Structural insights into the retroviral DNA integration apparatus.

Retroviral replication depends on successful integration of the viral genetic material into a host cell chromosome. Virally encoded integrase, an enzyme from the DDE(D) nucleotidyltransferase superfamily, is responsible for the key DNA cutting and joining steps associated with this process. Insights into the structural and mechanistic aspects of integration are directly relevant for the development of antiretroviral drugs. Recent breakthroughs have led to biochemical and structural characterization of the principal integration intermediates revealing the tetramer of integrase that catalyzes insertion of both 3' viral DNA ends into a sharply bent target DNA. This review discusses the mechanism of retroviral DNA integration and the mode of action of HIV-1 integrase strand transfer inhibitors in light of the recent visualization of the prototype foamy virus intasome, target DNA capture and strand transfer complexes.

[1]  A. Engelman,et al.  Retroviral intasome assembly and inhibition of DNA strand transfer , 2010, Nature.

[2]  M. Sudoł,et al.  A Substitution in Rous Sarcoma Virus Integrase That Separates Its Two Biologically Relevant Enzymatic Activities , 2005, Journal of Virology.

[3]  H. Varmus,et al.  Retroviral integration into minichromosomes in vitro. , 1992, The EMBO journal.

[4]  John M. Coffin,et al.  Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[5]  F. Bushman,et al.  Identification of discrete functional domains of HIV‐1 integrase and their organization within an active multimeric complex. , 1993, The EMBO journal.

[6]  F. Bushman,et al.  Human immunodeficiency virus type 1 preintegration complexes: studies of organization and composition , 1997, Journal of virology.

[7]  M. Sudoł,et al.  An Amino Acid in the Central Catalytic Domain of Three Retroviral Integrases That Affects Target Site Selection in Nonviral DNA , 2003, Journal of Virology.

[8]  Wei Yang,et al.  Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis , 2005, Cell.

[9]  David V Schaffer,et al.  Specific insertions of zinc finger domains into Gag-Pol yield engineered retroviral vectors with selective integration properties , 2010, Proceedings of the National Academy of Sciences.

[10]  W. Reznikoff,et al.  Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. , 2000, Science.

[11]  A. Skalka,et al.  Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases , 1992, Molecular and cellular biology.

[12]  A. Engelman,et al.  Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. , 1994, Science.

[13]  S. Burgess,et al.  Weak Palindromic Consensus Sequences Are a Common Feature Found at the Integration Target Sites of Many Retroviruses , 2005, Journal of Virology.

[14]  J. Leis,et al.  HIV-1 Integrase Interaction with U3 and U5 Terminal Sequences in Vitro Defined Using Substrates with Random Sequences* 210 , 2002, The Journal of Biological Chemistry.

[15]  Sridhar Hannenhalli,et al.  Selection of Target Sites for Mobile DNA Integration in the Human Genome , 2006, PLoS Comput. Biol..

[16]  D. Hazuda,et al.  Inhibition of Human Immunodeficiency Virus Type 1 Concerted Integration by Strand Transfer Inhibitors Which Recognize a Transient Structural Intermediate , 2007, Journal of Virology.

[17]  P. Tauc,et al.  Oligomeric states of the HIV-1 integrase as measured by time-resolved fluorescence anisotropy. , 2000, Biochemistry.

[18]  Fred Dyda,et al.  Integrating prokaryotes and eukaryotes: DNA transposases in light of structure , 2010, Critical reviews in biochemistry and molecular biology.

[19]  J A Grobler,et al.  Inhibitors of strand transfer that prevent integration and inhibit HIV-1 replication in cells. , 2000, Science.

[20]  P. Cherepanov,et al.  The Interaction Between Lentiviral Integrase and LEDGF: Structural and Functional Insights , 2009, Viruses.

[21]  Jae Young Lee,et al.  Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. , 2006, Molecular cell.

[22]  G. Gottlieb,et al.  Susceptibility of the human retrovirus XMRV to antiretroviral inhibitors , 2010, Retrovirology.

[23]  A. Engelman,et al.  Structural Basis for Functional Tetramerization of Lentiviral Integrase , 2009, PLoS pathogens.

[24]  E. Dimitriadis,et al.  Nucleoprotein intermediates in HIV-1 DNA integration visualized by atomic force microscopy. , 2010, Journal of molecular biology.

[25]  David B Haniford,et al.  Target DNA bending is an important specificity determinant in target site selection in Tn10 transposition. , 2003, Journal of molecular biology.

[26]  E. Wattel,et al.  Inhibitors of Strand Transfer That Prevent Integration and Inhibit Human T-Cell Leukemia Virus Type 1 Early Replication , 2008, Antimicrobial Agents and Chemotherapy.

[27]  Amy S. Espeseth,et al.  HIV-1 integrase inhibitors that compete with the target DNA substrate define a unique strand transfer conformation for integrase. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Amy S. Espeseth,et al.  Diketo acid inhibitor mechanism and HIV-1 integrase: Implications for metal binding in the active site of phosphotransferase enzymes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[29]  W. Haseltine,et al.  Determination of viral proteins present in the human immunodeficiency virus type 1 preintegration complex , 1991, Journal of virology.

[30]  E. Guiot,et al.  Insight into the Integrase-DNA Recognition Mechanism , 2008, Journal of Biological Chemistry.

[31]  T. Baker,et al.  DNA-promoted assembly of the active tetramer of the Mu transposase. , 1992, Genes & development.

[32]  A. Engelman,et al.  LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration. , 2007, Genes & development.

[33]  A. Engelman,et al.  The Lentiviral Integrase Binding Protein LEDGF/p75 and HIV-1 Replication , 2008, PLoS pathogens.

[34]  P. Roversi,et al.  Functional and structural characterization of the integrase from the prototype foamy virus , 2008, Nucleic acids research.

[35]  A. Telesnitsky.  Retroviruses: Molecular Biology, Genomics and Pathogenesis. , 2010, Future virology.

[36]  Sridhar Hannenhalli,et al.  Genome-wide analysis of retroviral DNA integration , 2005, Nature Reviews Microbiology.

[37]  D. Hazuda,et al.  Discovery of raltegravir, a potent, selective orally bioavailable HIV-integrase inhibitor for the treatment of HIV-AIDS infection. , 2008, Journal of medicinal chemistry.

[38]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[39]  Maxwell D. Cummings,et al.  Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance , 2010, Proceedings of the National Academy of Sciences.

[40]  A. Engelman,et al.  Structure-based modeling of the functional HIV-1 intasome and its inhibition , 2010, Proceedings of the National Academy of Sciences.

[41]  Goedele N. Maertens,et al.  The mechanism of retroviral integration through X-ray structures of its key intermediates , 2010, Nature.

[42]  D. Esposito,et al.  Sequence specificity of viral end DNA binding by HIV‐1 integrase reveals critical regions for protein–DNA interaction , 1998, The EMBO journal.

[43]  A. Engelman,et al.  Dynamic Modulation of HIV-1 Integrase Structure and Function by Cellular Lens Epithelium-derived Growth Factor (LEDGF) Protein* , 2008, Journal of Biological Chemistry.

[44]  M. Jaskólski,et al.  Piecing together the structure of retroviral integrase, an important target in AIDS therapy , 2009, The FEBS journal.

[45]  Wei Yang,et al.  Structure of a two‐domain fragment of HIV‐1 integrase: implications for domain organization in the intact protein , 2001, The EMBO journal.

[46]  F. Bushman,et al.  HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. , 2007, Genome research.

[47]  Xiaowu Chen,et al.  Strand transfer inhibitors of HIV-1 integrase: bringing IN a new era of antiretroviral therapy. , 2010, Antiviral research.

[48]  Mary K. Lewinski,et al.  Retroviral DNA integration--mechanism and consequences. , 2005, Advances in genetics.

[49]  M. Nowotny,et al.  Retroviral integrase superfamily: the structural perspective , 2009, EMBO reports.

[50]  Y. Pommier,et al.  Resistance to Integrase Inhibitors , 2010, Viruses.

[51]  F. Bushman,et al.  Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[52]  R. Craigie,et al.  Nucleoprotein complex intermediates in HIV-1 integration. , 2009, Methods.

[53]  R. Daniel,et al.  Integrase-Specific Enhancement and Suppression of Retroviral DNA Integration by Compacted Chromatin Structure In Vitro , 2004, Journal of Virology.

[54]  M. Walkinshaw,et al.  Molecular Architecture of the Mos1 Paired-End Complex: The Structural Basis of DNA Transposition in a Eukaryote , 2009, Cell.

[55]  Robert Craigie,et al.  Retroviral DNA integration: reaction pathway and critical intermediates , 2006, The EMBO journal.

[56]  Paul Shinn,et al.  A role for LEDGF/p75 in targeting HIV DNA integration , 2005, Nature Medicine.

[57]  H. Varmus,et al.  DNA bending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes. , 1994, The EMBO journal.