1
|
Senavirathne G, London J, Gardner A, Fishel R, Yoder KE. DNA strand breaks and gaps target retroviral intasome binding and integration. Nat Commun 2023; 14:7072. [PMID: 37923737 PMCID: PMC10624929 DOI: 10.1038/s41467-023-42641-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
Retrovirus integration into a host genome is essential for productive infections. The integration strand transfer reaction is catalyzed by a nucleoprotein complex (Intasome) containing the viral integrase (IN) and the reverse transcribed (RT) copy DNA (cDNA). Previous studies suggested that DNA target-site recognition limits intasome integration. Using single molecule Förster resonance energy transfer (smFRET), we show prototype foamy virus (PFV) intasomes specifically bind to DNA strand breaks and gaps. These break and gap DNA discontinuities mimic oxidative base excision repair (BER) lesion-processing intermediates that have been shown to affect retrovirus integration in vivo. The increased DNA binding events targeted strand transfer to the break/gap site without inducing substantial intasome conformational changes. The major oxidative BER substrate 8-oxo-guanine as well as a G/T mismatch or +T nucleotide insertion that typically introduce a bend or localized flexibility into the DNA, did not increase intasome binding or targeted integration. These results identify DNA breaks or gaps as modulators of dynamic intasome-target DNA interactions that encourage site-directed integration.
Collapse
Affiliation(s)
- Gayan Senavirathne
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - James London
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Anne Gardner
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Richard Fishel
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA.
- Molecular Carcinogenesis and Chemoprevention Program, The James Comprehensive Cancer Center and Ohio State University, Columbus, OH, 43210, USA.
| | - Kristine E Yoder
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA.
- Molecular Carcinogenesis and Chemoprevention Program, The James Comprehensive Cancer Center and Ohio State University, Columbus, OH, 43210, USA.
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
2
|
Pellaers E, Bhat A, Christ F, Debyser Z. Determinants of Retroviral Integration and Implications for Gene Therapeutic MLV-Based Vectors and for a Cure for HIV-1 Infection. Viruses 2022; 15:32. [PMID: 36680071 PMCID: PMC9861059 DOI: 10.3390/v15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
To complete their replication cycle, retroviruses need to integrate a DNA copy of their RNA genome into a host chromosome. Integration site selection is not random and is driven by multiple viral and cellular host factors specific to different classes of retroviruses. Today, overwhelming evidence from cell culture, animal experiments and clinical data suggests that integration sites are important for retroviral replication, oncogenesis and/or latency. In this review, we will summarize the increasing knowledge of the mechanisms underlying the integration site selection of the gammaretrovirus MLV and the lentivirus HIV-1. We will discuss how host factors of the integration site selection of retroviruses may steer the development of safer viral vectors for gene therapy. Next, we will discuss how altering the integration site preference of HIV-1 using small molecules could lead to a cure for HIV-1 infection.
Collapse
Affiliation(s)
| | | | | | - Zeger Debyser
- Molecular Virology and Gene Therapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| |
Collapse
|
3
|
Mechanisms of LTR-Retroelement Transposition: Lessons from Drosophila melanogaster. Viruses 2017; 9:v9040081. [PMID: 28420154 PMCID: PMC5408687 DOI: 10.3390/v9040081] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 01/02/2023] Open
Abstract
Long terminal repeat (LTR) retrotransposons occupy a special place among all mobile genetic element families. The structure of LTR retrotransposons that have three open reading frames is identical to DNA forms of retroviruses that are integrated into the host genome. Several lines of evidence suggest that LTR retrotransposons share a common ancestry with retroviruses and thus are highly relevant to understanding mechanisms of transposition. Drosophila melanogaster is an exceptionally convenient model for studying the mechanisms of retrotransposon movement because many such elements in its genome are transpositionally active. Moreover, two LTRretrotransposons of D. melanogaster, gypsy and ZAM, have been found to have infectious properties and have been classified as errantiviruses. Despite numerous studies focusing on retroviral integration process, there is still no clear understanding of integration specificity in a target site. Most LTR retrotransposons non-specifically integrate into a target site. Site-specificity of integration at vertebrate retroviruses is rather relative. At the same time, sequence-specific integration is the exclusive property of errantiviruses and their derivatives with two open reading frames. The possible basis for the errantivirus integration specificity is discussed in the present review.
Collapse
|
4
|
Integration specificity of LTR-retrotransposons and retroviruses in the Drosophila melanogaster genome. Virus Genes 2011; 42:297-306. [PMID: 21369828 DOI: 10.1007/s11262-010-0566-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 12/24/2010] [Indexed: 01/28/2023]
Abstract
Integration of DNA copies in a host genome is a necessary stage in the life cycle of retroviruses and LTR-retrotransposons. There is still no clear understanding of integration specificity of retroelements into a target site. The selection of the target DNA is believed to potentially affect a number of factors such as transcriptional status, association with histones and other DNA-binding proteins, and DNA bending. The authors performed a comprehensive computer analysis of the integration specificity of Drosophila melanogaster LTR-retrotransposons and retroviruses including an analysis of the nucleotide composition of targets, terminal sequences of LTRs, and integrase sequences. A classification of LTR-retrotransposons based on the integration specificity was developed. All the LTR-retrotransposons of the gypsy group with three open frames (errantiviruses) and their derivatives with two open frames demonstrate strict specificity to a target DNA selection. Such specificity correlates with the structural features of the target DNA: bendability, A-philicity, or protein-induced deformability. The remaining LTR-retrotransposons (copia and BEL groups, blastopia and 412 subgroups of the gypsy group) do not show specificity of integration. Chromodomain is present in the integrase structures of blastopia and 412 subgroup LTR-retrotransposons and may facilitate the process of non-specific integration.
Collapse
|
5
|
Malet I, Soulie C, Tchertanov L, Derache A, Amellal B, Traore O, Simon A, Katlama C, Mouscadet JF, Calvez V, Marcelin AG. Structural effects of amino acid variations between B and CRF02-AG HIV-1 integrases. J Med Virol 2008; 80:754-61. [PMID: 18360887 DOI: 10.1002/jmv.21169] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
HIV-1 integrase is one of the three essential enzyme required for viral replication and has a great potential as a novel target for anti-HIV drugs. The sequence variability of the entire integrase (IN) was examined in HIV-1 subtype B and CRF02-AG antiretroviral naïve infected patients for the presence of naturally occurring polymorphisms IN gene sequences and protein structures from both subtypes were compared. The phylogenetic analysis showed a total concordance between the 3 pol gene sequences for patients identified as subtype B whereas 3% of patients identified as CRF02-AG showed a mixture of subtypes. The analysis of IN aa sequences showed that 13 positions (K/R14, V/I31, L/I101, T/V112, T/A124, T/A125, G/N134, I/V135, K/T136, V/I201, T/S206, L/I234, and S/G283) differed between subtypes B and CRF02-AG. As observed in the 3D model of the preintegration complex, these differences may impact the functional property of IN. The fact that most variations were grouped suggests that some of them are linked together through compensatory mechanisms. This comparison allowed us to identify several variations of amino acids in HIV-1 IN subtype CRF02-AG that could have a putative impact on anti-integrase sensitivity. In particular, the region formed by Thr125, Thr124, Val31 contains at least one residue, T125, which variation has been involved in eliciting resistance to the naphtyridine carboxamide L870,810 IN inhibitor. In conclusion, virological response to anti-integrase should be studied carefully, according to the subtype, in clinical trials.
Collapse
|
6
|
Mutations associated with failure of raltegravir treatment affect integrase sensitivity to the inhibitor in vitro. Antimicrob Agents Chemother 2008; 52:1351-8. [PMID: 18227187 DOI: 10.1128/aac.01228-07] [Citation(s) in RCA: 227] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Raltegravir (MK-0518) is a potent inhibitor of human immunodeficiency virus (HIV) integrase and is clinically effective against viruses resistant to other classes of antiretroviral agents. However, it can select mutations in the HIV integrase gene. Nine heavily pretreated patients who received salvage therapy including raltegravir and who subsequently developed virological failure under raltegravir therapy were studied. For each patient, the sequences of the integrase-coding region were determined and compared to that at the beginning of the treatment. Four different mutation profiles were identified in these nine patients: E92Q, G140S Q148H, N155H, and E157Q mutations. For four patients, each harboring a different profile, the wild-type and mutated integrases were produced, purified, and assayed in vitro. All the mutations identified altered the activities of integrase protein: both 3' processing and strand transfer activities were moderately affected in the E92Q mutant; strand transfer was markedly impaired in the N155H mutant; both activities were strongly impaired in the G140S Q148H mutant; and the E157Q mutant was almost completely inactive. The sensitivities of wild-type and mutant integrases to raltegravir were compared. The E92Q and G140S Q148H profiles were each associated with a 7- to 8-fold decrease in sensitivity, and the N155H mutant was more than 14-fold less sensitive to raltegravir. At least four genetic profiles (E92Q, G140S Q148H, N155H, and E157Q) can be associated with in vivo treatment failure and resistance to raltegravir. These mutations led to strong impairment of enzymes in vitro in the absence of raltegravir: strand transfer activity was affected, and in some cases 3' processing was also impaired.
Collapse
|
7
|
Baranova S, Tuzikov FV, Zakharova OD, Tuzikova NA, Calmels C, Litvak S, Tarrago-Litvak L, Parissi V, Nevinsky GA. Small-angle X-ray characterization of the nucleoprotein complexes resulting from DNA-induced oligomerization of HIV-1 integrase. Nucleic Acids Res 2007; 35:975-87. [PMID: 17259219 PMCID: PMC1807944 DOI: 10.1093/nar/gkl1111] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Revised: 11/28/2006] [Accepted: 12/28/2006] [Indexed: 11/12/2022] Open
Abstract
HIV-1 integrase (IN) catalyses integration of a DNA copy of the viral genome into the host genome. Specific interactions between retroviral IN and long terminal repeats (LTR) are required for this insertion. To characterize quantitatively the influence of the determinants of DNA substrate specificity on the oligomerization status of IN, we used the small-angle X-ray scattering (SAXS) technique. Under certain conditions in the absence of ODNs IN existed only as monomers. IN preincubation with specific ODNs led mainly to formation of dimers, the relative amount of which correlated well with the increase in the enzyme activity in the 3'-processing reaction. Under these conditions, tetramers were scarce. Non-specific ODNs stimulated formation of catalytically inactive dimers and tetramers. Complexes of monomeric, dimeric and tetrameric forms of IN with specific and non-specific ODNs had varying radii of gyration (R(g)), suggesting that the specific sequence-dependent formation of IN tetramers can probably occur by dimerization of two dimers of different structure. From our data we can conclude that the DNA-induced oligomerization of HIV-1 IN is probably of importance to provide substrate specificity and to increase the enzyme activity.
Collapse
Affiliation(s)
- Svetlana Baranova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences. Lavrentieva Ave. 8, 630090, Russia; Institute of Catalysis, Siberian Division of Russian Academy of Sciences. Lavrentyeva Ave. 3, 630090, Russia and UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France and IFR 66 Bordeaux, France
| | - Fedor V. Tuzikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences. Lavrentieva Ave. 8, 630090, Russia; Institute of Catalysis, Siberian Division of Russian Academy of Sciences. Lavrentyeva Ave. 3, 630090, Russia and UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France and IFR 66 Bordeaux, France
| | - Olga D. Zakharova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences. Lavrentieva Ave. 8, 630090, Russia; Institute of Catalysis, Siberian Division of Russian Academy of Sciences. Lavrentyeva Ave. 3, 630090, Russia and UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France and IFR 66 Bordeaux, France
| | - Natalia A. Tuzikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences. Lavrentieva Ave. 8, 630090, Russia; Institute of Catalysis, Siberian Division of Russian Academy of Sciences. Lavrentyeva Ave. 3, 630090, Russia and UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France and IFR 66 Bordeaux, France
| | - Christina Calmels
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences. Lavrentieva Ave. 8, 630090, Russia; Institute of Catalysis, Siberian Division of Russian Academy of Sciences. Lavrentyeva Ave. 3, 630090, Russia and UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France and IFR 66 Bordeaux, France
| | - Simon Litvak
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences. Lavrentieva Ave. 8, 630090, Russia; Institute of Catalysis, Siberian Division of Russian Academy of Sciences. Lavrentyeva Ave. 3, 630090, Russia and UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France and IFR 66 Bordeaux, France
| | - Laura Tarrago-Litvak
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences. Lavrentieva Ave. 8, 630090, Russia; Institute of Catalysis, Siberian Division of Russian Academy of Sciences. Lavrentyeva Ave. 3, 630090, Russia and UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France and IFR 66 Bordeaux, France
| | - Vincent Parissi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences. Lavrentieva Ave. 8, 630090, Russia; Institute of Catalysis, Siberian Division of Russian Academy of Sciences. Lavrentyeva Ave. 3, 630090, Russia and UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France and IFR 66 Bordeaux, France
| | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences. Lavrentieva Ave. 8, 630090, Russia; Institute of Catalysis, Siberian Division of Russian Academy of Sciences. Lavrentyeva Ave. 3, 630090, Russia and UMR 5097 CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France and IFR 66 Bordeaux, France
| |
Collapse
|
8
|
Desfarges S, San Filippo J, Fournier M, Calmels C, Caumont-Sarcos A, Litvak S, Sung P, Parissi V. Chromosomal integration of LTR-flanked DNA in yeast expressing HIV-1 integrase: down regulation by RAD51. Nucleic Acids Res 2006; 34:6215-24. [PMID: 17090598 PMCID: PMC1693895 DOI: 10.1093/nar/gkl843] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
HIV-1 integrase (IN) is the key enzyme catalyzing the proviral DNA integration step. Although the enzyme catalyzes the integration step accurately in vitro, whether IN is sufficient for in vivo integration and how it interacts with the cellular machinery remains unclear. We set up a yeast cellular integration system where integrase was expressed as the sole HIV-1 protein and targeted the chromosomes. In this simple eukaryotic model, integrase is necessary and sufficient for the insertion of a DNA containing viral LTRs into the genome, thereby allowing the study of the isolated integration step independently of other viral mechanisms. Furthermore, the yeast system was used to identify cellular mechanisms involved in the integration step and allowed us to show the role of homologous recombination systems. We demonstrated physical interactions between HIV-1 IN and RAD51 protein and showed that HIV-1 integrase activity could be inhibited both in the cell and in vitro by RAD51 protein. Our data allowed the identification of RAD51 as a novel in vitro IN cofactor able to down regulate the activity of this retroviral enzyme, thereby acting as a potential cellular restriction factor to HIV infection.
Collapse
Affiliation(s)
- S. Desfarges
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
| | - J. San Filippo
- Deptartment of Molecular Biophysics and Biochemistry, Yale University School of Medicine333 Cedar Street, SHM C130, New Haven, CT 06520, USA
| | - M. Fournier
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
| | - C. Calmels
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
| | - A. Caumont-Sarcos
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
| | - S. Litvak
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
| | - P. Sung
- Deptartment of Molecular Biophysics and Biochemistry, Yale University School of Medicine333 Cedar Street, SHM C130, New Haven, CT 06520, USA
| | - V. Parissi
- UMR 5097-CNRS, BordeauxFrance
- Université Victor Segalen Bordeaux 2, BordeauxFrance
- IFR 66 ‘Pathologies Infectieuses et Cancers’, BordeauxFrance
- 146 rue Léo Saignat, 33076 Bordeaux cedexFrance
- To whom correspondence should be addressed. Tel: +33 5 57 57 1740; Fax: +33 5 57 57 1766;
| |
Collapse
|
9
|
Diamond TL, Bushman FD. Division of labor within human immunodeficiency virus integrase complexes: determinants of catalysis and target DNA capture. J Virol 2006; 79:15376-87. [PMID: 16306609 PMCID: PMC1316026 DOI: 10.1128/jvi.79.24.15376-15387.2005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Following the completion of reverse transcription, the human immunodeficiency virus integrase (IN) enzyme covalently links the viral cDNA to a host cell chromosome. An IN multimer carries out this reaction, but the roles of individual monomers within the complex are mostly unknown. Here we analyzed the distribution of functions for target DNA capture and catalysis within the IN multimer. We used forced complementation between pairs of IN deletion derivatives in vitro as a tool for probing cis-trans relationships and analyzed amino acid substitutions affecting either catalysis or target site selection within these complementing complexes. This allowed the demonstration that the IN variant contributing the active catalytic domain was also responsible for recognition of the integration target DNA. We were further able to establish that a single monomer is responsible for both functions by use of assay mixtures containing three different IN genotypes. These data specify the ligands bound at the catalytically relevant IN monomer and allow more-specific modeling of the mechanism of inhibitors that also bind this surface of IN.
Collapse
Affiliation(s)
- Tracy L Diamond
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA
| | | |
Collapse
|
10
|
Zhu HM, Chen WZ, Wang CX. Docking dinucleotides to HIV-1 integrase carboxyl-terminal domain to find possible DNA binding sites. Bioorg Med Chem Lett 2005; 15:475-7. [PMID: 15603976 DOI: 10.1016/j.bmcl.2004.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2004] [Revised: 10/02/2004] [Accepted: 10/04/2004] [Indexed: 11/17/2022]
Abstract
HIV-1 integrase mediates a processed viral DNA into the host genome DNA. The binding modes between HIV-1 integrase and viral/host DNA have not been clarified until now. The C-terminal domain of integrase has been found to be a DNA-binding domain. In this work, we have explored the possible DNA binding sites of dimeric C-terminal domain by docking dinucleotides to HIV-1 integrase. The docking results suggest that two symmetrical DNA-binding sites are likely located on the outside surface of the dimeric C-terminal domain and not located in the groove. Those sites are in agreement with the experimental data.
Collapse
Affiliation(s)
- Hai Mei Zhu
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
| | | | | |
Collapse
|
11
|
Grandgenett DP. Symmetrical recognition of cellular DNA target sequences during retroviral integration. Proc Natl Acad Sci U S A 2005; 102:5903-4. [PMID: 15840713 PMCID: PMC1087955 DOI: 10.1073/pnas.0502045102] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Duane P Grandgenett
- Institute for Molecular Virology, Saint Louis University Health Sciences Center, St. Louis, MO 63110, USA.
| |
Collapse
|
12
|
Lewinski MK, Bushman FD. Retroviral DNA integration--mechanism and consequences. ADVANCES IN GENETICS 2005; 55:147-81. [PMID: 16291214 DOI: 10.1016/s0065-2660(05)55005-3] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Integration of retroviral cDNA into the host cell chromosome is an essential step in its replication. This process is catalyzed by the retroviral integrase protein, which is conserved among retroviruses and retrotransposons. Integrase binds viral and host DNA in a complex, called the preintegration complex (PIC), with other viral and cellular proteins. While the PIC is capable of directing integration of the viral DNA into any chromosomal location, different retroviruses have clear preferences for integration in or near particular chromosomal features. The determinants of integration site selection are under investigation but may include retrovirus-specific interactions between integrase and tethering factors bound to the host cell chromosomes. Research into the mechanisms of retroviral integration site selection has shed light on the phenomena of insertional mutagenesis and viral latency.
Collapse
Affiliation(s)
- Mary K Lewinski
- Infectious Disease Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92186, USA
| | | |
Collapse
|
13
|
Ikeda T, Nishitsuji H, Zhou X, Nara N, Ohashi T, Kannagi M, Masuda T. Evaluation of the functional involvement of human immunodeficiency virus type 1 integrase in nuclear import of viral cDNA during acute infection. J Virol 2004; 78:11563-73. [PMID: 15479797 PMCID: PMC523288 DOI: 10.1128/jvi.78.21.11563-11573.2004] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nuclear import of viral cDNA is a critical step for establishing the proviral state of human immunodeficiency virus type 1 (HIV-1). The contribution of HIV-1 integrase (IN) to the nuclear import of viral cDNA is controversial, partly due to a lack of identification of its bona fide nuclear localization signal. In this study, to address this putative function of HIV-1 IN, the effects of mutations at key residues for viral cDNA recognition (PYNP at positions 142 to 145, K156, K159, and K160) were evaluated in the context of viral replication. During acute infection, some mutations (N144Q, PYNP>KL, and KKK>AAA) severely reduced viral gene expression to less than 1% the wild-type (WT) level. None of the mutations affected the synthesis of viral cDNA. Meanwhile, the levels of integrated viral cDNA produced by N144Q, PYNP>KL, and KKK>AAA mutants were severely reduced to less than 1% the WT level. Quantitative PCR analysis of viral cDNA in nuclei and fluorescence in situ hybridization analysis showed that these mutations significantly reduced the level of viral cDNA accumulation in nuclei. Further analysis revealed that IN proteins carrying the N144Q, PYNP>KL, and KKK>AAA mutations showed severely reduced binding to viral cDNA but kept their karyophilic properties. Taken together, these results indicate that mutations that reduced the binding of IN to viral cDNA resulted in severe impairment of virus infectivity, most likely by affecting the nuclear import of viral cDNA that proceeds integration. These results suggest that HIV-1 IN may be one of the critical constituents for the efficient nuclear import of viral cDNA.
Collapse
Affiliation(s)
- Tamako Ikeda
- Department of Immunotherapeutics, Graduate School of Medicine and Dentistry, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | | | | | | | | | | | | |
Collapse
|
14
|
Parveen Z, Mukhtar M, Goodrich A, Acheampong E, Dornburg R, Pomerantz RJ. Cross-packaging of human immunodeficiency virus type 1 vector RNA by spleen necrosis virus proteins: construction of a new generation of spleen necrosis virus-derived retroviral vectors. J Virol 2004; 78:6480-8. [PMID: 15163741 PMCID: PMC416548 DOI: 10.1128/jvi.78.12.6480-6488.2004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The ability of the nonlentiviral retrovirus spleen necrosis virus (SNV) to cross-package the genomic RNA of the distantly related human immunodeficiency virus type 1 (HIV-1) and vice versa was analyzed. Such a model may allow us to further study HIV-1 replication and pathogenesis, as well as to develop safe gene therapy vectors. Our results suggest that SNV can cross-package HIV-1 genomic RNA but with lower efficiency than HIV-1 proteins. However, HIV-1-specific proteins were unable to cross-package SNV RNA. We also constructed SNV-based gag-pol chimeric variants by replacing the SNV integrase with the HIV-1 integrase, based on multiple sequence alignments and domain analyses. These analyses revealed that there are conserved domains in all retroviral integrase open reading frames (orf), despite the divergence in the primary sequences. The transcomplementation assays suggested that SNV proteins recognized one of the chimeric variants. This demonstrated that HIV-1 integrase is functional in the SNV gag-pol orf with a lower transduction efficiency, utilizing homologous (SNV) RNA, as well as the heterologous vector RNA of HIV-1. These findings suggest that homology in the conserved sequences of the integrase protein may not be fully competent in the replacement of protein(s) from one retrovirus to another, and there are likely several other factors involved in each of the steps related to replication, integration, and infection. However, further studies to dissect the gag-pol region will be critical for understanding the mechanisms involved in the cleavage of reverse transcriptase, RNase H, and integrase. These studies should provide further insight into the design and development of novel molecular approaches to block HIV-1 replication and to construct a new generation of SNV-based vectors.
Collapse
Affiliation(s)
- Zahida Parveen
- Dorrance H. Hamilton Laboratories, Center for Human Virology and Biodefense, Department of Medicine, Jefferson Medical College, Thomas Jefferson University, 1020 Locust St., Ste. 329, Philadelphia, PA 19107, USA.
| | | | | | | | | | | |
Collapse
|
15
|
Calmels C, de Soultrait VR, Caumont A, Desjobert C, Faure A, Fournier M, Tarrago-Litvak L, Parissi V. Biochemical and random mutagenesis analysis of the region carrying the catalytic E152 amino acid of HIV-1 integrase. Nucleic Acids Res 2004; 32:1527-38. [PMID: 14999095 PMCID: PMC390286 DOI: 10.1093/nar/gkh298] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
HIV-1 integrase (IN) catalyzes the integration of the proviral DNA into the cellular genome. The catalytic triad D64, D116 and E152 of HIV-1 IN is involved in the reaction mechanism and the DNA binding. Since the integration and substrate binding processes are not yet exactly known, we studied the role of amino acids localized in the catalytic site. We focused our interest on the V151E152S153 region. We generated random mutations inside this domain and selected mutated active INs by using the IN-induced yeast lethality assay. In vitro analysis of the selected enzymes showed that the IN nuclease activities (specific 3'-processing and non-sequence-specific endonuclease), the integration and disintegration reactions and the binding of the various DNA substrates were affected differently. Our results support the hypothesis that the three reactions may involve different DNA binding sites, enzyme conformations or mechanisms. We also show that the V151E152S153 region involvement in the integration reaction is more important than for the 3'-processing activity and can be involved in the recognition of DNA. The IN mutants may lead to the development of new tools for studying the integration reaction, and could serve as the basis for the discovery of integration-specific inhibitors.
Collapse
Affiliation(s)
- C Calmels
- UMR-5097, CNRS-Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, and IFR 66 Pathologies Infectieuses et Cancers, Bordeaux, France
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Harper AL, Sudol M, Katzman M. An amino acid in the central catalytic domain of three retroviral integrases that affects target site selection in nonviral DNA. J Virol 2003; 77:3838-45. [PMID: 12610159 PMCID: PMC149511 DOI: 10.1128/jvi.77.6.3838-3845.2003] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrase can insert retroviral DNA into almost any site in cellular DNA; however, target site preferences are noted in vitro and in vivo. We recently demonstrated that amino acid 119, in the alpha2 helix of the central domain of the human immunodeficiency virus type 1 integrase, affected the choice of nonviral target DNA sites. We have now extended these findings to the integrases of a nonprimate lentivirus and a more distantly related alpharetrovirus. We found that substitutions at the analogous positions in visna virus integrase and Rous sarcoma virus integrase changed the target site preferences in five assays that monitor insertion into nonviral DNA. Thus, the importance of this protein residue in the selection of nonviral target DNA sites is likely to be a general property of retroviral integrases. Moreover, this amino acid might be part of the cellular DNA binding site on integrase proteins.
Collapse
Affiliation(s)
- Amy L Harper
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, The Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033, USA
| | | | | |
Collapse
|
17
|
Appa RS, Shin CG, Lee P, Chow SA. Role of the nonspecific DNA-binding region and alpha helices within the core domain of retroviral integrase in selecting target DNA sites for integration. J Biol Chem 2001; 276:45848-55. [PMID: 11585830 DOI: 10.1074/jbc.m107365200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Retroviral integrase plays an important role in choosing host chromosomal sites for integration of the cDNA copy of the viral genome. The domain responsible for target site selection has been previously mapped to the central core of the protein (amino acid residues 49-238). Chimeric integrases between human immunodeficiency virus type 1 (HIV-1) and feline immunodeficiency virus (FIV) were prepared to examine the involvement of a nonspecific DNA-binding region (residues 213-266) and certain alpha helices within the core domain in target site selection. Determination of the distribution and frequency of integration events of the chimeric integrases narrowed the target site-specifying motif to within residues 49-187 and showed that alpha 3 and alpha 4 helices (residues 123-166) were not involved in target site selection. Furthermore, the chimera with the alpha 2 helix (residues 118-121) of FIV identity displayed characteristic integration events from both HIV-1 and FIV integrases. The results indicate that the alpha 2 helix plays a role in target site preference as either part of a larger or multiple target site-specifying motif.
Collapse
Affiliation(s)
- R S Appa
- Department of Molecular and Medical Pharmacology, Molecular Biology Institute, and UCLA AIDS Institute, UCLA School of Medicine, Los Angeles, California 90095, USA
| | | | | | | |
Collapse
|
18
|
Yang F, Roth MJ. Assembly and catalysis of concerted two-end integration events by Moloney murine leukemia virus integrase. J Virol 2001; 75:9561-70. [PMID: 11559787 PMCID: PMC114526 DOI: 10.1128/jvi.75.20.9561-9570.2001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Retroviral integration results in the stable and coordinated insertion of the two termini of the linear viral DNA into the host genome. An in vitro concerted two-end integration reaction catalyzed by the Moloney murine leukemia virus (M-MuLV) integrase (IN) was used to investigate the binding and coordination of the two viral DNA ends. Comparison of the two-end integration and strand transfer assays indicates that zinc is required for efficient concerted integration utilizing plasmid DNA as target. Complementation assays using a pair of nonoverlapping integrase domains, consisting of the HHCC domain and the core/C-terminal region, yielded products containing the correct 4-base target site duplication. The efficiency of the coordinated two-end integration varied depending on the order of addition of the individual protein and DNA components in the complementation assay. Two-end integration was most efficient when the long terminal repeat (LTR) was premixed with either the target DNA or the HHCC domain. The preference for two-end integration through preincubation of the HHCC finger with the viral DNA supports the role of this domain in the recognition and/or positioning of the LTR.
Collapse
Affiliation(s)
- F Yang
- Department of Biochemistry, University of Medicine and Dentistry of New Jersey-- Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
| | | |
Collapse
|
19
|
Harper AL, Skinner LM, Sudol M, Katzman M. Use of patient-derived human immunodeficiency virus type 1 integrases to identify a protein residue that affects target site selection. J Virol 2001; 75:7756-62. [PMID: 11462051 PMCID: PMC115014 DOI: 10.1128/jvi.75.16.7756-7762.2001] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To identify parts of retroviral integrase that interact with cellular DNA, we tested patient-derived human immunodeficiency virus type 1 (HIV-1) integrases for alterations in the choice of nonviral target DNA sites. This strategy took advantage of the genetic diversity of HIV-1, which provided 75 integrase variants that differed by a small number of amino acids. Moreover, our hypothesis that biological pressures on the choice of nonviral sites would be minimal was validated when most of the proteins that catalyzed DNA joining exhibited altered target site preferences. Comparison of the sequences of proteins with the same preferences then guided mutagenesis of a laboratory integrase. The results showed that single amino acid substitutions at one particular residue yielded the same target site patterns as naturally occurring integrases that included these substitutions. Similar results were found with DNA joining reactions conducted with Mn(2+) or with Mg(2+) and were confirmed with a nonspecific alcoholysis assay. Other amino acid changes at this position also affected target site preferences. Thus, this novel approach has identified a residue in the central domain of HIV-1 integrase that interacts with or influences interactions with cellular DNA. The data also support a model in which integrase has distinct sites for viral and cellular DNA.
Collapse
Affiliation(s)
- A L Harper
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, The Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033, USA
| | | | | | | |
Collapse
|
20
|
Holmes-Son ML, Appa RS, Chow SA. Molecular genetics and target site specificity of retroviral integration. ADVANCES IN GENETICS 2001; 43:33-69. [PMID: 11037298 DOI: 10.1016/s0065-2660(01)43003-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Integration is an essential step in the life cycle of retroviruses, resulting in the stable joining of the viral cDNA to the host cell chromosomes. While this critical process makes retroviruses an attractive vector for gene delivery, it also presents a potential hazard. The sites where integration occurs are nonspecific. Therefore,it is possible that integration of retroviral DNA will affect host gene expression and disrupt normal cellular functions. The mechanism by which integration sites are chosen is not well understood, and is influenced by several factors, including DNA sequence and structure, DNA-binding proteins, DNA methylation, and transcription. Integrase, the viral enzyme responsible for catalyzing integration, also plays a key role in controlling the choice of target sites. The integrase domain responsible for target site selection has been mapped to the central core region. A better understanding of the interaction between the target-specifying motif of integrase and the target DNA may allow a means to manipulate integration into particular chromosomal sites. Another approach to directing integration is to fuse integrase with a sequence-specific DNA-binding protein, which results in a bias of integration in vitro into the recognition site of the fusion partner. Successful incorporation of the fusion protein into infectious virions and the identification of optimal proteins that can be fused to integrase will advance the development of site-specific vectors. Retroviruses are promising for the delivery of genes in experimental and therapeutic protocols. A better understanding of integration will aid in the design of safer and more effective gene transfer vectors.
Collapse
Affiliation(s)
- M L Holmes-Son
- Department of Molecular and Medical Pharmacology, UCLA AIDS Institute and Molecular Biology Institute, UCLA School of Medicine, Los Angeles, California 90095, USA
| | | | | |
Collapse
|
21
|
Dirac AM, Kjems J. Mapping DNA-binding sites of HIV-1 integrase by protein footprinting. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:743-51. [PMID: 11168414 DOI: 10.1046/j.1432-1327.2001.01932.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The HIV-1 integrase protein catalyzes integration of the viral genome into host cell DNA. Whereas the structures of the three domains of integrase have been solved separately, both the structural organization of the full-length protein and its interaction with DNA remain unresolved. A protein footprinting approach was employed to investigate the accessibility of residues in the full-length soluble integrase mutant, INF(185K,C280S), to proteolytic attack in the absence and presence of DNA. The N-terminal and C-terminal domains were relatively more accessible to proteolytic attack than the core domain. The susceptibility to proteolytic attack was specifically affected by DNA at residues Lys34, in the N-terminal domain, Lys111, Lys136, Glu138, Lys156-Lys160, Lys185-Lys188, in the core domain, and Asp207, Lys 215, Glu246, Lys258 and Lys273 in the linker and C-terminal domain, suggesting that these regions are involved in, or shielded by, DNA binding. Lys34 is positioned in a putative dimerization domain, consistent with the notion that DNA stabilizes the dimeric state of integrase.
Collapse
Affiliation(s)
- A M Dirac
- Department of Molecular and Structural Biology, Aarhus University, Denmark
| | | |
Collapse
|
22
|
Skinner LM, Sudol M, Harper AL, Katzman M. Nucleophile selection for the endonuclease activities of human, ovine, and avian retroviral integrases. J Biol Chem 2001; 276:114-24. [PMID: 11024025 DOI: 10.1074/jbc.m007032200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Retroviral integrases catalyze four endonuclease reactions (processing, joining, disintegration, and nonspecific alcoholysis) that differ in specificity for the attacking nucleophile and target DNA sites. To assess how the two substrates of this enzyme affect each other, we performed quantitative analyses, in three retroviral systems, of the two reactions that use a variety of nucleophiles. The integrase proteins of human immuno- deficiency virus type 1, visna virus, and Rous sarcoma virus exhibited distinct preferences for water or other nucleophiles during site-specific processing of viral DNA and during nonspecific alcoholysis of nonviral DNA. Although exogenous alcohols competed with water as the nucleophile for processing, the alcohols stimulated nicking of nonviral DNA. Moreover, different nucleophiles were preferred when the various integrases acted on different DNA targets. In contrast, the nicking patterns were independent of whether integrase was catalyzing hydrolysis or alcoholysis and were not influenced by the particular exogenous alcohol. Thus, although the target DNA influenced the choice of nucleophile, the nucleophile did not affect the choice of target sites. These results indicate that interaction with target DNA is the critical step before catalysis and suggest that integrase does not reach an active conformation until target DNA has bound to the enzyme.
Collapse
Affiliation(s)
- L M Skinner
- Department of Medicine, Pennsylvania State University College of Medicine, The Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033, USA
| | | | | | | |
Collapse
|
23
|
Berger N, Heller AE, Störmann KD, Pfaff E. Characterization of chimeric enzymes between caprine arthritis--encephalitis virus, maedi--visna virus and human immunodeficiency virus type 1 integrases expressed in Escherichia coli. J Gen Virol 2001; 82:139-148. [PMID: 11125167 DOI: 10.1099/0022-1317-82-1-139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In order to investigate the functions of the three putative lentiviral integrase (IN) protein domains on viral DNA specificity and target site selection, enzymatically active chimeric enzymes were constructed using the three wild-type IN proteins of caprine arthritis-encephalitis virus (CAEV), maedi-visna virus (MVV) and human immunodeficiency virus type 1 (HIV-1). The chimeric enzymes were expressed in Escherichia coli, purified by affinity chromatography and analysed in vitro for IN-specific endonuclease and integration activities on various DNA substrates. Of the 21 purified chimeric IN proteins constructed, 20 showed distinct site-specific cleavage activity with at least one substrate and six were able to catalyse an efficient integration reaction. Analysis of the chimeric IN proteins revealed that the central domain together with the C terminus determines the activity and substrate specificity of the enzyme. The N terminus appears to have no considerable influence. Furthermore, an efficient integration activity of CAEV wild-type IN was successfully demonstrated after detailed characterization of the reaction conditions that support optimal enzyme activities of CAEV IN. Also, under the same in vitro assay conditions, MVV and HIV-1 IN proteins exhibited endonuclease and integration activities, an indispensable prerequisite of domain-swapping experiments. Thus, the following report presents a detailed characterization of the activities of CAEV IN in vitro as well as the analysis of functional chimeric lentiviral IN proteins.
Collapse
Affiliation(s)
- Nicola Berger
- Federal Research Centre for Virus Diseases of Animals, Institute for Immunology, Paul-Ehrlich-Strasse 28, D-72076 Tübingen, Germany1
| | - Astrid E Heller
- Federal Research Centre for Virus Diseases of Animals, Institute for Immunology, Paul-Ehrlich-Strasse 28, D-72076 Tübingen, Germany1
| | - Klaus D Störmann
- Federal Research Centre for Virus Diseases of Animals, Institute for Immunology, Paul-Ehrlich-Strasse 28, D-72076 Tübingen, Germany1
| | - Eberhard Pfaff
- Federal Research Centre for Virus Diseases of Animals, Institute for Immunology, Paul-Ehrlich-Strasse 28, D-72076 Tübingen, Germany1
| |
Collapse
|
24
|
Morgan AL, Katzman M. Subterminal viral DNA nucleotides as specific recognition signals for human immunodeficiency virus type 1 and visna virus integrases under magnesium-dependent conditions. J Gen Virol 2000; 81:839-49. [PMID: 10675422 DOI: 10.1099/0022-1317-81-3-839] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many reports describe the characteristics of susceptible viral DNA substrates to various retroviral integrases during in vitro reactions in which manganese serves as the divalent cation cofactor for site-specific nicking. However, manganese is known to alter the specificity of some endonucleases and magnesium may be the divalent cation used during retroviral integration in vivo. To address these concerns, we identified conditions under which the integrases of human immunodeficiency virus type 1 and visna virus were optimally active with magnesium (the first time such activity was shown for visna virus integrase) and used these conditions to test the susceptibility of a series of oligodeoxynucleotide substrates. The data show that two base pairs immediately internal to the conserved CA dinucleotide near the termini of retroviral DNA are selectively recognized by the two integrases and that the final six base pairs of viral DNA contain sufficient sequence information for specific recognition and cleavage by each enzyme. The results validate the importance of the subterminal viral DNA positions even in the presence of magnesium and identify viral DNA positions that functionally interact with integrase. The data obtained under magnesium-dependent conditions, which were obtained with substrates containing single and multiple base-pair substitutions and two different retroviral integrases, are consistent with those previously obtained with manganese. Thus, the large body of manganese-dependent data identifying terminal viral DNA positions that are important in substrate recognition by various integrases likely reflects interactions that are biologically relevant.
Collapse
Affiliation(s)
- A L Morgan
- Department of Microbiology, The Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, PA 17033-0850, USA
| | | |
Collapse
|
25
|
Katzman M, Sudol M, Pufnock JS, Zeto S, Skinner LM. Mapping target site selection for the non-specific nuclease activities of retroviral integrase. Virus Res 2000; 66:87-100. [PMID: 10653920 DOI: 10.1016/s0168-1702(99)00126-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To identify the parts of retroviral integrase that interact with its DNA substrates, we compared the patterns of target site usage by chimeric enzymes and protein fragments in assays that reveal integrase's non-specific nuclease activities. The central region of 12 chimeric proteins between the human immunodeficiency virus type 1 and visna virus integrases was found to be responsible for selecting non-viral target DNA sites when small alcohols provide the attacking nucleophilic OH group during non-specific alcoholysis assays. Testing deletion derivatives of the integrase protein in this assay, which has similarities to the DNA joining reaction that occurs during retroviral integration, defined a smaller central domain that is sufficient for activity. Thus, this core domain likely contains both the host DNA site and the nucleophile site. Surprisingly, the region of integrase responsible for selecting non-viral target DNA sites when the viral DNA end is the attacking nucleophile could not similarly be mapped with the standard oligonucleotide joining assay. We therefore tested the proteins in a more sensitive assay that displays preferred sites of viral DNA insertion in a plasmid DNA target. All 12 chimeras yielded novel patterns compared with the wild-type enzymes in this assay, although local insertion patterns indicated that the central domain plays an important role in target site selection. Together, these data suggest that other protein regions must be involved when the attacking nucleophilic group is provided by viral DNA. Because specific recognition of viral DNA ends was previously mapped to the central domain, two different regions of integrase must interact with retroviral DNA.
Collapse
Affiliation(s)
- M Katzman
- Department of Medicine, Section of Infectious Diseases, Pennsylvania State University College of Medicine, The Milton S. Hershey Medical Center, 500 University Drive, Mail Services H036, Hershey, PA 17033-2390, USA.
| | | | | | | | | |
Collapse
|
26
|
Abstract
DNA integration is a unique enzymatic process shared by all retroviruses and retrotransposons. During integration, double-stranded linear viral DNA is inserted into the host genome in a process catalyzed by the virus-encoded integrase (IN). The mechanism involves a series of nucleophilic attacks, the first of which removes the terminal 2 bases from the 3' ends of the long terminal repeats and of the second which inserts the viral DNA into the host genome. IN specifically recognizes the DNA sequences at the termini of the viral DNA, juxtaposing both ends in an enzyme complex that inserts the viral DNA into a single site in a concerted manner. Small duplications of the host DNA, characteristic of the viral IN, are found at the sites of insertion. At least two host proteins, HMG-I(Y) and BAF, have been shown to increase the efficiency of the integration reaction.
Collapse
Affiliation(s)
- P Hindmarsh
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | | |
Collapse
|
27
|
Eijkelenboom AP, Sprangers R, Hård K, Puras Lutzke RA, Plasterk RH, Boelens R, Kaptein R. Refined solution structure of the C-terminal DNA-binding domain of human immunovirus-1 integrase. Proteins 1999; 36:556-64. [PMID: 10450096 DOI: 10.1002/(sici)1097-0134(19990901)36:4<556::aid-prot18>3.0.co;2-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The structure of the C-terminal DNA-binding domain of human immunovirus-1 integrase has been refined using nuclear magnetic resonance spectroscopy. The protein is a dimer in solution and shows a well-defined dimer interface. The folding topology of the monomer consists of a five-stranded beta-barrel that resembles that of Src homology 3 domains. Compared with our previously reported structure, the structure is now defined far better. The final 42 structures display a back-bone root mean square deviation versus the average of 0.46 A. Correlation of the structure with recent mutagenesis studies suggests two possible models for DNA binding. Proteins 1999;36:556-564.
Collapse
Affiliation(s)
- A P Eijkelenboom
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
28
|
Abstract
Substrate recognition by the retroviral IN enzyme is critical for retroviral integration. To catalyze this recombination event, IN must recognize and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity. Although particular sequences at the viral DNA termini are recognized by IN, many host DNA sequences can serve as the target for integration. Over the last decade, both in vitro and in vivo data have contributed to our understanding of how IN recognizes its substrates. This review provides an overview of the sequence and structure requirements for recognition of viral and host DNA by different retroviral INs and discusses recent progress in mapping protein domains involved in these interactions.
Collapse
Affiliation(s)
- M Katzman
- Department of Medicine, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey 17033-0850, USA
| | | |
Collapse
|
29
|
Abstract
Integration of the viral DNA into a host cell chromosome is an essential step for HIV replication and maintenance of persistent infection. Two viral factors are essential for integration: the viral DNA termini (the att sites) and IN. Accruing knowledge of the IN structure, catalytic mechanisms, and interactions with other proteins can be used to design strategies to block integration. A large number of inhibitors have been identified that can be used as leads for the development of potent and selective anti-IN drugs with antiviral activity.
Collapse
Affiliation(s)
- Y Pommier
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland 20892-4255, USA
| | | |
Collapse
|
30
|
Yi J, Asante-Appiah E, Skalka AM. Divalent cations stimulate preferential recognition of a viral DNA end by HIV-1 integrase. Biochemistry 1999; 38:8458-68. [PMID: 10387092 DOI: 10.1021/bi982870n] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the presence of a divalent metal cofactor (Mg2+ or Mn2+), retroviral-encoded integrase (IN) catalyzes two distinct reactions: site-specific cleavage of two nucleotides from both 3' ends of viral DNA, and sequence-independent joining of the recessed viral ends to staggered phosphates in a target DNA. Here we investigate human immunodeficiency virus type 1 (HIV-1) IN-DNA interactions using surface plasmon resonance. The results show that IN forms tight complexes both with duplex oligonucleotides that represent the viral DNA ends and with duplex oligonucleotides with an unrelated sequence that represent a target DNA substrate. The IN-DNA complexes are stable in 4.0 M NaCl, or 50% (v/v) methanol, but they are not resistant to low concentrations of SDS, indicating that their stability is highly dependent on structural features of the protein. Divalent metal cofactors exert two distinct effects on the IN-DNA interaction. Mn2+ inhibits IN binding to a model target DNA with the apparent Kd increasing approximately 3-fold in the presence of this cation. On the other hand, Mn2+ (or Mg2+) stimulates the binding of IN to a model viral DNA end, decreasing the apparent Kd of this IN-viral DNA complex approximately 6-fold. Such metal-mediated stimulation of the binding of IN to the viral DNA is totally abolished by substitution of the subterminal conserved CA/GT bp with a GT/CA bp, and is greatly diminished when the viral DNA end is recessed or "pre-processed." IN binds to a viral duplex oligonucleotide whose end was extended with nonviral sequences with kinetics similar to the nonviral model target DNA. This suggests that IN can distinguish the integrated DNA product from the viral donor DNA in the presence of divalent metal ion. Thus, our results show that preferential recognition of viral DNA by HIV-1 IN is achieved only in the presence of metal cofactor, and requires a free, wild-type viral DNA end.
Collapse
Affiliation(s)
- J Yi
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | | | | |
Collapse
|
31
|
van den Ent FM, Vos A, Plasterk RH. Dissecting the role of the N-terminal domain of human immunodeficiency virus integrase by trans-complementation analysis. J Virol 1999; 73:3176-83. [PMID: 10074170 PMCID: PMC104080 DOI: 10.1128/jvi.73.4.3176-3183.1999] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus (HIV) integrase protein (IN) catalyzes two reactions required to integrate HIV DNA into the human genome: 3' processing of the viral DNA ends and integration. IN has three domains, the N-terminal zinc-binding domain, the catalytic core, and the C-terminal SH3 domain. Previously, it was shown that IN proteins mutated in different domains could complement each other. We now report that this does not require any overlap between the two complementing proteins; an N-terminal domain, provided in trans, can restore IN activity of a mutant lacking this domain. Only the zinc-coordinating form of the N-terminal domain can efficiently restore IN activity of an N-terminal deletion mutant. This suggests that interaction between different domains of IN is needed for functional multimerization. We find that the N-terminal domain of feline immunodeficiency virus IN can support IN activity of an N-terminal deletion mutant of HIV type 2 IN. These cross-complementation experiments indicate that the N-terminal domain contributes to the recognition of specific viral DNA ends.
Collapse
Affiliation(s)
- F M van den Ent
- Division of Molecular Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | | | | |
Collapse
|
32
|
Esposito D, Craigie R. Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction. EMBO J 1998; 17:5832-43. [PMID: 9755183 PMCID: PMC1170911 DOI: 10.1093/emboj/17.19.5832] [Citation(s) in RCA: 233] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 integrase specifically recognizes and cleaves viral end DNA during the initial step of retroviral integration. The protein and DNA determinants of the specificity of viral end DNA binding have not been clearly identified. We have used mutational analysis of the viral end LTR sequence, in vitro selection of optimal viral end sequences, and specific photocrosslinking to identify regions of integrase that interact with specific bases in the LTR termini. The results highlight the involvement of the disordered loop of the integrase core domain, specifically residues Q148 and Y143, in binding to the terminal portion of the viral DNA ends. Additionally, we have identified positions upstream in the LTR termini which interact with the C-terminal domain of integrase, providing evidence for the role of that domain in stabilization of viral DNA binding. Finally, we have located a region centered 12 bases from the viral DNA terminus which appears essential for viral end DNA binding in the presence of magnesium, but not in the presence of manganese, suggesting a differential effect of divalent cations on sequence-specific binding. These results help to define important regions of contact between integrase and viral DNA, and assist in the formulation of a molecular model of this vital interaction.
Collapse
Affiliation(s)
- D Esposito
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, 5 Center Drive MSC0560, Bethesda, MD 20892, USA
| | | |
Collapse
|