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Stephan Oroszlan and the Proteolytic Processing of Retroviral Proteins: Following A Pro. Viruses 2021; 13:v13112218. [PMID: 34835024 PMCID: PMC8621278 DOI: 10.3390/v13112218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 12/26/2022] Open
Abstract
Steve Oroszlan determined the sequences at the ends of virion proteins for a number of different retroviruses. This work led to the insight that the amino-terminal amino acid of the mature viral CA protein is always proline. In this remembrance, we review Steve’s work that led to this insight and show how that insight was a necessary precursor to the work we have done in the subsequent years exploring the cleavage rate determinants of viral protease processing sites and the multiple roles the amino-terminal proline of CA plays after protease cleavage liberates it from its position in a protease processing site.
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Abstract
I was fortunate to be associated with the lab of Stephen Oroszlan at the US National Cancer Institute from ~1982 until his conversion to Emeritus status in 1995. His lab made groundbreaking discoveries on retroviral proteins during that time, including many features that could not have been inferred or anticipated from straightforward sequence information. Building on the Oroszlan lab results, my colleagues and I demonstrated that the zinc fingers in nucleocapsid proteins play a crucial role in genomic RNA encapsidation; that the N-terminal myristylation of the Gag proteins of many retroviruses is important for their association with the plasma membrane before particle assembly is completed; and that gammaretroviruses initially synthesize their Env protein as an inactive precursor and then truncate the cytoplasmic tail of the transmembrane protein, activating Env fusogenicity, during virus maturation. We also elucidated several aspects of the mechanism of translational suppression in pol gene expression in gammaretroviruses; amazingly, this is a fundamentally different mechanism of suppression from that in most other retroviral genera.
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Affiliation(s)
- Alan Rein
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
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Aceituno-Valenzuela U, Micol-Ponce R, Ponce MR. Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans. Cell Mol Life Sci 2020; 77:3991-4014. [PMID: 32303790 PMCID: PMC11105112 DOI: 10.1007/s00018-020-03518-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/22/2022]
Abstract
The diverse eukaryotic proteins that contain zinc fingers participate in many aspects of nucleic acid metabolism, from DNA transcription to RNA degradation, post-transcriptional gene silencing, and small RNA biogenesis. These proteins can be classified into at least 30 types based on structure. In this review, we focus on the CCHC-type zinc fingers (ZCCHC), which contain an 18-residue domain with the CX2CX4HX4C sequence, where C is cysteine, H is histidine, and X is any amino acid. This motif, also named the "zinc knuckle", is characteristic of the retroviral Group Antigen protein and occurs alone or with other motifs. Many proteins containing zinc knuckles have been identified in eukaryotes, but only a few have been studied. Here, we review the available information on ZCCHC-containing factors from three evolutionarily distant eukaryotes-Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens-representing fungi, plants, and metazoans, respectively. We performed systematic searches for proteins containing the CX2CX4HX4C sequence in organism-specific and generalist databases. Next, we analyzed the structural and functional information for all such proteins stored in UniProtKB. Excluding retrotransposon-encoded proteins and proteins harboring uncertain ZCCHC motifs, we found seven ZCCHC-containing proteins in yeast, 69 in Arabidopsis, and 34 in humans. ZCCHC-containing proteins mainly localize to the nucleus, but some are nuclear and cytoplasmic, or exclusively cytoplasmic, and one localizes to the chloroplast. Most of these factors participate in RNA metabolism, including transcriptional elongation, polyadenylation, translation, pre-messenger RNA splicing, RNA export, RNA degradation, microRNA and ribosomal RNA biogenesis, and post-transcriptional gene silencing. Several human ZCCHC-containing factors are derived from neofunctionalized retrotransposons and act as proto-oncogenes in diverse neoplastic processes. The conservation of ZCCHCs in orthologs of these three phylogenetically distant eukaryotes suggests that these domains have biologically relevant functions that are not well known at present.
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Affiliation(s)
- Uri Aceituno-Valenzuela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
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Boyd PS, Brown JB, Brown JD, Catazaro J, Chaudry I, Ding P, Dong X, Marchant J, O’Hern CT, Singh K, Swanson C, Summers MF, Yasin S. NMR Studies of Retroviral Genome Packaging. Viruses 2020; 12:v12101115. [PMID: 33008123 PMCID: PMC7599994 DOI: 10.3390/v12101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/03/2022] Open
Abstract
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
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Mutations in the Basic Region of the Mason-Pfizer Monkey Virus Nucleocapsid Protein Affect Reverse Transcription, Genomic RNA Packaging, and the Virus Assembly Site. J Virol 2018; 92:JVI.00106-18. [PMID: 29491167 DOI: 10.1128/jvi.00106-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/20/2018] [Indexed: 12/19/2022] Open
Abstract
In addition to specific RNA-binding zinc finger domains, the retroviral Gag polyprotein contains clusters of basic amino acid residues that are thought to support Gag-viral genomic RNA (gRNA) interactions. One of these clusters is the basic K16NK18EK20 region, located upstream of the first zinc finger of the Mason-Pfizer monkey virus (M-PMV) nucleocapsid (NC) protein. To investigate the role of this basic region in the M-PMV life cycle, we used a combination of in vivo and in vitro methods to study a series of mutants in which the overall charge of this region was more positive (RNRER), more negative (AEAEA), or neutral (AAAAA). The mutations markedly affected gRNA incorporation and the onset of reverse transcription. The introduction of a more negative charge (AEAEA) significantly reduced the incorporation of M-PMV gRNA into nascent particles. Moreover, the assembly of immature particles of the AEAEA Gag mutant was relocated from the perinuclear region to the plasma membrane. In contrast, an enhancement of the basicity of this region of M-PMV NC (RNRER) caused a substantially more efficient incorporation of gRNA, subsequently resulting in an increase in M-PMV RNRER infectivity. Nevertheless, despite the larger amount of gRNA packaged by the RNRER mutant, the onset of reverse transcription was delayed in comparison to that of the wild type. Our data clearly show the requirement for certain positively charged amino acid residues upstream of the first zinc finger for proper gRNA incorporation, assembly of immature particles, and proceeding of reverse transcription.IMPORTANCE We identified a short sequence within the Gag polyprotein that, together with the zinc finger domains and the previously identified RKK motif, contributes to the packaging of genomic RNA (gRNA) of Mason-Pfizer monkey virus (M-PMV). Importantly, in addition to gRNA incorporation, this basic region (KNKEK) at the N terminus of the nucleocapsid protein is crucial for the onset of reverse transcription. Mutations that change the positive charge of the region to a negative one significantly reduced specific gRNA packaging. The assembly of immature particles of this mutant was reoriented from the perinuclear region to the plasma membrane. On the contrary, an enhancement of the basic character of this region increased both the efficiency of gRNA packaging and the infectivity of the virus. However, the onset of reverse transcription was delayed even in this mutant. In summary, the basic region in M-PMV Gag plays a key role in the packaging of genomic RNA and, consequently, in assembly and reverse transcription.
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Drici N, Krallafa MA. Effect of mutation on the stabilization energy of HIV-1 zinc fingers: a hybrid local self-consistent field/molecular mechanics investigation. J Biol Inorg Chem 2016; 22:109-119. [DOI: 10.1007/s00775-016-1411-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/03/2016] [Indexed: 11/27/2022]
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Cross- and Co-Packaging of Retroviral RNAs and Their Consequences. Viruses 2016; 8:v8100276. [PMID: 27727192 PMCID: PMC5086612 DOI: 10.3390/v8100276] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/03/2016] [Accepted: 10/03/2016] [Indexed: 12/23/2022] Open
Abstract
Retroviruses belong to the family Retroviridae and are ribonucleoprotein (RNP) particles that contain a dimeric RNA genome. Retroviral particle assembly is a complex process, and how the virus is able to recognize and specifically capture the genomic RNA (gRNA) among millions of other cellular and spliced retroviral RNAs has been the subject of extensive investigation over the last two decades. The specificity towards RNA packaging requires higher order interactions of the retroviral gRNA with the structural Gag proteins. Moreover, several retroviruses have been shown to have the ability to cross-/co-package gRNA from other retroviruses, despite little sequence homology. This review will compare the determinants of gRNA encapsidation among different retroviruses, followed by an examination of our current understanding of the interaction between diverse viral genomes and heterologous proteins, leading to their cross-/co-packaging. Retroviruses are well-known serious animal and human pathogens, and such a cross-/co-packaging phenomenon could result in the generation of novel viral variants with unknown pathogenic potential. At the same time, however, an enhanced understanding of the molecular mechanisms involved in these specific interactions makes retroviruses an attractive target for anti-viral drugs, vaccines, and vectors for human gene therapy.
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In silico structure-based design and synthesis of novel anti-RSV compounds. Antiviral Res 2015; 122:46-50. [PMID: 26259810 DOI: 10.1016/j.antiviral.2015.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/04/2015] [Accepted: 08/06/2015] [Indexed: 12/20/2022]
Abstract
Respiratory syncytial virus (RSV) is the major cause for respiratory tract disease in infants and young children. Currently, no licensed vaccine or a selective antiviral drug against RSV infections are available. Here, we describe a structure-based drug design approach that led to the synthesis of a novel series of zinc-ejecting compounds active against RSV replication. 30 compounds, sharing a common dithiocarbamate moiety, were designed and prepared to target the zinc finger motif of the M2-1 protein. A library of ∼ 12,000 small fragments was docked to explore the area surrounding the zinc ion. Among these, seven ligands were selected and used for the preparation of the new derivatives. The results reported here may help the development of a lead compound for the treatment of RSV infections.
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Retrospective on the all-in-one retroviral nucleocapsid protein. Virus Res 2014; 193:2-15. [PMID: 24907482 PMCID: PMC7114435 DOI: 10.1016/j.virusres.2014.05.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/11/2014] [Accepted: 05/11/2014] [Indexed: 01/08/2023]
Abstract
This retrospective reviews 30 years of research on the retroviral nucleocapsid protein (NC) focusing on HIV-1 NC. Originally considered as a non-specific nucleic-acid binding protein, NC has seminal functions in virus replication. Indeed NC turns out to be a all-in-one viral protein that chaperones viral DNA synthesis and integration, and virus formation. As a chaperone NC provides assistance to genetic recombination thus allowing the virus to escape the immune response and antiretroviral therapies against HIV-1.
This review aims at briefly presenting a retrospect on the retroviral nucleocapsid protein (NC), from an unspecific nucleic acid binding protein (NABP) to an all-in-one viral protein with multiple key functions in the early and late phases of the retrovirus replication cycle, notably reverse transcription of the genomic RNA and viral DNA integration into the host genome, and selection of the genomic RNA together with the initial steps of virus morphogenesis. In this context we will discuss the notion that NC protein has a flexible conformation and is thus a member of the growing family of intrinsically disordered proteins (IDPs) where disorder may account, at least in part, for its function as a nucleic acid (NA) chaperone and possibly as a protein chaperone vis-à-vis the viral DNA polymerase during reverse transcription. Lastly, we will briefly review the development of new anti-retroviral/AIDS compounds targeting HIV-1 NC because it represents an ideal target due to its multiple roles in the early and late phases of virus replication and its high degree of conservation.
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Determinants of Moloney murine leukemia virus Gag-Pol and genomic RNA proportions. J Virol 2014; 88:7267-75. [PMID: 24741085 DOI: 10.1128/jvi.03513-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The Moloney murine leukemia virus (MoMLV) ribonucleoprotein complex is composed of an approximately 20:1 mixture of Gag and Gag-Pol polyproteins plus a single genomic RNA (gRNA) dimer. The mechanisms that regulate these proportions are unknown. Here, we examined whether virion proportions of Gag, Gag-Pol, and gRNA were determined by sampling (that is, if they reflected expression ratios or intracellular concentrations) or more specific recruitment. To this end, MoMLV Gag, Gag-Pol, and gRNA were expressed separately or together in various ratios. Varying the expression ratios of Gag and Gag-Pol revealed that Gag-Pol incorporation was stochastic and that the conserved 20:1 Gag/Gag-Pol ratio coincided with maximal particle production. When skewed expression ratios resulted in excess Gag-Pol, the released virions maintained the intracellular Gag/Gag-Pol ratios and the infectivity per virion was largely maintained, but virion production decreased sharply with high levels of Gag-Pol. The determinants of gRNA proportions were addressed by manipulating the amounts and contexts of functional nucleocapsid (NC) and the ratios of Gag to gRNA. The results showed that the NC domain of either Gag or Gag-Pol could provide gRNA packaging functions equally well. Unlike Gag-Pol, gRNA incorporation was saturable. An upper limit of gRNA incorporation was observed, and particle production was not disrupted by excess gRNA expression. These results indicate that the determinants of Gag/Gag-Pol proportions differ from those for Gag/gRNA. On the basis of the assumption that MoMLV evolved to produce virion components in optimal proportions, these data provide a means of estimating the proportion of unspliced MoMLV RNA that serves as genomic RNA. IMPORTANCE Viruses assemble their progeny from within the cells that they parasitize, where they must sort through a rich milieu of host proteins and nucleic acids to gather together their own building blocks, which are also proteins and nucleic acids. The research described here addresses whether or not the proportions of viral proteins and nucleic acids that are brought together to form a retroviral particle are determined by random sampling from the cell-and thus dictated by the components' availabilities within the cell-or if the amounts of each molecule are specified by the virus replication process. The results indicated that protein components of the murine retrovirus studied here are recruited by chance but that a specific counting mechanism defines the amount of nucleic acid incorporated into each progeny virion.
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Turpin JA. The next generation of HIV/AIDS drugs: novel and developmental antiHIV drugs and targets. Expert Rev Anti Infect Ther 2014; 1:97-128. [PMID: 15482105 DOI: 10.1586/14787210.1.1.97] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
There are presently 42 million people worldwide living with HIV/AIDS, the majority of which have limited access to antiretrovirals. Even if worldwide penetration was possible, our current chemotherapeutic strategies still suffer from issues of cost, patient compliance, deleterious acute and chronic side effects, emerging single and multidrug resistance, and generalized treatment and economic issues. Even our best antiretroviral therapeutic strategy, highly active antiretroviral therapy (HAART), falls short of completely suppressing HIV replication. Therefore, expansion of current therapeutic options by discovering new antiretrovirals and targets will be critical in the coming years. This review addresses the current status of reverse transcriptase and protease inhibitor development, and summarizes the progress in emerging classes of HIV inhibitors, including entry (T-20, T-1249), coreceptor (SCH-C, SCH-D), integrase (beta-Diketos) and p7 nucleocapsid Zn finger inhibitors (thioesters and PATEs). In addition, the processes of virus entry, PIC transport to the nucleus, HIV interaction with nuclear pores, Tat function, Rev function and virus budding (Tsg101 and ubiquitination) are examined, and proof of concept inhibitors and potential antiviral targets discussed.
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Affiliation(s)
- Jim A Turpin
- HowPin Consulting International, PO Box B Frederick, MD 21705, USA.
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Johnson SF, Garcia EL, Summers MF, Telesnitsky A. Moloney murine leukemia virus genomic RNA packaged in the absence of a full complement of wild type nucleocapsid protein. Virology 2012; 430:100-9. [PMID: 22633243 DOI: 10.1016/j.virol.2012.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 03/26/2012] [Accepted: 05/07/2012] [Indexed: 11/17/2022]
Abstract
The current model for MLV genomic RNA (gRNA) packaging predicts that of the thousands of Gag proteins in a budding virion, only a small number (≤1%) may be necessary to recruit gRNA. Here, we examined the threshold limits of functional Gag required to package gRNA using wild-type (WT) and packaging deficient mutant nucleocapsid (NC) phenotypically mixed virions. Although gRNA packaging was severely diminished for the NC mutant, the residual encapsidated RNA dimer displayed motility on gels, thermostability, and integrity that was indistinguishable from that of WT. In phenotypically mixed virions, gRNA encapsidation recovered to within approximately two-fold of WT levels when the amount of WT NC was 5-10% of the total. Our results demonstrate that NC's roles in gRNA dimerization and packaging are genetically separable. Additionally, MLV gRNA packaging does not require 100% WT NC, but the amount of functional NC required is greater than the predicted minimum.
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Affiliation(s)
- Silas F Johnson
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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Chaurasiya KR, Geertsema H, Cristofari G, Darlix JL, Williams MC. A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3. Nucleic Acids Res 2012; 40:751-60. [PMID: 21917850 PMCID: PMC3258130 DOI: 10.1093/nar/gkr726] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/09/2011] [Accepted: 08/23/2011] [Indexed: 12/18/2022] Open
Abstract
Reverse transcription in retroviruses and retrotransposons requires nucleic acid chaperones, which drive the rearrangement of nucleic acid conformation. The nucleic acid chaperone properties of the human immunodeficiency virus type-1 (HIV-1) nucleocapsid (NC) protein have been extensively studied, and nucleic acid aggregation, duplex destabilization and rapid binding kinetics have been identified as major components of its activity. However, the properties of other nucleic acid chaperone proteins, such as retrotransposon Ty3 NC, a likely ancestor of HIV-1 NC, are not well understood. In addition, it is unclear whether a single zinc finger is sufficient to optimize the properties characteristic of HIV-1 NC. We used single-molecule DNA stretching as a method for detailed characterization of Ty3 NC chaperone activity. We found that wild type Ty3 NC aggregates single- and double-stranded DNA, weakly stabilizes dsDNA, and exhibits rapid binding kinetics. Single-molecule studies in the presence of Ty3 NC mutants show that the N-terminal basic residues and the unique zinc finger at the C-terminus are required for optimum chaperone activity in this system. While the single zinc finger is capable of optimizing Ty3 NC's DNA interaction kinetics, two zinc fingers may be necessary in order to facilitate the DNA destabilization exhibited by HIV-1 NC.
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Affiliation(s)
- Kathy R. Chaurasiya
- Department of Physics, Northeastern University, Boston, MA, USA, Unité de Virologie Humaine INSERM 758, IFR 128 Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon, France and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA, USA
| | - Hylkje Geertsema
- Department of Physics, Northeastern University, Boston, MA, USA, Unité de Virologie Humaine INSERM 758, IFR 128 Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon, France and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA, USA
| | - Gaël Cristofari
- Department of Physics, Northeastern University, Boston, MA, USA, Unité de Virologie Humaine INSERM 758, IFR 128 Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon, France and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA, USA
| | - Jean-Luc Darlix
- Department of Physics, Northeastern University, Boston, MA, USA, Unité de Virologie Humaine INSERM 758, IFR 128 Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon, France and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA, USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA, USA, Unité de Virologie Humaine INSERM 758, IFR 128 Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon, France and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA, USA
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Lu K, Heng X, Summers MF. Structural determinants and mechanism of HIV-1 genome packaging. J Mol Biol 2011; 410:609-33. [PMID: 21762803 DOI: 10.1016/j.jmb.2011.04.029] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/11/2011] [Accepted: 04/11/2011] [Indexed: 11/30/2022]
Abstract
Like all retroviruses, the human immunodeficiency virus selectively packages two copies of its unspliced RNA genome, both of which are utilized for strand-transfer-mediated recombination during reverse transcription-a process that enables rapid evolution under environmental and chemotherapeutic pressures. The viral RNA appears to be selected for packaging as a dimer, and there is evidence that dimerization and packaging are mechanistically coupled. Both processes are mediated by interactions between the nucleocapsid domains of a small number of assembling viral Gag polyproteins and RNA elements within the 5'-untranslated region of the genome. A number of secondary structures have been predicted for regions of the genome that are responsible for packaging, and high-resolution structures have been determined for a few small RNA fragments and protein-RNA complexes. However, major questions regarding the RNA structures (and potentially the structural changes) that are responsible for dimeric genome selection remain unanswered. Here, we review efforts that have been made to identify the molecular determinants and mechanism of human immunodeficiency virus type 1 genome packaging.
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Affiliation(s)
- Kun Lu
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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Chaurasiya KR, Paramanathan T, McCauley MJ, Williams MC. Biophysical characterization of DNA binding from single molecule force measurements. Phys Life Rev 2010; 7:299-341. [PMID: 20576476 DOI: 10.1016/j.plrev.2010.06.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/19/2010] [Accepted: 05/20/2010] [Indexed: 11/25/2022]
Abstract
Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.
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Affiliation(s)
- Kathy R Chaurasiya
- Department of Physics, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
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Boukhvalova MS, Prince GA, Blanco JCG. Inactivation of respiratory syncytial virus by zinc finger reactive compounds. Virol J 2010; 7:20. [PMID: 20102602 PMCID: PMC2823672 DOI: 10.1186/1743-422x-7-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 01/26/2010] [Indexed: 11/26/2022] Open
Abstract
Background Infectivity of retroviruses such as HIV-1 and MuLV can be abrogated by compounds targeting zinc finger motif in viral nucleocapsid protein (NC), involved in controlling the processivity of reverse transcription and virus infectivity. Although a member of a different viral family (Pneumoviridae), respiratory syncytial virus (RSV) contains a zinc finger protein M2-1 also involved in control of viral polymerase processivity. Given the functional similarity between the two proteins, it was possible that zinc finger-reactive compounds inactivating retroviruses would have a similar effect against RSV by targeting RSV M2-1 protein. Moreover, inactivation of RSV through modification of an internal protein could yield a safer whole virus vaccine than that produced by RSV inactivation with formalin which modifies surface proteins. Results Three compounds were evaluated for their ability to reduce RSV infectivity: 2,2'-dithiodipyridine (AT-2), tetraethylthiuram disulfide and tetramethylthiuram disulfide. All three were capable of inactivating RSV, with AT-2 being the most potent. The mechanism of action of AT-2 was analyzed and it was found that AT-2 treatment indeed results in the modification of RSV M2-1. Altered intramolecular disulfide bond formation in M2-1 protein of AT-2-treated RSV virions might have been responsible for abrogation of RSV infectivity. AT-2-inactivated RSV was found to be moderately immunogenic in the cotton rats S.hispidus and did not cause a vaccine-enhancement seen in animals vaccinated with formalin-inactivated RSV. Increasing immunogenicity of AT-2-inactivated RSV by adjuvant (Ribi), however, led to vaccine-enhanced disease. Conclusions This work presents evidence that compounds that inactivate retroviruses by targeting the zinc finger motif in their nucleocapsid proteins are also effective against RSV. AT-2-inactivated RSV vaccine is not strongly immunogenic in the absence of adjuvants. In the adjuvanted form, however, vaccine induces immunopathologic response. The mere preservation of surface antigens of RSV, therefore may not be sufficient to produce a highly-efficacious inactivated virus vaccine that does not lead to an atypical disease.
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Matsui T, Tanaka T, Endoh H, Sato K, Tanaka H, Miyauchi E, Kawashima Y, Nagai-Makabe M, Komatsu H, Kohno T, Maeda T, Kodera Y. The RNA Recognition Mechanism of Human Immunodeficiency Virus (HIV) Type 2 NCp8 Is Different from That of HIV-1 NCp7. Biochemistry 2009; 48:4314-23. [DOI: 10.1021/bi802364b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takashi Matsui
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
- Mitsubishi Kagaku Institute of Life Sciences (MITILS), Machida, Tokyo 194-8511, Japan
| | - Takeshi Tanaka
- Mitsubishi Kagaku Institute of Life Sciences (MITILS), Machida, Tokyo 194-8511, Japan
| | - Hiroshi Endoh
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Kazuki Sato
- Department of Environmental Science, School of Science, Fukuoka Women’s University, Higashi-ku, Fukuoka 813-8529, Japan
| | - Hidekazu Tanaka
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Emi Miyauchi
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Yusuke Kawashima
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Misa Nagai-Makabe
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Hiroyoshi Komatsu
- Department of Clinical Laboratory Medicine, Faculty of Health Science Technology, Bunkyo Gakuin University, Bunkyo-ku, Tokyo 113-0023, Japan
| | - Toshiyuki Kohno
- Mitsubishi Kagaku Institute of Life Sciences (MITILS), Machida, Tokyo 194-8511, Japan
| | - Tadakazu Maeda
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Yoshio Kodera
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
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18
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Vo MN, Barany G, Rouzina I, Musier-Forsyth K. HIV-1 nucleocapsid protein switches the pathway of transactivation response element RNA/DNA annealing from loop-loop "kissing" to "zipper". J Mol Biol 2009; 386:789-801. [PMID: 19154737 DOI: 10.1016/j.jmb.2008.12.070] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2008] [Revised: 12/20/2008] [Accepted: 12/29/2008] [Indexed: 11/24/2022]
Abstract
The chaperone activity of HIV-1 (human immunodeficiency virus type 1) nucleocapsid protein (NC) facilitates multiple nucleic acid rearrangements that are critical for reverse transcription of the single-stranded RNA genome into double-stranded DNA. Annealing of the transactivation response element (TAR) RNA hairpin to a complementary TAR DNA hairpin is an essential step in the minus-strand transfer step of reverse transcription. Previously, we used truncated 27-nt mini-TAR RNA and DNA constructs to investigate this annealing reaction pathway in the presence and in the absence of HIV-1 NC. In this work, full-length 59-nt TAR RNA and TAR DNA constructs were used to systematically study TAR hairpin annealing kinetics. In the absence of NC, full-length TAR hairpin annealing is approximately 10-fold slower than mini-TAR annealing. Similar to mini-TAR annealing, the reaction pathway for TAR in the absence of NC involves the fast formation of an unstable "kissing" loop intermediate, followed by a slower conversion to an extended duplex. NC facilitates the annealing of TAR by approximately 10(5)-fold by stabilizing the bimolecular intermediate ( approximately 10(4)-fold) and promoting the subsequent exchange reaction ( approximately 10-fold). In contrast to the mini-TAR annealing pathway, wherein NC-mediated annealing can initiate through both loop-loop kissing and a distinct "zipper" pathway involving nucleation at the 3'-/5'-terminal ends, full-length TAR hairpin annealing switches predominantly to the zipper pathway in the presence of saturated NC.
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Affiliation(s)
- My-Nuong Vo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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19
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Retroviral nucleocapsid proteins display nonequivalent levels of nucleic acid chaperone activity. J Virol 2008; 82:10129-42. [PMID: 18684831 DOI: 10.1128/jvi.01169-08] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) is a nucleic acid chaperone that facilitates the remodeling of nucleic acids during various steps of the viral life cycle. Two main features of NC's chaperone activity are its abilities to aggregate and to destabilize nucleic acids. These functions are associated with NC's highly basic character and with its zinc finger domains, respectively. While the chaperone activity of HIV-1 NC has been extensively studied, less is known about the chaperone activities of other retroviral NCs. In this work, complementary experimental approaches were used to characterize and compare the chaperone activities of NC proteins from four different retroviruses: HIV-1, Moloney murine leukemia virus (MLV), Rous sarcoma virus (RSV), and human T-cell lymphotropic virus type 1 (HTLV-1). The different NCs exhibited significant differences in their overall chaperone activities, as demonstrated by gel shift annealing assays, decreasing in the order HIV-1 approximately RSV > MLV >> HTLV-1. In addition, whereas HIV-1, RSV, and MLV NCs are effective aggregating agents, HTLV-1 NC, which exhibits poor overall chaperone activity, is unable to aggregate nucleic acids. Measurements of equilibrium binding to single- and double-stranded oligonucleotides suggested that all four NC proteins have moderate duplex destabilization capabilities. Single-molecule DNA-stretching studies revealed striking differences in the kinetics of nucleic acid dissociation between the NC proteins, showing excellent correlation between nucleic acid dissociation kinetics and overall chaperone activity.
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20
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Morcock DR, Thomas JA, Sowder RC, Henderson LE, Crise BJ, Gorelick RJ. HIV-1 inactivation by 4-vinylpyridine is enhanced by dissociating Zn(2+) from nucleocapsid protein. Virology 2008; 375:148-58. [PMID: 18304600 DOI: 10.1016/j.virol.2008.01.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 12/06/2007] [Accepted: 01/30/2008] [Indexed: 11/29/2022]
Abstract
Selective inactivation of critical cysteine residues in human immunodeficiency virus type one (HIV-1) was observed after treatment with 4-vinylpyridine (4-VP), with and without the membrane-permeable metal chelator N,N,N',N'-tetrakis(2-pyridylmethyl)-ethylenediamine (TPEN). Chromatographic analysis showed that cysteines contained within nucleocapsid zinc fingers, in the context of whole virus or purified protein, were essentially unreactive, but became reactive when a chelator was included. Virus treated with 4-VP showed only a modest decrease in infectivity; after TPEN addition, nearly complete inactivation of HIV-1 occurred. Similarly, quantitation of viral DNA products from 4-VP-treated virus infections showed no significant effects on reverse transcription, but did show a 14-fold reduction in proviruses; when TPEN was added, a 10(5)-fold decrease in late reverse transcription products was observed and no proviruses were detected. Since 4-VP effectiveness was greatly enhanced by TPEN, this strongly suggests that modification of nucleocapsid zinc fingers is necessary and sufficient for HIV-1 inactivation by sulfhydryl reagents.
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Affiliation(s)
- David R Morcock
- AIDS Vaccine Program, Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Building 535, 4th floor, P.O. Box B, Frederick, Maryland 21702-1201, USA
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21
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Nucleocapsid protein function in early infection processes. Virus Res 2008; 134:39-63. [PMID: 18279991 DOI: 10.1016/j.virusres.2007.12.006] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 12/13/2007] [Accepted: 12/13/2007] [Indexed: 01/15/2023]
Abstract
The role of nucleocapsid protein (NC) in the early steps of retroviral replication appears largely that of a facilitator for reverse transcription and integration. Using a wide variety of cell-free assay systems, the properties of mature NC proteins (e.g. HIV-1 p7(NC) or MLV p10(NC)) as nucleic acid chaperones have been extensively investigated. The effect of NC on tRNA annealing, reverse transcription initiation, minus-strand-transfer, processivity of reverse transcription, plus-strand-transfer, strand-displacement synthesis, 3' processing of viral DNA by integrase, and integrase-mediated strand-transfer has been determined by a large number of laboratories. Interestingly, these reactions can all be accomplished to varying degrees in the absence of NC; some are facilitated by both viral and non-viral proteins and peptides that may or may not be involved in vivo. What is one to conclude from the observation that NC is not strictly required for these necessary reactions to occur? NC likely enhances the efficiency of each of these steps, thereby vastly improving the productivity of infection. In other words, one of the major roles of NC is to enhance the effectiveness of early infection, thereby increasing the probability of productive replication and ultimately of retrovirus survival.
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22
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Berg JM. Metal-Binding Domains in Nucleic Acid-Binding and Gene-Regulatory Proteins. PROGRESS IN INORGANIC CHEMISTRY 2007. [DOI: 10.1002/9780470166383.ch3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Matsui T, Kodera Y, Endoh H, Miyauchi E, Komatsu H, Sato K, Tanaka T, Kohno T, Maeda T. RNA recognition mechanism of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein. J Biochem 2007; 141:269-77. [PMID: 17202191 DOI: 10.1093/jb/mvm037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
NCp8 of HIV-2 contains two CCHC-type zinc fingers connected by a linker, and is involved in many critical steps of the virus life cycle. It was previously shown that the first zinc finger flanked by the linker is the minimal active domain for specific binding to viral RNA. In our previous study, we determined the three-dimensional structure of NCp8-f1, including the minimal active domain, and found that a hydrogen bond between Asn(11) N(delta)H and Arg(27) O stabilized the conformation of the linker in the vicinity of the zinc finger [Kodera et al. (1998) Biochemistry 37, 17704-17713]. In this study, RNA binding activities of NCp8-f1 and three types of its mutant peptides were analysed by native PAGE assay. The activity and three-dimensional structure of NCp8-f1/N11A, in which alanine is substituted for Asn(11) thereby affecting the conformation of the linker, was analyzed and compared with those of NCp8-f1. We demonstrated that the existence of Arg(4) and/or Lys(5) and Arg(26) and/or Arg(27) were necessary for binding RNA. Furthermore, the linker's flexible orientation, which is controlled by the hydrogen bond between Asn(11) N(delta)H and Arg(27) O, appears to be a structural basis for NCp8 existing as a multi-functional protein.
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Affiliation(s)
- Takashi Matsui
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
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24
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Kankia BI, Musier-Forsyth K. The HIV-1 central DNA flap region contains a "flapping" third strand. Biophys Chem 2006; 127:64-8. [PMID: 17215070 DOI: 10.1016/j.bpc.2006.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Accepted: 12/12/2006] [Indexed: 11/16/2022]
Abstract
Due to the discontinuous nature of HIV-1 plus-strand DNA synthesis, a 99-nt plus-strand overhang termed the "central DNA flap" is present near the center of the proviral DNA prior to integration. The flap appears to have stabilizing and/or protective effects on viral DNA, which has been hypothesized to be due to a specific conformation adopted by the three-stranded region. The 5' end of the flap sequence is very purine rich and has the potential to adopt different secondary structures (e.g., duplex, triplex or quadruplex). In the present work, circular dichroism spectroscopy and thermal unfolding techniques were used to characterize an 89-nt long DNA sequence designed to mimic the three-stranded region at the 5' end of HIV-1 proviral DNA. The effect of addition of the HIV-1 nucleocapsid protein (NC) on the nucleic acid structure was also examined. Although, guanine-rich short oligonucleotides derived from the DNA flap demonstrated CD spectra characteristic to parallel quadruplexes, this analysis reveals that the extended 89-nt construct folds into a canonical duplex with a "flapping" third strand both in the absence and presence of NC.
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Affiliation(s)
- Besik I Kankia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
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25
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Levin JG, Guo J, Rouzina I, Musier-Forsyth K. Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. ACTA ACUST UNITED AC 2006; 80:217-86. [PMID: 16164976 DOI: 10.1016/s0079-6603(05)80006-6] [Citation(s) in RCA: 285] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Judith G Levin
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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26
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Abstract
As retroviruses assemble in infected cells, two copies of their full-length, unspliced RNA genomes are selected for packaging from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Understanding the molecular details of genome packaging is important for the development of new antiviral strategies and to enhance the efficacy of retroviral vectors used in human gene therapy. Recent studies of viral RNA structure in vitro and in vivo and high-resolution studies of RNA fragments and protein-RNA complexes are helping to unravel the mechanism of genome packaging and providing the first glimpses of the initial stages of retrovirus assembly.
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Affiliation(s)
- Victoria D'Souza
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
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27
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Liu HW, Cosa G, Landes CF, Zeng Y, Kovaleski BJ, Mullen DG, Barany G, Musier-Forsyth K, Barbara PF. Single-molecule FRET studies of important intermediates in the nucleocapsid-protein-chaperoned minus-strand transfer step in HIV-1 reverse transcription. Biophys J 2005; 89:3470-9. [PMID: 16100256 PMCID: PMC1366842 DOI: 10.1529/biophysj.105.065326] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The minus-strand transfer step of HIV-1 reverse transcription is chaperoned by the nucleocapsid protein (NC), which has been shown to facilitate the annealing between the transactivation response element (TAR) RNA and complementary TAR DNA stem-loop structures. In this work, potential intermediates in the mechanism of NC-chaperoned TAR DNA/TAR RNA annealing have been examined using single-molecule fluorescence resonance energy transfer. The interaction between TAR DNA and various DNA oligonucleotides designed to mimic the initial annealing step was monitored to capture potential intermediates along the reaction pathway. Two possible mechanisms of annealing were examined, namely nucleation through the 3'/5' termini, termed the "zipper" complex, or nucleation through the hairpin loops in a "kissing" complex. Intermediates associated with both mechanisms were observed in the presence of NC, and the kinetics of formation of these intermediates were also measured. Thus, the single-molecule experiments support the notion that NC-assisted annealing of TAR DNA:TAR RNA may occur through multiple pathways.
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Affiliation(s)
- Hsiao-Wei Liu
- Department of Chemistry and Biochemistry, Center for Nano and Molecular Science and Technology, University of Texas, Austin, TX 78712, USA
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28
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Heilman-Miller SL, Wu T, Levin JG. Alteration of nucleic acid structure and stability modulates the efficiency of minus-strand transfer mediated by the HIV-1 nucleocapsid protein. J Biol Chem 2004; 279:44154-65. [PMID: 15271979 DOI: 10.1074/jbc.m401646200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During human immunodeficiency virus type 1 minus-strand transfer, the nucleocapsid protein (NC) facilitates annealing of the complementary repeat regions at the 3'-ends of acceptor RNA and minus-strand strong-stop DNA ((-) SSDNA). In addition, NC destabilizes the highly structured complementary trans-activation response element (TAR) stem-loop (TAR DNA) at the 3'-end of (-) SSDNA and inhibits TAR-induced self-priming, a dead-end reaction that competes with minus-strand transfer. To investigate the relationship between nucleic acid secondary structure and NC function, a series of truncated (-) SSDNA and acceptor RNA constructs were used to assay minus-strand transfer and self-priming in vitro. The results were correlated with extensive enzymatic probing and mFold analysis. As the length of (-) SSDNA was decreased, self-priming increased and was highest when the DNA contained little more than TAR DNA, even if NC and acceptor were both present; in contrast, truncations within TAR DNA led to a striking reduction or elimination of self-priming. However, destabilization of TAR DNA was not sufficient for successful strand transfer: the stability of acceptor RNA was also crucial, and little or no strand transfer occurred if the RNA was highly stable. Significantly, NC may not be required for in vitro strand transfer if (-) SSDNA and acceptor RNA are small, relatively unstructured molecules with low thermodynamic stabilities. Collectively, these findings demonstrate that for efficient NC-mediated minus-strand transfer, a delicate thermodynamic balance between the RNA and DNA reactants must be maintained.
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Affiliation(s)
- Susan L Heilman-Miller
- Laboratory of Molecular Genetics, NICHD, National Institutes of Health, Bethesda, Maryland 20892-2780, USA
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29
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Derebail SS, Heath MJ, DeStefano JJ. Evidence for the differential effects of nucleocapsid protein on strand transfer in various regions of the HIV genome. J Biol Chem 2003; 278:15702-12. [PMID: 12595541 DOI: 10.1074/jbc.m211701200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
An in vitro strand transfer assay that mimicked recombinational events occurring during reverse transcription in HIV-1 was used to assess the role of nucleocapsid protein (NC) in strand transfer. Strand transfer in highly structured nucleic acid species from the U3 3' long terminal repeats, gag-pol frameshift region, and Rev response element were strongly enhanced by NC. In contrast, weakly structured templates from the env and pol-vif regions transferred well without NC and showed lower enhancement. The lack of strong polymerase pause sites in the latter regions demonstrated that non-pause driven mechanisms could also promote transfer. Assays conducted using NC zinc finger mutants supported a differential role for the two fingers in strand transfer with finger 1 (N-terminal) being more important on highly structured RNAs. Overall this report suggests a role for structural intricacies of RNA templates in determining the extent of influence of NC on recombination and illustrates that strand transfer may occur by several different mechanisms depending on the structural nature of the RNA.
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Affiliation(s)
- Suchitra S Derebail
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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30
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Chen Y, Balakrishnan M, Roques BP, Fay PJ, Bambara RA. Mechanism of minus strand strong stop transfer in HIV-1 reverse transcription. J Biol Chem 2003; 278:8006-17. [PMID: 12499370 DOI: 10.1074/jbc.m210959200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Retrovirus minus strand strong stop transfer (minus strand transfer) requires reverse transcriptase-associated RNase H, R sequence homology, and viral nucleocapsid protein. The minus strand transfer mechanism in human immunodeficiency virus-1 was examined in vitro with purified protein and substrates. Blocking donor RNA 5'-end cleavage inhibited transfers when template homology was 19 nucleotides (nt) or less. Cleavage of the donor 5'-end occurred prior to formation of transfer products. This suggests that when template homology is short, transfer occurs through a primer terminus switch-initiated mechanism, which requires cleavage of the donor 5' terminus. On templates with 26-nt and longer homology, transfer occurred before cleavage of the donor 5' terminus. Transfer was unaffected when donor 5'-end cleavages were blocked but was reduced when internal cleavages within the donor were restricted. Based on the overall data, we conclude that in human immunodeficiency virus-1, which contains a 97-nt R sequence, minus strand transfer occurs through an acceptor invasion-initiated mechanism. Transfer is initiated at internal regions of the homologous R sequence without requiring cleavage at the donor 5'-end. The acceptor invades at gaps created by reverse transcriptase-RNase H in the donor-cDNA hybrid. The fragmented donor is eventually strand-displaced by the acceptor, completing the transfer.
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Affiliation(s)
- Yan Chen
- Department of Biochemistry and Biophysics, University of Rochester, New York 14642, USA
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31
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Buckman JS, Bosche WJ, Gorelick RJ. Human immunodeficiency virus type 1 nucleocapsid zn(2+) fingers are required for efficient reverse transcription, initial integration processes, and protection of newly synthesized viral DNA. J Virol 2003; 77:1469-80. [PMID: 12502862 PMCID: PMC140799 DOI: 10.1128/jvi.77.2.1469-1480.2003] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) containing mutations in the nucleocapsid (NC) Zn(2+) finger domains have greatly reduced infectivity, even though genome packaging is largely unaffected in certain cases. To examine replication defects, viral DNA (vDNA) was isolated from cells infected with viruses containing His-to-Cys changes in their Zn(2+) fingers (NC(H23C) and NC(H44C)), an integrase mutant (IN(D116N)), a double mutant (NC(H23C)/IN(D116N)), or wild-type HIV-1. In vitro assays have established potential roles for NC in reverse transcription and integration. In vivo results for these processes were obtained by quantitative PCR, cloning of PCR products, and comparison of the quantity and composition of vDNA generated at discrete points during reverse transcription. Quantitative analysis of the reverse transcription intermediates for these species strongly suggests decreased stability of the DNA produced. Both Zn(2+) finger mutants appear to be defective in DNA synthesis, with the minus- and plus-strand transfer processes being affected while interior portions of the vDNA remain more intact. Sequences obtained from PCR amplification and cloning of 2-LTR circle junction fragments revealed that the NC mutants had a phenotype similar to the IN mutant; removal of the terminal CA dinucleotides necessary for integration of the vDNA is disabled by the NC mutations. Thus, the loss of infectivity in these NC mutants in vivo appears to result from defective reverse transcription and integration processes stemming from decreased protection of the full-length vDNA. Finally, these results indicate that the chaperone activity of NC extends from the management of viral RNA through to the full-length vDNA.
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Affiliation(s)
- James S Buckman
- AIDS Vaccine Program, SAIC Frederick, Inc., National Cancer Institute at Frederick, Maryland 21702-1201, USA
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32
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Guo J, Wu T, Kane BF, Johnson DG, Henderson LE, Gorelick RJ, Levin JG. Subtle alterations of the native zinc finger structures have dramatic effects on the nucleic acid chaperone activity of human immunodeficiency virus type 1 nucleocapsid protein. J Virol 2002; 76:4370-8. [PMID: 11932404 PMCID: PMC155087 DOI: 10.1128/jvi.76.9.4370-4378.2002] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleocapsid protein (NC) of human immunodeficiency virus type 1 has two zinc fingers, each containing the invariant CCHC zinc-binding motif; however, the surrounding amino acid context is not identical in the two fingers. Recently, we demonstrated that zinc coordination is required when NC unfolds complex secondary structures in RNA and DNA minus- and plus-strand transfer intermediates; this property of NC reflects its nucleic acid chaperone activity. Here we have analyzed the chaperone activities of mutants having substitutions of alternative zinc-coordinating residues, i.e., CCHH or CCCC, for the wild-type CCHC motif. We also investigated the activities of mutants that retain the CCHC motifs but have mutations that exchange or duplicate the zinc fingers (mutants 1-1, 2-1, and 2-2); these changes affect amino acid context. Our results indicate that in general, for optimal activity in an assay that measures stimulation of minus-strand transfer and inhibition of nonspecific self-priming, the CCHC motif in the zinc fingers cannot be replaced by CCHH or CCCC and the amino acid context of the fingers must be conserved. Context changes also reduce the ability of NC to facilitate primer removal in plus-strand transfer. In addition, we found that the first finger is a more crucial determinant of nucleic acid chaperone activity than the second finger. Interestingly, comparison of the in vitro results with earlier in vivo replication data raises the possibility that NC may adopt multiple conformations that are responsible for different NC functions during virus replication.
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Affiliation(s)
- Jianhui Guo
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA
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33
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Abstract
Recombination is a major source of genetic variability in retroviruses. Each viral particle contains two single-stranded genomic RNAs. Recombination mostly results from a switch in template between these two RNAs during reverse transcription. Here we emphasize the main mechanisms underlying recombination that are emerging from recent advances in biochemical and cell culture techniques. Increasing evidence supporting the involvement of RNA secondary structures now complements the predominant role classically attributed to enzyme pausing during reverse transcription. Finally, the implications of recombination on the dynamics of emergence of genomic aberrations in retroviruses are discussed.
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Affiliation(s)
- M Negroni
- Unité de Regulation Enzymatique des Activités Cellulaires, FRE 2364-CNRS, Paris, France.
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34
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Morcock DR, Kane BP, Casas-Finet JR. Fluorescence and nucleic acid binding properties of the human T-cell leukemia virus-type 1 nucleocapsid protein. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1481:381-94. [PMID: 11018730 DOI: 10.1016/s0167-4838(00)00181-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We used intrinsic tryptophan fluorescence to study the nucleocapsid protein from human T-cell leukemia virus-type one, HTLV-1 p15, an 85-amino-acid protein with two Trp-containing zinc-finger motifs. Fluorescence spectra suggested an interaction between the two zinc fingers and another interaction involving the C-terminal tail and the zinc fingers. Titrations with nucleic acid revealed similar, sub-micromolar affinity for poly(dT) and poly(U) in 1 mM sodium phosphate, pH 7. Double-stranded DNA bound an order of magnitude weaker, suggesting helix-destabilizing activity. Base preference of p15 was T approximately U>I approximately C approximately G>A; affinity spanned about one order of magnitude. HTLV-1 p15 bound weaker and with less variation than reported values for either human or simian immunodeficiency virus homologues. The low affinity of p15 for nonspecific nucleic acids distinguishes it from other nucleocapsid proteins, and may suggest its involvement in additional steps of the virus life cycle other than RNA packaging.
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Affiliation(s)
- D R Morcock
- AIDS Vaccine Program, SAIC Frederick, National Cancer Institute - Frederick Cancer Research and Development Center, Bldg. 535, 4th floor, P.O. Box B, Frederick, MD 21702, USA
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35
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Morcock DR, Sowder RC, Casas-Finet JR. Role of the histidine residues of visna virus nucleocapsid protein in metal ion and DNA binding. FEBS Lett 2000; 476:190-3. [PMID: 10913611 DOI: 10.1016/s0014-5793(00)01723-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Zinc finger (ZF) domains in retroviral nucleocapsid proteins usually contain one histidine per metal ion coordination complex (Cys-X(2)-Cys-X(4)-His-X(4)-Cys). Visna virus nucleocapsid protein, p8, has two additional histidines (in the second of its two ZFs) that could potentially bind metal ions. Absorption spectra of cobalt-bound ZF2 peptides were altered by Cys alkylation and mutation, but not by mutation of the extra histidines. Our results show that visna p8 ZFs involve three Cys and one His in the canonical spacing in metal ion coordination, and that the two additional histidines appear to interact with nucleic acid bases in p8-DNA complexes.
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Affiliation(s)
- D R Morcock
- AIDS Vaccine Program, SAIC Frederick, National Cancer Institute-Frederick Cancer Research and Development Center, Building 535-4, P.O. Box B, Frederick, MD 21702, USA
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36
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Abstract
The human immunodeficiency virus (HIV) genome encodes a total of three structural proteins, two envelope proteins, three enzymes, and six accessory proteins. Studies over the past ten years have provided high-resolution three-dimensional structural information for all of the viral enzymes, structural proteins and envelope proteins, as well as for three of the accessory proteins. In some cases it has been possible to solve the structures of the intact, native proteins, but in most cases structural data were obtained for isolated protein domains, peptidic fragments, or mutants. Peptide complexes with two regulatory RNA fragments and a protein complex with an RNA recognition/encapsidation element have also been structurally characterized. This article summarizes the high-resolution structural information that is currently available for HIV proteins and reviews current structure-function and structure-biological relationships.
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Affiliation(s)
- B G Turner
- Howard Hughes Medical Institute, Department of Chemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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37
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Kodera Y, Sato K, Tsukahara T, Komatsu H, Maeda T, Kohno T. High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein. Biochemistry 1998; 37:17704-13. [PMID: 9922136 DOI: 10.1021/bi981818o] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The retroviral nucleocapsid (NC) protein is a multifunctional protein essential for RNA genome packaging and viral infectivity. The NC protein, NCp8, of the human immunodeficiency virus type-II (HIV-2) is a 49 amino acid peptide containing two zinc fingers, of the type C-X2-C-X4-H-X4-C, connected by seven amino acid residues, called the "basic amino acid cluster." It has been shown that the N-terminal zinc finger flanked by the basic amino acid cluster is the minimal active domain for the specific binding to viral RNA and other functions. However, the structure-activity relationships of NCp8 have not been investigated in detail. In the present study, the three-dimensional structure of a 29 amino acid peptide, including the minimal active domain (NCp8-fl), was determined by two-dimensional 1H NMR spectroscopy with simulated annealing calculations. A total of 15 converged structures of NCp8-fl were obtained on the basis of 355 experimental constraints, including 343 distance constraints obtained from nuclear Overhauser effect connectivities, 12 torsion angle (phi, chi1) constraints, and four constraints for zinc binding. The root-mean-square deviation of the 15 converged structures was 0.29 +/- 0.04 A for the backbone atoms (N, C(alpha), C) and 1.27 +/- 0.13 A for all heavy atoms. Interestingly, the basic amino acid cluster itself was defined well, with a loop-like conformation in which three arginine residues in the cluster and one arginine residue in the zinc finger are located approximately in the same plane of the molecule and are exposed to the solvent. The structure-activity relationships are discussed on the basis of the comparison of this well-defined structure with those of other NC proteins.
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Affiliation(s)
- Y Kodera
- Mitsubishi Kasei Institute of Life Sciences, Machida, Tokyo, Japan
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38
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Lehmann E, Zenobi R. Detektion spezifischer nichtkovalenter Zinkfingerpeptid-Oligodesoxynucleotid-Komplexe durch matrixunterstützte Laserdesorptions/Ionisations-Massenspektrometrie. Angew Chem Int Ed Engl 1998. [DOI: 10.1002/(sici)1521-3757(19981217)110:24<3600::aid-ange3600>3.0.co;2-g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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Lee SY, Howard TM, Rasheed S. Genetic analysis of the rat leukemia virus: influence of viral sequences in transduction of the c-ras proto-oncogene and expression of its transforming activity. J Virol 1998; 72:9906-17. [PMID: 9811727 PMCID: PMC110503 DOI: 10.1128/jvi.72.12.9906-9917.1998] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rat leukemia virus (RaLV) is an endogenous retrovirus that is spontaneously released by Sprague-Dawley rat embryo cells. The overall structure of the RaLV genome resembles that of other simple, replication-competent retroviruses, but the sequence of the long terminal repeats (LTR) is unique and unrelated to the known retroviruses. Phylogenetically, the RaLV genome appears to be more closely related to the feline leukemia virus group of retroviruses than to the murine leukemia virus group. A remarkable feature of RaLV is that it is capable of transducing a ras proto-oncogene from rat tumor cells in the form of an acutely transforming virus, designated the Rasheed strain of the rat sarcoma virus (RaSV). With the exception of the c-ras sequence, the genomes of both RaLV and RaSV are collinear. The RaSV-encoded oncogene v-Ra-ras expresses a fusion protein with a molecular mass of 29 kDa, and it exhibits a unique structure that has not been described previously for any known virus. The 5' end of this gene is derived from sequences encoding RaLV matrix followed by 20 bp derived from the U5 region of the RaLV LTR (RS-U5 element) which is joined at its 3' end to sequences derived from all six (coding and noncoding) exons of the c-ras proto-oncogene at the 3' end. This recombinational event represents a novel mechanism among the acutely transforming viruses that have been studied.
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MESH Headings
- 3T3 Cells
- Amino Acid Sequence
- Animals
- Base Sequence
- Cats
- Cells, Cultured
- DNA, Viral/genetics
- Evolution, Molecular
- Gammaretrovirus/genetics
- Gene Expression
- Genes, ras
- Genome, Viral
- Mice
- Molecular Sequence Data
- Phylogeny
- RNA, Viral/genetics
- Rats
- Recombination, Genetic
- Sequence Homology, Nucleic Acid
- Terminal Repeat Sequences
- Transduction, Genetic
- Transformation, Genetic
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Affiliation(s)
- S Y Lee
- Laboratory of Viral Oncology and AIDS Research, Department of Pathology, School of Medicine, University of Southern California, Los Angeles, California 90032-3626, USA
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40
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Davis WR, Gabbara S, Hupe D, Peliska JA. Actinomycin D inhibition of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase and nucleocapsid protein. Biochemistry 1998; 37:14213-21. [PMID: 9760259 DOI: 10.1021/bi9814890] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Actinomycin D was found to be a potent inhibitor of HIV-1 reverse transcriptase catalyzed DNA strand transfer reactions. Using an oligonucleotide model system, actinomycin D inhibition of DNA strand transfer was examined to elucidate the mechanism of inhibition and further define the mechanism of DNA strand transfer. Our results show that actinomycin D inhibits HIV-1 reverse transcriptase catalyzed DNA strand transfer without inhibiting RNA-dependent or DNA-dependent DNA polymerase activity. Actinomycin D was found to strongly inhibit annealing of a primary DNA product to the DNA acceptor template, preventing the formation of a key reaction intermediate. The HIV-1 nucleocapsid protein has been shown to participate in catalytic events during reverse transcription including DNA strand transfer. Recombinant nucleocapsid protein was used in conjunction with actinomycin D in this model system to investigate how NC may participate in the mechanism of inhibition by actinomycin D and in DNA strand transfer. The inclusion of nucleocapsid protein was found to partially relieve both DNA annealing and strand transfer inhibition caused by actinomycin D. This study suggests a potential new mechanism for inhibiting retroviral replication by preventing the formation of replication intermediates.
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Affiliation(s)
- W R Davis
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor 48109-0606, USA
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41
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Rossio JL, Esser MT, Suryanarayana K, Schneider DK, Bess JW, Vasquez GM, Wiltrout TA, Chertova E, Grimes MK, Sattentau Q, Arthur LO, Henderson LE, Lifson JD. Inactivation of human immunodeficiency virus type 1 infectivity with preservation of conformational and functional integrity of virion surface proteins. J Virol 1998; 72:7992-8001. [PMID: 9733838 PMCID: PMC110135 DOI: 10.1128/jvi.72.10.7992-8001.1998] [Citation(s) in RCA: 339] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole inactivated viral particles have been successfully used as vaccines for some viruses, but procedures historically used for inactivation can denature virion proteins. Results have been inconsistent, with enhancement of disease rather than protection seen in some notable instances following vaccination. We used the compound 2,2'-dithiodipyridine (aldrithiol-2; AT-2) to covalently modify the essential zinc fingers in the nucleocapsid (NC) protein of human immunodeficiency virus type 1 (HIV-1) or simian immunodeficiency virus (SIV) virions, thereby inactivating infectivity. The inactivated virus was not detectably infectious in vitro (up to 5 log units of inactivation). However, in contrast to virions inactivated by conventional methods such as heat or formalin treatment, viral and host cell-derived proteins on virion surfaces retained conformational and functional integrity. Thus, immunoprecipitation of AT-2-treated virions was comparable to precipitation of matched untreated virus, even when using antibodies to conformational determinants on gp120. AT-2 inactivated virions bound to CD4(+) target cells and mediated virus-induced, CD4-dependent "fusion from without" comparably to native virions. However, viral entry assays demonstrated that the viral life cycle of AT-2-treated virions was arrested before initiation of reverse transcription. The major histocompatibility complex (MHC) class II molecules on the surface of AT-2-treated virions produced from MHC class II-expressing cells retained the ability to support class II-dependent, superantigen-triggered proliferative responses by resting T lymphocytes. These findings indicate that inactivation via this method results in elimination of infectivity with preservation of conformational and functional integrity of virion surface proteins, including both virally encoded determinants and proteins derived from the host cells in which the virus was produced. Such inactivated virions should provide a promising candidate vaccine antigen and a useful reagent for experimentally probing the postulated involvement of virion surface proteins in indirect mechanisms of HIV-1 pathogenesis.
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Affiliation(s)
- J L Rossio
- Retroviral Pathogenesis Laboratory, AIDS Vaccine Program, SAIC Frederick, National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, Maryland 21702, USA
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42
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Brown JP, Gee NS. Cloning and deletion mutagenesis of the alpha2 delta calcium channel subunit from porcine cerebral cortex. Expression of a soluble form of the protein that retains [3H]gabapentin binding activity. J Biol Chem 1998; 273:25458-65. [PMID: 9738015 DOI: 10.1074/jbc.273.39.25458] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The anti-epileptic, anti-hyperalgesic, and anxiolytic agent gabapentin (1-(aminomethyl)-cyclohexane acetic acid or Neurontin) has previously been shown to bind with high affinity to the alpha2delta subunit of voltage-dependent calcium channels (Gee, N. S. , Brown, J. P., Dissanayake, V. U. K., Offord, J., Thurlow, R., and Woodruff, G.N. (1996) J. Biol. Chem. 271, 5768-5776). We report here the cloning, sequencing, and deletion mutagenesis of the alpha2delta subunit from porcine brain. The deduced protein sequence has a 95.9 and 98.2% identity to the rat and human neuronal alpha2 delta sequences, respectively. [3H]Gabapentin binds with a KD of 37.5 +/- 10.4 nM to membranes prepared from COS-7 cells transfected with wild-type porcine alpha2 delta cDNA. Six deletion mutants (B-G) that lack the delta polypeptide, together with varying amounts of the alpha2 component, failed to bind [3H]gabapentin. C-terminal deletion mutagenesis of the delta polypeptide identified a segment (residues 960-994) required for correct assembly of the [3H]gabapentin binding pocket. Mutant L, which lacks the putative membrane anchor in the delta sequence, was found in both membrane-associated and soluble secreted forms. The soluble form was not proteolytically cleaved into separate alpha2 and delta chains but still retained a high affinity (KD = 30.7 +/- 8.1 nM) for [3H]gabapentin. The production of a soluble alpha2delta mutant supports the single transmembrane model of the alpha2 delta subunit and is an important step toward the large-scale recombinant expression of the protein.
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Affiliation(s)
- J P Brown
- Parke-Davis Neuroscience Research Centre, Cambridge University Forvie Site, Robinson Way, Cambridge, CB2 2QB, United Kingdom.
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43
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Lee BM, De Guzman RN, Turner BG, Tjandra N, Summers MF. Dynamical behavior of the HIV-1 nucleocapsid protein. J Mol Biol 1998; 279:633-49. [PMID: 9641983 DOI: 10.1006/jmbi.1998.1766] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The HIV-1 nucleocapsid protein (NC) contains two CCHC-type zinc knuckle domains that are essential for genome recognition, packaging and infectivity. The solution structure of the protein has been determined independently by three groups. Although the structures of the individual zinc knuckle domains are similar, two of the studies indicated that the knuckles behave as independently folded, non-interacting domains connected by a flexible tether, whereas one study revealed the presence of interknuckle NOE cross-peaks, which were interpreted in terms of a more compact structure in which the knuckles are in close proximity. We have collected multidimensional NMR data for the recombinant, isotopically labeled HIV-1 NC protein, and confirmed the presence of weak interknuckle NOEs. However, the NOE data are not consistent with a single protein conformation. 15N NMR relaxation studies reveal that the two zinc knuckle domains possess different effective rotational correlation times, indicating that the knuckles are not tumbling as a single globular domain. In addition, the 1H NMR chemical shifts of isolated zinc knuckle peptides are very similar to those of the intact protein. The combined results indicate that the interknuckle interactions, which involve the close approach of the side-chains of Phe16 and Trp37, are transitory. The solution behavior of NC may be best considered as a rapid equilibrium between conformations with weakly interacting and non-interacting knuckle domains. This inherent conformational flexibility may be functionally important, enabling adaptive binding of NC to different recognition elements within the HIV-1 psi-RNA packaging signal.
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Affiliation(s)
- B M Lee
- Howard Hughes Medical Institute, University of Maryland, Baltimore County 21250, USA
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44
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Huang M, Maynard A, Turpin JA, Graham L, Janini GM, Covell DG, Rice WG. Anti-HIV agents that selectively target retroviral nucleocapsid protein zinc fingers without affecting cellular zinc finger proteins. J Med Chem 1998; 41:1371-81. [PMID: 9554870 DOI: 10.1021/jm9708543] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Agents that target the two highly conserved Zn fingers of the human immunodeficiency virus (HIV) nucleocapsid p7 (NCp7) protein are under development as antivirals. These agents covalently modify Zn-coordinating cysteine thiolates of the fingers, causing Zn ejection, loss of native protein structure and nucleic acid binding capacity, and disruption of virus replication. Concentrations of three antiviral agents that promoted in vitro Zn ejection from NCp7 and inhibited HIV replication did not impact the functions of cellular Zn finger proteins, including poly(ADP-ribose) polymerase and the Sp1 and GATA-1 transcription factors, nor did the compounds inhibit HeLa nuclear extract mediated transcription. Selectivity of interactions of these agents with NCp7 was supported by molecular modeling analysis which (1) identified a common saddle-shaped nucleophilic region on the surfaces of both NCp7 Zn fingers, (2) indicated a strong correspondence between computationally docked positions for the agents tested and overlap of frontier orbitals within the nucleophilic loci of the NCp7 Zn fingers, and (3) revealed selective steric exclusion of the agents from the core of the GATA-1 Zn finger. Further modeling analysis suggests that the thiolate of Cys49 in the carboxy-terminal finger is the site most susceptible to electrophilic attack. These data provide the first experimental evidence and rationale for antiviral agents that selectively target retroviral nucleocapsid protein Zn fingers.
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Affiliation(s)
- M Huang
- Laboratory of Antiviral Drug Mechanisms, National Cancer Institute-Frederick Cancer Research and Development Center, SAIC Frederick, Frederick, Maryland 21702-1201, USA
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45
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Yee KS, Yu VC. Isolation and characterization of a novel member of the neural zinc finger factor/myelin transcription factor family with transcriptional repression activity. J Biol Chem 1998; 273:5366-74. [PMID: 9478997 DOI: 10.1074/jbc.273.9.5366] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myelin transcription factor 1 (MyT1) and neural zinc finger factor 1 (NZF-1) represent the first two members of an emerging family of neural specific, zinc finger-containing DNA-binding proteins. MyT1 has been shown recently to play a critical role in neuronal cell differentiation during development. We have cloned the third member of the NZF/MyT family, referred to as neural zinc finger factor 3 (NZF-3). The cDNA sequence predicts a protein of 1,032 amino acids which contains two clusters of zinc fingers similar to MyT1 and NZF-1. Unlike MyT1 and NZF-1, NZF-3 does not contain an acidic domain at the amino terminus or a serine/threonine-rich region between the two finger clusters. NZF-3 binds to a DNA element containing a single copy of the previously described AAAGTTT consensus motif for these factors but exhibits a marked enhancement in relative affinity to a bipartite element containing two copies of the consensus motif. In contrast to MyT1 and NZF-1, which are known to activate transcription, cotransfection experiments revealed that NZF-3 confers repression on the basal activity of promoters containing the consensus binding elements. The identification of an additional member of the NZF/MyT family provides an opportunity to investigate the relative contribution of members of this family of transcription factors to the complex regulatory processes in neural development and homeostasis.
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Affiliation(s)
- K S Yee
- Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609, Republic of Singapore
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46
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De Guzman RN, Wu ZR, Stalling CC, Pappalardo L, Borer PN, Summers MF. Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element. Science 1998; 279:384-8. [PMID: 9430589 DOI: 10.1126/science.279.5349.384] [Citation(s) in RCA: 551] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The three-dimensional structure of the human immunodeficiency virus-type 1 (HIV-1) nucleocapsid protein (NC) bound to the SL3 stem-loop recognition element of the genomic Psi RNA packaging signal has been determined by heteronuclear magnetic resonance spectroscopy. Tight binding (dissociation constant, approximately 100 nM) is mediated by specific interactions between the amino- and carboxyl-terminal CCHC-type zinc knuckles of the NC protein and the G7 and G9 nucleotide bases, respectively, of the G6-G7-A8-G9 RNA tetraloop. A8 packs against the amino-terminal knuckle and forms a hydrogen bond with conserved Arg32, and residues Lys3 to Arg10 of NC form a 310 helix that binds to the major groove of the RNA stem and also packs against the amino-terminal zinc knuckle. The structure provides insights into the mechanism of viral genome recognition, explains extensive amino acid conservation within NC, and serves as a basis for the development of inhibitors designed to interfere with genome encapsidation.
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Affiliation(s)
- R N De Guzman
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland-Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
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47
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McDonnell NB, De Guzman RN, Rice WG, Turpin JA, Summers MF. Zinc ejection as a new rationale for the use of cystamine and related disulfide-containing antiviral agents in the treatment of AIDS. J Med Chem 1997; 40:1969-76. [PMID: 9207937 DOI: 10.1021/jm970147+] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The highly conserved and mutationally intolerant retroviral zinc finger motif of the HIV-1 nucleocapsid protein (NC) is an attractive target for drug therapy due to its participation in multiple stages of the viral replication cycle. A literature search identified cystamine, thiamine disulfide, and disulfiram as compounds that have been shown to inhibit HIV-1 replication by poorly defined mechanisms and that have electrophilic functional groups that might react with the metal-coordinating sulfur atoms of the retroviral zinc fingers and cause zinc ejection. 1H NMR studies reveal that these compounds readily eject zinc from synthetic peptides with sequences corresponding to the HIV-1 NC zinc fingers, as well as from the intact HIV-1 NC protein. In contrast, the reduced forms of disulfiram and cystamine, diethyl dithiocarbamate and cysteamine, respectively, were found to be ineffective at zinc ejection, although cysteamine formed a transient complex with the zinc fingers. Studies with HIV-1-infected human T-cells and monocyte/macrophage cultures revealed that cystamine and cysteamine possess significant antiviral properties at nontoxic concentrations, which warrant their consideration as therapeutically useful anti-HIV agents.
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Affiliation(s)
- N B McDonnell
- Howard Hughes Medical Institute, University of Maryland Baltimore County 21228, USA
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48
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Wu JQ, Maki AH, Ozarowski A, Urbaneja MA, Henderson LE, Casas-Finet JR. Fluorescence, phosphorescence, and optically detected magnetic resonance studies of the nucleic acid association of the nucleocapsid protein of the murine leukemia virus. Biochemistry 1997; 36:6115-23. [PMID: 9166782 DOI: 10.1021/bi962951o] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fluorescence, phosphorescence, and optical detection of triplet state magnetic resonance (ODMR) are employed to investigate the interaction of p10, the nucleocapsid protein of the Moloney murine leukemia virus, with nucleic acids. p10 is a 55-amino acid protein containing a single zinc finger motif, C26C29H34C39, that includes Y at position 28 and W at position 35. In addition, the interactions of a zinc finger peptide, p10-ZF, comprising residues 24-41 of p10, and a doubly mutated 24-41 peptide, p10-ZF' in which the positions of Y and W are interchanged, also are reported. The measurements focus on the direct involvement of the sole W residue in the nucleic acid interaction. Fluorescence quenching and salt-back titrations indicate complex formation of p10 with several octanucleotides--(dT)8, (dI)8, (dU)7dT, and (5-BrdU)7dT--and with the polynucleotides poly(dT) and poly(dI). Poly(dI) binds with the highest affinity. Apparent binding constants and salt-back midpoints are reported. Neither p10-ZF nor p10-ZF' exhibits significant fluorescence quenching by these DNA substrates. Binding of p10-ZF to fluorescent poly(ethenoadenylic acid) was detected with greatly reduced affinity relative to p10, but binding of p10-ZF' was undetectable. These results are in general agreement with phosphorescence and ODMR measurements monitoring W. Addition of poly(I) to p10 leads to a phosphorescence red shift, reduction in the zero-field splitting (ZFS) parameters D and E, and a significantly reduced phosphorescence lifetime, each consistent with aromatic stacking interactions between W and the nucleobases. These effects are smaller with p10-ZF and undetectable with p10-ZF'. Poly(U) produces no significant changes in the triplet state parameters of W; no stacking interactions are observed even for p10. (5-BrdU)7dT yields large phosphorescence red shifts in p10 and p10-ZF, and reductions of D, but no significant heavy atom effects. These effects probably are due to enhanced local polarizability caused by Br, but any stacking interactions in these complexes would exclude van der Waals contacts between W and the Br atoms.
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Affiliation(s)
- J Q Wu
- Department of Chemistry, University of California, Davis 95616, USA
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49
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Lapadat-Tapolsky M, Gabus C, Rau M, Darlix JL. Possible roles of HIV-1 nucleocapsid protein in the specificity of proviral DNA synthesis and in its variability. J Mol Biol 1997; 268:250-60. [PMID: 9159468 DOI: 10.1006/jmbi.1997.0978] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Retroviral nucleocapsid (NC) protein is an integral part of the virion nucleocapsid where it coats the dimeric RNA genome. Due to its nucleic acid binding and annealing activities, NC protein directs the annealing of the tRNA primer to the primer binding site and greatly facilitates minus strand DNA elongation and transfer while protecting the nucleic acids against nuclease degradation. To understand the role of NCp7 in viral DNA synthesis, we examined the influence of NCp7 on self-primed versus primer-specific reverse transcription. The results show that HIV-1 NCp7 can extensively inhibit self-primed reverse transcription of viral and cellular RNAs while promoting primer-specific synthesis of proviral DNA. The role of NCp7 vis-a-vis the presence of mutations in the viral DNA during minus strand elongation was examined. NCp7 maximized the annealing between a cDNA(-) primer containing one to five consecutive errors and an RNA representing the 3' end of the genome. The ability of reverse transcriptase (RT) in the presence of NCp7 to subsequently extend the mutated primers depended upon the position of the mismatch within the primer:template complex. When the mutations were at the polymerisation site, primer extension by RT in the presence of NCp7 was very high, about 40% for one mismatch and 3% for five consecutive mismatches. Mutations within the DNA primer or at its 5' end had little effect on the extension of viral DNA by RT. Taken together these results indicate that NCp7 plays major roles in proviral DNA synthesis within the virion core due to its ability to promote prime-specific proviral DNA synthesis while concurrently inhibiting non-specific reverse transcription of viral and cellular RNAs. Moreover, the observation that NCp7 enhances the incorporation of mutations during minus strand DNA elongation favours the notion that NCp7 is a factor contributing to the high mutation rate of HIV-1.
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Affiliation(s)
- M Lapadat-Tapolsky
- LaboRetro Unité de Virologie Humaine 412, Ecole Normale Supérieure deLyon, France
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50
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Jackson FR, Banfi S, Guffanti A, Rossi E. A novel zinc finger-containing RNA-binding protein conserved from fruitflies to humans. Genomics 1997; 41:444-52. [PMID: 9169144 DOI: 10.1006/geno.1997.4704] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Drosophila lark gene encodes an essential RNA-binding protein of the RNA recognition motif (RRM) class that is required during embryonic development. Genetic analysis demonstrates that it also functions as a molecular element of a circadian clock output pathway, mediating the temporal regulation of adult emergence in the fruitfly. We now report the molecular characterization of a human gene with significant similarity to lark. Based on fluorescence in situ hybridization and radiation hybrid mapping, the human gene has been localized to chromosome region 11q13; it is closely linked to several identified genes including the locus of Bardet-Biedl syndrome type 1. The lark-homologous human gene expresses a single 1.8-kb size class of mRNA in most or all tissues including brain. Additional database searches have identified a mouse counterpart that is virtually identical to the human protein. Similar to lark protein, both mammalian proteins contain two copies of the RRM-type consensus RNA-binding motif. Unlike most RRM family members, however, the Drosophila and mammalian proteins also contain a retroviral-type (RT) zinc finger that is situated 43 residues C-terminal to the second RRM element. Within a 184-residue segment spanning the RRM elements and the RT zinc finger, the human and mouse proteins are 61% similar to the Drosophila lark sequence. These common sequence features and comparisons among a large collection of RRM proteins suggest that the human and mouse proteins represent homologues of Drosophila lark.
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Affiliation(s)
- F R Jackson
- Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.
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