbusch HWM, Mastroeni D, Coleman P, Lemere CA, Hof PR, van den Hove DLA, Rutten BPF. The epigenetics of aging and neurodegeneration. Prog Neurobiol 2015; 131:21-64. [PMID: 26072273 PMCID: PMC6477921 DOI: 10.1016/j.pneurobio.2015.05.002] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/14/2022]
Abstract
Epigenetics is a quickly growing field encompassing mechanisms regulating gene expression that do not involve changes in the genotype. Epigenetics is of increasing relevance to neuroscience, with epigenetic mechanisms being implicated in brain development and neuronal differentiation, as well as in more dynamic processes related to cognition. Epigenetic regulation covers multiple levels of gene expression; from direct modifications of the DNA and histone tails, regulating the level of transcription, to interactions with messenger RNAs, regulating the level of translation. Importantly, epigenetic dysregulation currently garners much attention as a pivotal player in aging and age-related neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, where it may mediate interactions between genetic and environmental risk factors, or directly interact with disease-specific pathological factors. We review current knowledge about the major epigenetic mechanisms, including DNA methylation and DNA demethylation, chromatin remodeling and non-coding RNAs, as well as the involvement of these mechanisms in normal aging and in the pathophysiology of the most common neurodegenerative diseases. Additionally, we examine the current state of epigenetics-based therapeutic strategies for these diseases, which either aim to restore the epigenetic homeostasis or skew it to a favorable direction to counter disease pathology. Finally, methodological challenges of epigenetic investigations and future perspectives are discussed.
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Affiliation(s)
- Roy Lardenoije
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Artemis Iatrou
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Gunter Kenis
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Konstantinos Kompotis
- Center for Integrative Genomics, University of Lausanne, Genopode Building, 1015 Lausanne-Dorigny, Switzerland
| | - Harry W M Steinbusch
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Diego Mastroeni
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands; L.J. Roberts Alzheimer's Disease Center, Banner Sun Health Research Institute, 10515 W. Santa Fe Drive, Sun City, AZ 85351, USA
| | - Paul Coleman
- L.J. Roberts Alzheimer's Disease Center, Banner Sun Health Research Institute, 10515 W. Santa Fe Drive, Sun City, AZ 85351, USA
| | - Cynthia A Lemere
- Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Daniel L A van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands; Laboratory of Translational Neuroscience, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Fuechsleinstrasse 15, 97080 Wuerzburg, Germany
| | - Bart P F Rutten
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands.
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6
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Differential sensitivity of porcine endogenous retrovirus to APOBEC3-mediated inhibition. Arch Virol 2015; 160:1901-8. [DOI: 10.1007/s00705-015-2450-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 05/07/2015] [Indexed: 01/30/2023]
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Gekonge B, Bardin MC, Montaner LJ. Short communication: Nitazoxanide inhibits HIV viral replication in monocyte-derived macrophages. AIDS Res Hum Retroviruses 2015; 31:237-41. [PMID: 25303025 PMCID: PMC4313412 DOI: 10.1089/aid.2014.0015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We document the anti-HIV activity of nitazoxanide (NTZ), the first member of the thiazolide class of antiinfective drugs, originally effective against enteritis caused by Cryptosporidium parvum and Giardia lamblia. NTZ has been administered extensively worldwide, with no severe toxicities associated with its use. Here, we show for the first time that NTZ decreases HIV-1 replication in monocyte-derived macrophages (MDM) if present before or during HIV-1 infection. This NTZ effect is associated with downregulation of HIV-1 receptors CD4 and CCR5, and increasing gene expression of host cell anti-HIV resistance factors APOBEC3A/3G and tetherin. As NTZ is already in clinical use for other conditions, this newly described anti-HIV activity in MDM may facilitate innovative intensification strategies against HIV-1 when combined with current antiretroviral drug regimens.
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Affiliation(s)
- Bethsebah Gekonge
- HIV Immunopathogenesis Laboratory, Wistar Institute, Philadelphia, Pennsylvania
| | | | - Luis J. Montaner
- HIV Immunopathogenesis Laboratory, Wistar Institute, Philadelphia, Pennsylvania
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8
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Hardy I, Brenner B, Quashie P, Thomas R, Petropoulos C, Huang W, Moisi D, Wainberg MA, Roger M. Evolution of a novel pathway leading to dolutegravir resistance in a patient harbouring N155H and multiclass drug resistance. J Antimicrob Chemother 2014; 70:405-11. [PMID: 25281399 DOI: 10.1093/jac/dku387] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Dolutegravir has been recently approved for treatment-naive and -experienced HIV-infected subjects, including integrase inhibitor (INI)-experienced patients. Dolutegravir is a second-generation INI that can overcome many prior raltegravir and elvitegravir failures. Here, we report the evolution of resistance to dolutegravir in a highly treatment-experienced patient harbouring the major N155H mutation consequent to raltegravir treatment failure. METHODS Genotypic and phenotypic analyses were done on longitudinal samples to determine viral resistance to INIs. Integrase amino acid sequence interactions with raltegravir and dolutegravir were assessed by molecular modelling and docking simulations. RESULTS Five mutations (A49P, L68FL, T97A, E138K and L234V) were implicated in emergent dolutegravir resistance, with a concomitant severe compromise in viral replicative capacity. Molecular modelling and docking simulations revealed that dolutegravir binding to integrase was affected by these acquired dolutegravir mutations. CONCLUSIONS Our findings identify a novel mutational pathway involving integrase mutations A49P and L234V, leading to dolutegravir resistance in a patient with the N155H raltegravir mutation.
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Affiliation(s)
- Isabelle Hardy
- Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Bluma Brenner
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Peter Quashie
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Réjean Thomas
- Clinique Médicale L'Actuel, Montréal, Québec, Canada
| | | | - Wei Huang
- Monogram Biosciences, South San Francisco, CA, USA
| | - Daniela Moisi
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Mark A Wainberg
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Michel Roger
- Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
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9
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Lackey L, Law EK, Brown WL, Harris RS. Subcellular localization of the APOBEC3 proteins during mitosis and implications for genomic DNA deamination. Cell Cycle 2013; 12:762-72. [PMID: 23388464 DOI: 10.4161/cc.23713] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Humans have seven APOBEC3 DNA cytosine deaminases. The activity of these enzymes allows them to restrict a variety of retroviruses and retrotransposons, but may also cause pro-mutagenic genomic uracil lesions. During interphase the APOBEC3 proteins have different subcellular localizations: cell-wide, cytoplasmic or nuclear. This implies that only a subset of APOBEC3s have contact with nuclear DNA. However, during mitosis, the nuclear envelope breaks down and cytoplasmic proteins may enter what was formerly a privileged zone. To address the hypothesis that all APOBEC3 proteins have access to genomic DNA, we analyzed the localization of the APOBEC3 proteins during mitosis. We show that APOBEC3A, APOBEC3C and APOBEC3H are excluded from condensed chromosomes, but become cell-wide during telophase. However, APOBEC3B, APOBEC3D, APOBEC3F and APOBEC3G are excluded from chromatin throughout mitosis. After mitosis, APOBEC3B becomes nuclear, and APOBEC3D, APOBEC3F and APOBEC3G become cytoplasmic. Both structural motifs as well as size may be factors in regulating chromatin exclusion. Deaminase activity was not dependent on cell cycle phase. We also analyzed APOBEC3-induced cell cycle perturbations as a measure of each enzyme's capacity to inflict genomic DNA damage. AID, APOBEC3A and APOBEC3B altered the cell cycle profile, and, unexpectedly, APOBEC3D also caused changes. We conclude that several APOBEC3 family members have access to the nuclear compartment and can impede the cell cycle, most likely through DNA deamination and the ensuing DNA damage response. Such genomic damage may contribute to carcinogenesis, as demonstrated by AID in B cell cancers and, recently, APOBEC3B in breast cancers.
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Affiliation(s)
- Lela Lackey
- Department of Biochemistry, Molecular Biology and Biophysics, Institute of Molecular Virology, University of Minnesota, Minneapolis, MN, USA
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Cruz NVG, Amorim R, Oliveira FE, Speranza FAC, Costa LJ. Mutations in the nef and vif genes associated with progression to AIDS in elite controller and slow-progressor patients. J Med Virol 2013; 85:563-74. [PMID: 23417613 DOI: 10.1002/jmv.23512] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2012] [Indexed: 11/07/2022]
Abstract
Progression towards AIDS can vary from 5 to 10 years from the establishment of the primary infection by HIV-1 to more than 10 years in the complete absence of antiretroviral therapy. Several factors can contribute to the outcome of HIV infection, including host genetic and viral replicating characteristics. Historically, nef-deleted viral genomes have been associated with disease progression. Therefore, the lentiviral Nef protein is regarded as a progression factor. The objective of this work was to characterize the nef gene from a group of treatment naive patients infected with HIV-1 for more than 10 years. These patients were classified as long-term non-progressors, elite controller, and slow-progressors according to clinical and laboratorial data. A premature stop codon within the nef gene leading to the expression of a truncated peptide was observed on samples from the elite controller patient. For the slow-progressor patients, several degrees of deletions at the C-terminal of Nef were observed predicting a loss of function of this protein. The vif gene was characterized for these patients and a rare mutation that predicts a miss localization of the Vif protein to the nucleus of infected cells that could prevent its function as an APOBEC neutralization factor was also observed. These data indicate the importance of the HIV accessory proteins as factors that contribute to the outcome of AIDS.
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Affiliation(s)
- Nadia V G Cruz
- Department of Virology, Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Chen Z, Zhang L, Ying S. SAMHD1: a novel antiviral factor in intrinsic immunity. Future Microbiol 2012; 7:1117-26. [DOI: 10.2217/fmb.12.81] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Some intracellular/membranous factors exert intrinsic immunity against viral pathogens. Most recently, SAMHD1 has been shown to be one of these factors. SAMHD1 is a nucleus-localized protein, and mutations in the gene are associated with Aicardi–Goutières syndrome. As a triphosphohydrolase, it depletes the intracellular pool of dNTPs in myeloid cells, such as macrophages and dendritic cells, to a low level that establishes a precursor-deficient environment for the synthesis of lentiviral cDNA, thereby restricting viral replication in these host cells. However, some viruses evolve Vpx to recruit SAMHD1 onto the CRL4DCAF1 E3 ubiquitin ligase in the cytoplasm for proteasome-dependent degradation, by which these viruses relieve SAMHD1-mediated restriction of primate lentivirus infection. In this review, we describe the latest knowledge of SAMHD1 biology.
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Affiliation(s)
- Zhangming Chen
- Department of Immunology, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Linjie Zhang
- Department of Immunology, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Songcheng Ying
- Department of Immunology, Anhui Medical University, Hefei, Anhui Province 230032, China
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12
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HIV-1 Reverse Transcriptase Still Remains a New Drug Target: Structure, Function, Classical Inhibitors, and New Inhibitors with Innovative Mechanisms of Actions. Mol Biol Int 2012; 2012:586401. [PMID: 22778958 PMCID: PMC3388302 DOI: 10.1155/2012/586401] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/03/2012] [Indexed: 12/21/2022] Open
Abstract
During the retrotranscription process, characteristic of all retroviruses, the viral ssRNA genome is converted into integration-competent dsDNA. This process is accomplished by the virus-coded reverse transcriptase (RT) protein, which is a primary target in the current treatments for HIV-1 infection. In particular, in the approved therapeutic regimens two classes of drugs target RT, namely, nucleoside RT inhibitors (NRTIs) and nonnucleoside RT inhibitors (NNRTIs). Both classes inhibit the RT-associated polymerase activity: the NRTIs compete with the natural dNTP substrate and act as chain terminators, while the NNRTIs bind to an allosteric pocket and inhibit polymerization noncompetitively. In addition to these two classes, other RT inhibitors (RTIs) that target RT by distinct mechanisms have been identified and are currently under development. These include translocation-defective RTIs, delayed chain terminators RTIs, lethal mutagenesis RTIs, dinucleotide tetraphosphates, nucleotide-competing RTIs, pyrophosphate analogs, RT-associated RNase H function inhibitors, and dual activities inhibitors. This paper describes the HIV-1 RT function and molecular structure, illustrates the currently approved RTIs, and focuses on the mechanisms of action of the newer classes of RTIs.
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Boga JA, Coto-Montes A, Rosales-Corral SA, Tan DX, Reiter RJ. Beneficial actions of melatonin in the management of viral infections: a new use for this "molecular handyman"? Rev Med Virol 2012; 22:323-38. [PMID: 22511571 PMCID: PMC7169144 DOI: 10.1002/rmv.1714] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/08/2012] [Accepted: 02/09/2012] [Indexed: 12/24/2022]
Abstract
Melatonin (N‐acetyl‐5‐methoxytryptamine) is a multifunctional signaling molecule that has a variety of important functions. Numerous clinical trials have examined the therapeutic usefulness of melatonin in different fields of medicine. Clinical trials have shown that melatonin is efficient in preventing cell damage under acute (sepsis, asphyxia in newborns) and chronic states (metabolic and neurodegenerative diseases, cancer, inflammation, aging). The beneficial effects of melatonin can be explained by its properties as a potent antioxidant and antioxidant enzyme inducer, a regulator of apoptosis and a stimulator of immune functions. These effects support the use of melatonin in viral infections, which are often associated with inflammatory injury and increases in oxidative stress. In fact, melatonin has been used recently to treat several viral infections, which are summarized in this review. The role of melatonin in infections is also discussed herein. Copyright © 2012 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jose Antonio Boga
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, Texas, USA
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14
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Hsu CYM, Uludağ H. Nucleic-acid based gene therapeutics: delivery challenges and modular design of nonviral gene carriers and expression cassettes to overcome intracellular barriers for sustained targeted expression. J Drug Target 2012; 20:301-28. [PMID: 22303844 DOI: 10.3109/1061186x.2012.655247] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The delivery of nucleic acid molecules into cells to alter physiological functions at the genetic level is a powerful approach to treat a wide range of inherited and acquired disorders. Biocompatible materials such as cationic polymers, lipids, and peptides are being explored as safer alternatives to viral gene carriers. However, the comparatively low efficiency of nonviral carriers currently hampers their translation into clinical settings. Controlling the size and stability of carrier/nucleic acid complexes is one of the primary hurdles as the physicochemical properties of the complexes can define the uptake pathways, which dictate intracellular routing, endosomal processing, and nucleocytoplasmic transport. In addition to nuclear import, subnuclear trafficking, posttranscriptional events, and immune responses can further limit transfection efficiency. Chemical moieties, reactive linkers or signal peptide have been conjugated to carriers to prevent aggregation, induce membrane destabilization and localize to subcellular compartments. Genetic elements can be inserted into the expression cassette to facilitate nuclear targeting, delimit expression to targeted tissue, and modulate transgene expression. The modular option afforded by both gene carriers and expression cassettes provides a two-tier multicomponent delivery system that can be optimized for targeted gene delivery in a variety of settings.
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Affiliation(s)
- Charlie Yu Ming Hsu
- Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Cananda
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15
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Roy-Engel AM. LINEs, SINEs and other retroelements: do birds of a feather flock together? Front Biosci (Landmark Ed) 2012; 17:1345-61. [PMID: 22201808 DOI: 10.2741/3991] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mobile elements account for almost half of the mass of the human genome. Only the retroelements from the non-LTR (long terminal repeat) retrotransposon family, which include the LINE-1 (L1) and its non-autonomous partners, are currently active and contributing to new insertions. Although these elements seem to share the same basic amplification mechanism, the activity and success of the different types of retroelements varies. For example, Alu-induced mutagenesis is responsible for the majority of the documented instances of human disease induced by insertion of retroelements. Using copy number in mammals as an indicator, some SINEs have been vastly more successful than other retroelements, such as the retropseudogenes and even L1, likely due to differences in post-insertion selection and ability to overcome cellular controls. SINE and LINE integration can be differentially influenced by cellular factors, indicating some differences between in their amplification mechanisms. We focus on the known aspects of this group of retroelements and highlight their similarities and differences that may significantly influence their biological impact.
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Affiliation(s)
- Astrid M Roy-Engel
- Tulane University, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane Cancer Center, SL-66 1430 Tulane Ave., New Orleans, LA 70112.
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16
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Fehrholz M, Kendl S, Prifert C, Weissbrich B, Lemon K, Rennick L, Duprex PW, Rima BK, Koning FA, Holmes RK, Malim MH, Schneider-Schaulies J. The innate antiviral factor APOBEC3G targets replication of measles, mumps and respiratory syncytial viruses. J Gen Virol 2011; 93:565-576. [PMID: 22170635 DOI: 10.1099/vir.0.038919-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The cytidine deaminase APOBEC3G (apolipoprotein B mRNA-editing enzyme-catalytic polypeptide 3G; A3G) exerts antiviral activity against retroviruses, hepatitis B virus, adeno-associated virus and transposable elements. We assessed whether the negative-strand RNA viruses measles, mumps and respiratory syncytial might be affected by A3G, and found that their infectivity was reduced by 1-2 logs (90-99 %) in A3G overexpressing Vero cells, and in T-cell lines expressing A3G at physiological levels. Viral RNA was co-precipitated with HA-tagged A3G and could be amplified by RT-PCR. Interestingly, A3G reduced viral transcription and protein expression in infected cells by 50-70 %, and caused an increased mutation frequency of 0.95 mutations per 1000 nt in comparison to the background level of 0.22/1000. The observed mutations were not specific for A3G [cytidine to uridine (C→U) or guanine to adenine (G→A) hypermutations], nor specific for ADAR (adenosine deaminase acting on RNA, A→G and U→C transitions, with preference for next neighbour-nucleotides U = A>C>G). In addition, A3G mutants with inactivated catalytic deaminase (H257R and E259Q) were inhibitory, indicating that the deaminase activity is not required for the observed antiviral activity. In combination, impaired transcription and increased mutation frequencies are sufficient to cause the observed reduction in viral infectivity and eliminate virus replication within a few passages in A3G-expressing cells.
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Affiliation(s)
- Markus Fehrholz
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Sabine Kendl
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Christiane Prifert
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Benedikt Weissbrich
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Ken Lemon
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, UK
| | - Linda Rennick
- Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston University, Boston, USA
| | - Paul W Duprex
- Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston University, Boston, USA
| | - Bert K Rima
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, UK
| | | | | | - Michael H Malim
- Department of Infectious Diseases, King's College, London, UK
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Dietrich I, Hosie MJ, Willett BJ. The role of BST2/tetherin in feline retrovirus infection. Vet Immunol Immunopathol 2011; 143:255-64. [PMID: 21715020 DOI: 10.1016/j.vetimm.2011.06.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Pathogenic retroviral infections of mammals have induced the evolution of cellular anti-viral restriction factors and have shaped their biological activities. This intrinsic immunity plays an important role in controlling viral replication and imposes a barrier to viral cross-species transmission. Well-studied examples of such host restriction factors are TRIM5α, an E3 ubiquitin ligase that binds incoming retroviral capsids in the cytoplasm via its C-terminal PRY/SPRY (B30.2) domain and targets them for proteasomal degradation, and APOBEC3 proteins, cytidine deaminases that induce hypermutation and impair viral reverse transcription. Tetherin (BST-2, CD317) is an interferon-inducible transmembrane protein that potently inhibits the release of nascent retrovirus particles in single-cycle replication assays. However, whether the primary biological activity of tetherin in vivo is that of a restriction factor remains uncertain as recent studies on human tetherin suggest that it is unable to prevent spreading infection of human immunodeficiency virus type 1 (HIV-1). The feline tetherin homologue resembles human tetherin in amino acid sequence, protein topology and anti-viral activity. Transiently expressed feline tetherin displays potent inhibition of feline immunodeficiency virus (FIV) and HIV-1 particle release. However, stable ectopic expression of feline tetherin in a range of feline cell lines has no inhibitory effect on the growth of either primary or cell culture-adapted strains of FIV. By comparing and contrasting the activities of the felid and primate tetherins against their respective immunodeficiency-causing lentiviruses we may gain insight into the contribution of tetherins to the control of lentiviral replication and the evolution of lentiviral virulence.
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Affiliation(s)
- Isabelle Dietrich
- Retrovirus Research Laboratory, MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G611QH, United Kingdom.
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18
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Mattick JS. The central role of RNA in human development and cognition. FEBS Lett 2011; 585:1600-16. [DOI: 10.1016/j.febslet.2011.05.001] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 05/03/2011] [Indexed: 12/22/2022]
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Lee J, Choi JY, Lee HJ, Kim KC, Choi BS, Oh YK, Kim YB. Repression of porcine endogenous retrovirus infection by human APOBEC3 proteins. Biochem Biophys Res Commun 2011; 407:266-70. [PMID: 21396348 DOI: 10.1016/j.bbrc.2011.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 03/04/2011] [Indexed: 01/07/2023]
Abstract
It has been shown that porcine endogenous retrovirus (PERV) can infect human cells, indicating that PERV transmission poses a serious concern in pig-to-human xenotransplantation. A number of recent studies have reported on retrovirus interference by antiviral proteins. The most potent antiviral proteins are members of the APOBEC family of cytidine deaminases, which are involved in defense against retroviral attack. These proteins are present in the cytoplasm of mammalian cells and inhibit retroviral replication. To evaluate the inhibition of PERV transmission by human APOBEC3 proteins, we co-transfected 293T cells with a PERV molecular clone and human APOBEC3F or APOBEC3G expression vectors, and monitored PERV replication competency using a quantitative analysis of PERV pol genes. The replication of PERVs in cells co-expressing human APOBEC3s was reduced by 60-90% compared with PERV-only control. These results suggest that human APOBEC3G and APOBEC3F might serve a potential barrier function against PERV transmission in xenotransplantation.
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Affiliation(s)
- Jungeun Lee
- Department of Animal Biotechnology, College of Animal Bioscience and Technology, Konkuk University, Seoul 143-701, South Korea.
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20
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Mattick JS. RNA as the substrate for epigenome-environment interactions: RNA guidance of epigenetic processes and the expansion of RNA editing in animals underpins development, phenotypic plasticity, learning, and cognition. Bioessays 2011; 32:548-52. [PMID: 20544741 DOI: 10.1002/bies.201000028] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- John S Mattick
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia.
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21
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Okeoma CM, Huegel AL, Lingappa J, Feldman MD, Ross SR. APOBEC3 proteins expressed in mammary epithelial cells are packaged into retroviruses and can restrict transmission of milk-borne virions. Cell Host Microbe 2010; 8:534-43. [PMID: 21147467 PMCID: PMC3023938 DOI: 10.1016/j.chom.2010.11.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 10/05/2010] [Accepted: 11/02/2010] [Indexed: 11/19/2022]
Abstract
Viruses, including retroviruses like human immunodeficiency virus (HIV) and mouse mammary tumor virus (MMTV), are transmitted from mother to infants through milk. Lymphoid cells and antibodies are thought to provide mammary gland and milk-borne immunity. In contrast, little is known about the role of mammary epithelial cells (MECs). The APOBEC3 family of retroviral restriction factors is highly expressed in macrophages and lymphoid and dendritic cells. We now show that APOBEC3 proteins are also expressed in mouse and human MECs. Lymphoid cell-expressed APOBEC3 restricts in vivo spread of MMTV to lymphoid and mammary tissue. In contrast, mammary gland-expressed APOBEC3 is packaged into MMTV virions and decreases the infectivity of milk-borne viruses. Moreover, APOBEC3G and other APOBEC3 genes are expressed in human mammary cells and have the potential to restrict viruses produced in this cell type. These data point to a role for APOBEC3 proteins in limiting infectivity of milk-transmitted viruses.
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MESH Headings
- APOBEC Deaminases
- Animals
- Cells, Cultured
- Cytidine Deaminase/biosynthesis
- Cytidine Deaminase/physiology
- Cytosine Deaminase/biosynthesis
- Cytosine Deaminase/physiology
- Epithelial Cells/metabolism
- Epithelial Cells/virology
- Female
- HIV-1/pathogenicity
- Humans
- Infectious Disease Transmission, Vertical
- Lymphocytes/metabolism
- Mammary Glands, Animal/metabolism
- Mammary Glands, Animal/virology
- Mammary Glands, Human/metabolism
- Mammary Glands, Human/virology
- Mammary Tumor Virus, Mouse/pathogenicity
- Mammary Tumor Virus, Mouse/physiology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Milk/virology
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/virology
- Retroviridae Infections/metabolism
- Retroviridae Infections/transmission
- Retroviridae Infections/virology
- Tumor Virus Infections/metabolism
- Tumor Virus Infections/transmission
- Tumor Virus Infections/virology
- Virion/physiology
- Virus Assembly
- vif Gene Products, Human Immunodeficiency Virus/physiology
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Affiliation(s)
- Chioma M. Okeoma
- Department of Microbiology and Abramson Cancer Center, University of Pennsylvania School of Medicine
| | - Alyssa L. Huegel
- Department of Microbiology and Abramson Cancer Center, University of Pennsylvania School of Medicine
| | | | - Michael D. Feldman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine
| | - Susan R. Ross
- Department of Microbiology and Abramson Cancer Center, University of Pennsylvania School of Medicine
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22
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Levin JG, Mitra M, Mascarenhas A, Musier-Forsyth K. Role of HIV-1 nucleocapsid protein in HIV-1 reverse transcription. RNA Biol 2010; 7:754-74. [PMID: 21160280 DOI: 10.4161/rna.7.6.14115] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The HIV-1 nucleocapsid protein (NC) is a nucleic acid chaperone, which remodels nucleic acid structures so that the most thermodynamically stable conformations are formed. This activity is essential for virus replication and has a critical role in mediating highly specific and efficient reverse transcription. NC's function in this process depends upon three properties: (1) ability to aggregate nucleic acids; (2) moderate duplex destabilization activity; and (3) rapid on-off binding kinetics. Here, we present a detailed molecular analysis of the individual events that occur during viral DNA synthesis and show how NC's properties are important for almost every step in the pathway. Finally, we also review biological aspects of reverse transcription during infection and the interplay between NC, reverse transcriptase, and human APOBEC3G, an HIV-1 restriction factor that inhibits reverse transcription and virus replication in the absence of the HIV-1 Vif protein.
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Affiliation(s)
- Judith G Levin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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23
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Towards Inhibition of Vif-APOBEC3G Interaction: Which Protein to Target? Adv Virol 2010; 2010:649315. [PMID: 22347227 PMCID: PMC3275931 DOI: 10.1155/2010/649315] [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: 05/02/2010] [Revised: 07/31/2010] [Accepted: 08/14/2010] [Indexed: 11/17/2022] Open
Abstract
APOBEC proteins appeared in the cellular battle against HIV-1 as part of intrinsic cellular immunity. The antiretroviral activity of some of these proteins is overtaken by the action of HIV-1 Viral Infectivity Factor (Vif) protein. Since the discovery of APOBEC3G (A3G) as an antiviral factor, many advances have been made to understand its mechanism of action in the cell and how Vif acts in order to counteract its activity. The mainstream concept is that Vif overcomes the innate antiviral activity of A3G by direct protein binding and promoting its degradation via the cellular ubiquitin/proteasomal pathway. Vif may also inhibit A3G through mechanisms independent of proteasomal degradation. Binding of Vif to A3G is essential for its degradation since disruption of this interaction is predicted to stimulate intracellular antiviral immunity. In this paper we will discuss the different binding partners between both proteins as one of the major challenges for the development of new antiviral drugs.
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24
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The glycosylated Gag protein of a murine leukemia virus inhibits the antiretroviral function of APOBEC3. J Virol 2010; 84:10933-6. [PMID: 20702647 DOI: 10.1128/jvi.01023-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
APOBEC proteins have evolved as innate defenses against retroviral infections. Human immunodeficiency virus (HIV) encodes the Vif protein to evade human APOBEC3G; however, mouse retroviruses do not encode a Vif homologue, and it has not been understood how they evade mouse APOBEC3. We report here a murine leukemia virus (MuLV) that utilizes its glycosylated Gag protein (gGag) to evade APOBEC3. gGag is critical for infection of in vitro cell lines in the presence of APOBEC3. Furthermore, a gGag-deficient virus restricted for replication in wild-type mice replicates efficiently in APOBEC3 knockout mice, implying a novel role of gGag in circumventing the action of APOBEC3 in vivo.
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25
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Herschhorn A, Hizi A. Retroviral reverse transcriptases. Cell Mol Life Sci 2010; 67:2717-47. [PMID: 20358252 PMCID: PMC11115783 DOI: 10.1007/s00018-010-0346-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Revised: 02/22/2010] [Accepted: 03/08/2010] [Indexed: 12/22/2022]
Abstract
Reverse transcription is a critical step in the life cycle of all retroviruses and related retrotransposons. This complex process is performed exclusively by the retroviral reverse transcriptase (RT) enzyme that converts the viral single-stranded RNA into integration-competent double-stranded DNA. Although all RTs have similar catalytic activities, they significantly differ in several aspects of their catalytic properties, their structures and subunit composition. The RT of human immunodeficiency virus type-1 (HIV-1), the virus causing acquired immunodeficiency syndrome (AIDS), is a prime target for the development of antiretroviral drug therapy of HIV-1/AIDS carriers. Therefore, despite the fundamental contributions of other RTs to the understanding of RTs and retrovirology, most recent RT studies are related to HIV-1 RT. In this review we summarize the basic properties of different RTs. These include, among other topics, their structures, enzymatic activities, interactions with both viral and host proteins, RT inhibition and resistance to antiretroviral drugs.
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Affiliation(s)
- Alon Herschhorn
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Amnon Hizi
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
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26
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27
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APOBEC3G directly binds Hepatitis B virus core protein in cell and cell free systems. Virus Res 2010; 151:213-9. [PMID: 20510315 PMCID: PMC7173111 DOI: 10.1016/j.virusres.2010.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 05/13/2010] [Accepted: 05/18/2010] [Indexed: 02/08/2023]
Abstract
APOBEC3G (A3G) is an intrinsic antiretroviral factor which can inhibit Hepatitis B virus (HBV) replication. This antiviral activity mainly depends on A3G incorporation into viral particles. However, the mechanisms of A3G packaging into HBV particles have not been well characterized. In this paper, we demonstrated that A3G interacted with the HBV core protein (HBc) directly in co-transfected HepG2 cells using the fluorescence resonance energy transfer (FRET) approach. In addition, we further found that this interaction did not require other factors in vitro using surface plasmon resonance (SPR) technology on BIAcore 3000. While cellular RNA or viral RNA was added to A3G protein solution before flow through the BIAcore chip, the interaction was not affected. In conclusion, these results suggest the possibility that A3G is incorporated into HBV viral particles via direct binding with HBc protein.
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28
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Qureshi IA, Mattick JS, Mehler MF. Long non-coding RNAs in nervous system function and disease. Brain Res 2010; 1338:20-35. [PMID: 20380817 DOI: 10.1016/j.brainres.2010.03.110] [Citation(s) in RCA: 356] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 03/26/2010] [Accepted: 03/30/2010] [Indexed: 12/14/2022]
Abstract
Central nervous system (CNS) development, homeostasis, stress responses, and plasticity are all mediated by epigenetic mechanisms that modulate gene expression and promote selective deployment of functional gene networks in response to complex profiles of interoceptive and environmental signals. Thus, not surprisingly, disruptions of these epigenetic processes are implicated in the pathogenesis of a spectrum of neurological and psychiatric diseases. Epigenetic mechanisms involve chromatin remodeling by relatively generic complexes that catalyze DNA methylation and various types of histone modifications. There is increasing evidence that these complexes are directed to their sites of action by long non-protein-coding RNAs (lncRNAs), of which there are tens if not hundreds of thousands specified in the genome. LncRNAs are transcribed in complex intergenic, overlapping and antisense patterns relative to adjacent protein-coding genes, suggesting that many lncRNAs regulate the expression of these genes. LncRNAs also participate in a wide array of subcellular processes, including the formation and function of cellular organelles. Most lncRNAs are transcribed in a developmentally regulated and cell type specific manner, particularly in the CNS, wherein over half of all lncRNAs are expressed. While the numerous biological functions of lncRNAs are yet to be characterized fully, a number of recent studies suggest that lnRNAs are important for mediating cell identity. This function seems to be especially important for generating the enormous array of regional neuronal and glial cell subtypes that are present in the CNS. Further studies have also begun to elucidate additional roles played by lncRNAs in CNS processes, including homeostasis, stress responses and plasticity. Herein, we review emerging evidence that highlights the expression and function of lncRNAs in the CNS and suggests that lncRNA deregulation is an important factor in various CNS pathologies including neurodevelopmental, neurodegenerative and neuroimmunological disorders, primary brain tumors, and psychiatric diseases.
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Affiliation(s)
- Irfan A Qureshi
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461, USA
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29
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Menéndez-Arias L. Mutation rates and intrinsic fidelity of retroviral reverse transcriptases. Viruses 2009; 1:1137-65. [PMID: 21994586 PMCID: PMC3185545 DOI: 10.3390/v1031137] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 12/03/2009] [Accepted: 12/03/2009] [Indexed: 11/27/2022] Open
Abstract
Retroviruses are RNA viruses that replicate through a DNA intermediate, in a process catalyzed by the viral reverse transcriptase (RT). Although cellular polymerases and host factors contribute to retroviral mutagenesis, the RT errors play a major role in retroviral mutation. RT mutations that affect the accuracy of the viral polymerase have been identified by in vitro analysis of the fidelity of DNA synthesis, by using enzymological (gel-based) and genetic assays (e.g., M13mp2 lacZ forward mutation assays). For several amino acid substitutions, these observations have been confirmed in cell culture using viral vectors. This review provides an update on studies leading to the identification of the major components of the fidelity center in retroviral RTs.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" [Consejo Superior de Investigaciones Científicas (CSIC) & Universidad Autónoma de Madrid], Campus de Cantoblanco, 28049 Madrid, Spain; E-Mail: ; Tel.: +34 91 196 4494
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30
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Shen W, Gao L, Balakrishnan M, Bambara RA. A recombination hot spot in HIV-1 contains guanosine runs that can form a G-quartet structure and promote strand transfer in vitro. J Biol Chem 2009; 284:33883-93. [PMID: 19822521 DOI: 10.1074/jbc.m109.055368] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The co-packaged RNA genomes of human immunodeficiency virus-1 recombine at a high rate. Recombination can mix mutations to generate viruses that escape immune response. A cell-culture-based system was designed previously to map recombination events in a 459-bp region spanning the primer binding site through a portion of the gag protein coding region. Strikingly, a strong preferential site for recombination in vivo was identified within a 112-nucleotide-long region near the beginning of gag. Strand transfer assays in vitro revealed that three pause bands in the gag hot spot each corresponded to a run of guanosine (G) residues. Pausing of reverse transcriptase is known to promote recombination by strand transfer both in vivo and in vitro. To assess the significance of the G runs, we altered them by base substitutions. Disruption of the G runs eliminated both the associated pausing and strand transfer. Some G-rich sequences can develop G-quartet structures, which were first proposed to form in telomeric DNA. G-quartet structure formation is highly dependent on the presence of specific cations. Incubation in cations discouraging G-quartets altered gel mobility of the gag template consistent with breakdown of G-quartet structure. The same cations faded G-run pauses but did not affect pauses caused by hairpins, indicating that quartet structure causes pausing. Moreover, gel analysis with cations favoring G-quartet structure indicated no structure in mutated templates. Overall, results point to reverse transcriptase pausing at G runs that can form quartets as a unique feature of the gag recombination hot spot.
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Affiliation(s)
- Wen Shen
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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31
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Narvaiza I, Linfesty DC, Greener BN, Hakata Y, Pintel DJ, Logue E, Landau NR, Weitzman MD. Deaminase-independent inhibition of parvoviruses by the APOBEC3A cytidine deaminase. PLoS Pathog 2009; 5:e1000439. [PMID: 19461882 PMCID: PMC2678267 DOI: 10.1371/journal.ppat.1000439] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 04/22/2009] [Indexed: 12/17/2022] Open
Abstract
The APOBEC3 proteins form a multigene family of cytidine deaminases with inhibitory activity against viruses and retrotransposons. In contrast to APOBEC3G (A3G), APOBEC3A (A3A) has no effect on lentiviruses but dramatically inhibits replication of the parvovirus adeno-associated virus (AAV). To study the contribution of deaminase activity to the antiviral activity of A3A, we performed a comprehensive mutational analysis of A3A. By mutation of non-conserved residues, we found that regions outside of the catalytic active site contribute to both deaminase and antiviral activities. Using A3A point mutants and A3A/A3G chimeras, we show that deaminase activity is not required for inhibition of recombinant AAV production. We also found that deaminase-deficient A3A mutants block replication of both wild-type AAV and the autonomous parvovirus minute virus of mice (MVM). In addition, we identify specific residues of A3A that confer activity against AAV when substituted into A3G. In summary, our results demonstrate that deaminase activity is not necessary for the antiviral activity of A3A against parvoviruses. The APOBEC3 proteins constitute a family of seven cytidine deaminases. Cytidine deaminases are editing enzymes able to remove the amine group from cytidine in single-strand DNA (ssDNA) and RNA, converting it to uracil. APOBEC3 proteins have potent antiviral activity against retroviruses, retrotransposons, and DNA viruses. APOBEC3 generated high interest because of the ability of APOBEC3G (A3G) to inhibit HIV. APOBEC3A (A3A) is a member of the family that inhibits the human parvovirus adeno-associated virus (AAV) and the retrotransposon LINE-1. Parvoviruses are simple ssDNA viruses that do not require a retrotranscription step for their replication. In contrast to A3G, which is predominantly cytoplasmic, A3A is located in both the nucleus and cytoplasm. In addition, A3A consists of a single cytidine deaminase catalytic domain, whereas A3G has two. The dependence of the antiviral function on deaminase activity is controversial. In this study, we identify numerous A3A residues required for deaminase and antiviral activities. We show that A3A not only inhibits AAV but also the minute virus of mice (MVM). Importantly, we demonstrate that A3A does not require its deaminase activity to block the replication of both parvoviruses. Thus, exploiting the simplicity of parvoviruses together with the single-domain cytidine deaminase A3A, we are able to demonstrate that cytidine deaminase activity is not required for APOBEC3 mediated viral inhibition.
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Affiliation(s)
- Iñigo Narvaiza
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Daniel C. Linfesty
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Benjamin N. Greener
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Yoshiyuki Hakata
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - David J. Pintel
- Department of Molecular Microbiology and Immunology, University of Missouri–Columbia, School of Medicine, Life Sciences Center, Columbia, Missouri, United States of America
| | - Eric Logue
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Nathaniel R. Landau
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Matthew D. Weitzman
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- * E-mail:
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32
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Affiliation(s)
- Susan R Ross
- Department of Microbiology and Abramson Family Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
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Abstract
Interferons represent a family of cytokines, which is of central importance in the innate immune response to virus infections. All interferons act as secreted ligands of specific cell surface receptors, eliciting the transcription of hundreds of interferon-stimulated genes whose protein products have antiviral activity, as well as antimicrobial, antiproliferative/antitumor, and immunomodulatory effects. Expression of type I and III interferons is induced in virtually all cell types upon recognition of viral molecular patterns, especially nucleic acids, by cytoplasmic and endosomal receptors, whereas type II interferon is induced by cytokines such as IL-12, and its expression is restricted to immune cells such as T cells and NK cells. The effectiveness of the interferon system in counteracting viral infections is reflected by the multitude of inhibitors of interferon induction or interferon action that are encoded by many viruses, preventing their eradication and resulting in the continued coexistence of viruses and vertebrates. The unique biological functions of interferons have led to their therapeutic use in the treatment of diseases such as hepatitis, multiple sclerosis, and certain leukemias.
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Affiliation(s)
- Volker Fensterl
- Department of Molecular Genetics, The Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
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Jochmans D. Novel HIV-1 reverse transcriptase inhibitors. Virus Res 2008; 134:171-85. [PMID: 18308412 DOI: 10.1016/j.virusres.2008.01.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 01/07/2008] [Accepted: 01/08/2008] [Indexed: 10/22/2022]
Abstract
HIV-1 reverse transcriptase (RT) was the first viral enzyme to be targeted by anti-HIV drugs. Despite 20 years of experience with RT inhibitors, new ways to inhibit this target and address viral resistance continue to emerge. In both licensed RT inhibitor classes, nucleosides (NRTIs) and non-nucleosides (NNRTIs), compounds with better resistance, pharmacokinetic and toxicity profiles are being developed. Second-generation NNRTIs active against HIV-1 strains resistant to current NNRTIs are being clinically evaluated. Beyond the classical NRTIs, nucleoside analogs that are no longer obligate chain terminators but nevertheless impede reverse transcription or even lead to viral ablation after several replication cycles, are being studied. RT inhibitor research has also yielded additional mechanisms to block RT. Driven by new insights the RNase H field remains in evolution. In addition, the binding of both substrates (deoxynucleotide and primer/template) to RT is now subject to competition by novel inhibitors. Further development of aptamers bears promise for gene therapy but perhaps more importantly, reveals additional new platforms for the development of small-molecule RT inhibitors. This promising research provides much optimism that RT inhibitors will continue to evolve with subsequent clinical benefit.
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Affiliation(s)
- Dirk Jochmans
- Tibotec BVBA, Gen De Wittelaan L 11B 3, 2800 Mechelen, Belgium.
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Strand transfer events during HIV-1 reverse transcription. Virus Res 2008; 134:19-38. [PMID: 18279992 DOI: 10.1016/j.virusres.2007.12.017] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 12/19/2007] [Accepted: 12/20/2007] [Indexed: 11/20/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) and other retroviruses replicate through reverse transcription, a process in which the single stranded RNA of the viral genome is converted to a double stranded DNA. The virally encoded reverse transcriptase (RT) mediates reverse transcription through DNA polymerase and RNase H activities. Conversion of the plus strand RNA to plus/minus strand RNA/DNA hybrid involves a transfer of the growing DNA strand from one site on the genomic RNA to another. This is called minus strong-stop DNA transfer. Later synthesis of the second or plus DNA strand involves a second strand transfer, involving a similar mechanism as the minus strand transfer. A basic feature of the strand transfer mechanism is the use of the RT RNase H to remove segments of the RNA template strand from the growing DNA strand, freeing a single stranded region to anneal to the second site. Viral nucleocapsid protein (NC) functions to promote transfer by facilitating this strand exchange process. Two copies of the RNA genomes, sometimes non-identical, are co-packaged in the genomes of retroviruses. The properties of the reverse transcriptase allow a transfer of the growing DNA strand between these genomes to occur occasionally at any point during reverse transcription, producing recombinant viral progeny. Recombination promotes structural diversity of the virus that helps it to survive host immunity and drug therapy. Recombination strand transfer can be forced by a break in the template, or can occur at sites where folding structure of the template pauses the RT, allowing a concentration of RNase H cleavages that promote transfers. Transfer can be a simple one-step process, or can proceed by a complex multi-step invasion mechanism. In this latter process, the second RNA template interacts with the growing DNA strand well behind the DNA 3'-terminus. The newly formed RNA-DNA hybrid expands by branch migration and eventually catches the elongating DNA primer 3'-terminus to complete the transfer. Transfers are also promoted by interactions between the two RNA templates, which accelerate transfer by a proximity effect. Other details of the role of strand transfers in reverse transcription and the biochemical features of the transfer reaction are discussed.
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