Asymmetric Processing of Human Immunodeficiency Virus Type 1 cDNA In Vivo: Implications for Functional End Coupling during the Chemical Steps of DNA Transposition

REFERENCES

• Agrawal, A., Q. M. Eastman, and D. G. Schatz. 1998. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394:744–751.
   PubMed Web of Science ®Google Scholar
• Bainton, R., P. Gamas, and N. L. Craig. 1991. Tn7 transposition in vitro proceeds through an excised transposon intermediate generated by staggered breaks in DNA. Cell 65:805–816.
   PubMedGoogle Scholar
• Baker, T. A., E. Kremenstova, and L. Luo. 1994. Complete transposition requires four active monomers in the Mu transposase tetramer. Genes Dev. 8:2416–2428.
   PubMedGoogle Scholar
• Brown, H. E. V., H. Chen, and A. Engelman. 1999. Structure-based mutagenesis of the human immunodeficiency virus DNA attachment site: effects on integration and cDNA synthesis. J. Virol. 73:9011–9020.
   PubMedGoogle Scholar
• Brown, P. O.. 1997. Integration. Retroviruses.. J. M. Coffin, S. H. Hughes, and H. E. Varmus. 161–203. Cold Spring Harbor Laboratory Press, Plainview, N.Y
   Google Scholar
• Brown, P. O., B. Bowerman, H. E. Varmus, and J. M. Bishop. 1987. Correct integration of retroviral DNA in vitro. Cell 49:347–356.
   PubMed Web of Science ®Google Scholar
• Carteau, S., S. C. Batson, L. Poljak, J.-F. Mouscadet, H. Rocquigny, J.-L. Darlix, B. P. Roques, E. Kas, and C. Auclair. 1997. Human immunodeficiency virus type 1 nucleocapsid protein specifically stimulates Mg2+-dependent DNA integration in vitro. J. Virol. 71:6225–6229.
   PubMed Web of Science ®Google Scholar
• Chaconas, G., B. D. Lavoie, and M. A. Watson. 1996. DNA transposition: jumping gene machine, some assembly required. Curr. Biol. 6:817–820.
   PubMedGoogle Scholar
• Chen, H., and A. Engelman. 1998. The barrier-to-autointegration protein is a host factor for HIV type 1 integration. Proc. Natl. Acad. Sci. USA 95:15270–15274.
   PubMed Web of Science ®Google Scholar
• Chen, H., and A. Engelman. 2000. Characterization of a replication-defective human immunodeficiency virus type 1 att site mutant that is blocked after the 3′ processing step of retroviral integration. J. Virol. 74:8188–8193.
   PubMedGoogle Scholar
• Chen, H., S.-Q. Wei, and A. Engelman. 1999. Multiple integrase functions are required to form the native structure of the human immunodeficiency virus type 1 intasome. J. Biol. Chem. 274:17358–17364.
   PubMed Web of Science ®Google Scholar
• Derbyshire, K. M., L. Hwang, and N. D. F. Grindley. 1987. Genetic analysis of the interaction of the insertion sequence IS903 transposase with its terminal inverted repeats. Proc. Natl. Acad. Sci. USA 84:8049–8053.
   PubMedGoogle Scholar
• Eastman, Q. M., and D. G. Schatz. 1997. Nicking is asynchronous and stimulated by synapsis in 12/23 rule-regulated V(D)J cleavage. Nucleic Acids Res. 25:4370–4378.
   PubMedGoogle Scholar
• Engelman, A., and R. Craigie. 1992. Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J. Virol. 66:6361–6369.
   PubMed Web of Science ®Google Scholar
• Engelman, A., G. Englund, J. M. Orenstein, M. A. Martin, and R. Craigie. 1995. Multiple effects of mutations in human immunodeficiency virus type 1 integrase on viral replication. J. Virol. 69:2729–2736.
   PubMed Web of Science ®Google Scholar
• Farnet, C. M., and W. A. Haseltine. 1990. Integration of human immunodeficiency virus type 1 DNA in vitro. Proc. Natl. Acad. Sci. USA 87:4164–4168.
   PubMed Web of Science ®Google Scholar
• Fugmann, S. D., A. I. Lee, P. E. Shockett, I. J. Villey, and D. G. Schatz. 2000. The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annu. Rev. Immunol. 18:495–527.
   PubMed Web of Science ®Google Scholar
• Fujiwara, T., and K. Mizuuchi. 1988. Retroviral DNA integration: structure of an integration intermediate. Cell 54:497–504.
   PubMed Web of Science ®Google Scholar
• Goodzari, G., G.-J. Im, K. Brackmann, and D. P. Grandgenett. 1995. Concerted integration of retrovirus-like DNA by human immunodeficiency virus type 1 integrase. J. Virol. 69:6090–6097.
   PubMedGoogle Scholar
• Haniford, D., and N. Kleckner. 1994. Tn10 transposition in vivo: temporal separation of cleavages at the two transposon ends and roles of terminal basepairs subsequent to interaction of ends. EMBO J. 13:3401–3411.
   PubMedGoogle Scholar
• Haniford, D. B., H. W. Benjamin, and N. Kleckner. 1991. Kinetic and structural analysis of a cleaved donor intermediate and a strand transfer intermediate in Tn10 transposition. Cell 11:171–179.
   Google Scholar
• Hiom, K., M. Melek, and M. Gellert. 1998. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94:463–470.
   PubMedGoogle Scholar
• Huisman, O., P. R. Errada, L. Signon, and N. Kleckner. 1989. Mutational analysis of IS10's outside end. EMBO J. 8:2101–2109.
   PubMedGoogle Scholar
• Kennedy, A. K., A. Guhathakurta, N. Kleckner, and D. B. Haniford. 1998. Tn10 transposition via a DNA hairpin intermediate. Cell 95:125–134.
   PubMedGoogle Scholar
• Lavoie, B. D., B. S. Chan, R. G. Allison, and G. Chaconas. 1991. Structural aspects of a higher order nucleoprotein complex: induction of an altered DNA structure at the Mu-host junction of the type 1 transpososome. EMBO J. 10:3051–3059.
   PubMedGoogle Scholar
• Leavitt, A. D., R. B. Rose, and H. E. Varmus. 1992. Both substrate and target oligonucleotide sequences affect in vitro integration mediated by the human immunodeficiency virus type 1 integrase protein produced in Saccharomyces cerevisiae. J. Virol. 66:2359–2368.
   PubMedGoogle Scholar
• Masuda, T., M. J. Kuroda, and S. Harada. 1998. Specific and independent recognition of U3 and U5 att sites by human immunodeficiency virus type 1 integrase in vivo. J. Virol. 72:8396–8402.
   PubMed Web of Science ®Google Scholar
• Miller, M. D., C. M. Farnet, and F. D. Bushman. 1997. Human immunodeficiency type 1 preintegration complexes: studies of organization and function. J. Virol. 71:5382–5390.
   PubMed Web of Science ®Google Scholar
• Mizuuchi, M., T. A. Baker, and K. Mizuuchi. 1992. Assembly of the active form of the transposase-Mu DNA complex: a critical control point in Mu transposition. Cell 70:303–311.
   PubMedGoogle Scholar
• Murphy, J. E., and S. P. Goff. 1992. A mutation at one end of Moloney murine leukemia virus DNA blocks cleavage at both ends by the viral integrase in vivo. J. Virol. 66:5092–5095.
   PubMed Web of Science ®Google Scholar
• Namgoong, S.-Y., and R. M. Harshey. 1998. The same two monomers within a MuA tetramer provide the DDE domains for the strand cleavage and strand transfer steps of transposition. EMBO J. 17:3775–3785.
   PubMedGoogle Scholar
• Pauza, C. D.. 1990. Two bases are deleted from the termini of HIV-1 linear DNA during integrative recombination. Virology 179:886–889.
   PubMed Web of Science ®Google Scholar
• Roth, M. J., P. L. Schwartzberg, and S. P. Goff. 1989. Structure of the termini of DNA intermediates in the integration of retroviral DNA: dependence on IN function and terminal DNA sequence. Cell 58:47–54.
   PubMed Web of Science ®Google Scholar
• Savilhati, H., and K. Mizuuchi. 1996. Mu transpositional recombination: donor DNA cleavage and strand transfer in trans by the Mu transposase. Cell 85:271–280.
   PubMedGoogle Scholar
• Sherman, P. A., M. L. Dickson, and J. A. Fyfe. 1992. Human immunodeficiency virus type 1 integration protein: DNA sequence requirements for cleavage and joining reaction. J. Virol. 66:3593–3601.
   PubMed Web of Science ®Google Scholar
• Surette, M. G., T. Harkness, and G. Chaconas. 1991. Stimulation of the Mu A protein-mediated strand cleavage reaction by the Mu B protein, and the requirement of DNA nicking for stable type 1 transpososome formation. J. Biol. Chem. 266:3118–3124.
   PubMedGoogle Scholar
• Vink, C., D. C. van Gent, Y. Elgersma, and R. H. A. Plasterk. 1991. Human immunodeficiency virus integrase protein requires a subterminal position of its viral DNA recognition sequence for efficient cleavage. J. Virol. 65:4636–4644.
   PubMed Web of Science ®Google Scholar
• Wei, S.-Q., K. Mizuuchi, and R. Craigie. 1997. A large nucleoprotein assembly at the ends of the viral DNA mediates retroviral DNA integration. EMBO J. 16:7511–7520.
   PubMedGoogle Scholar
• Wei, S.-Q., K. Mizuuchi, and R. Craigie. 1998. Footprints on the viral DNA ends in Moloney murine leukemia virus preintegration complexes reflect a specific association with integrase. Proc. Natl. Acad. Sci. USA 95:10535–10540.
   PubMedGoogle Scholar
• West, R. B., and M. R. Lieber. 1998. The RAG-HMG1 complex enforces the 12/23 rule of V(D)J recombination specifically at the double-hairpin formation step. Mol. Cell. Biol. 18:6408–6415.
   PubMedGoogle Scholar
• Williams, T. L., E. L. Jackson, A. Carritte, and T. A. Baker. 1999. Organization and dynamics of the Mu transpososome: recombination by communication between two active sites. Genes Dev. 13:2725–2737.
   PubMedGoogle Scholar
• Yu, K., and M. R. Lieber. 2000. The nicking step in V(D)J recombination is independent of synapsis: implications for the immune repertoire. Mol. Cell. Biol. 20:7914–7921.
   PubMedGoogle Scholar