Dimerization of HIV-1Lai RNA at Low Ionic Strength

Genomic human immunodeficiency virus type 1 (HIV-1) RNA consists of two identical RNA molecules joined noncovalently near their 5′ ends in a region called the dimer linkage structure (DLS). Previous work has shown that the putative DLS is localized in a 113-nucleotide domain encompassing the 5′ end of the gag gene. This region contains conserved purine tracks that are thought to mediate dimerization through purine quartets. However, recently, an HIV-1Ma1 RNA dimerization model was proposed as the HIV-1Ma1 RNA dimerization initiation site, involving another region upstream from the splice donor site and possibly confined within a stem-loop. In the present study, we have investigated the dimerization of HIV-1Lai RNA, using in vitro dimerization assays under conditions of low ionic strength, predictive RNA secondary structures determined by computer folding, and antisense DNA oligonucleotides in order to discriminate between these two models. Our results suggest that purine quartets are not involved in the dimer structure of HIV-1Lai RNA and have led to the identification of a region upstream from the splice donor site. This region, comprising an autocomplementary sequence in a possible stem-loop structure, is responsible for the formation of dimeric HIV-1Lai RNA.

[1]  Wei-Shau Hu,et al.  Genetic consequences of packaging two RNA genomes in one retroviral particle: pseudodiploidy and high rate of genetic recombination. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[2]  O. Uhlenbeck,et al.  Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. , 1987, Nucleic acids research.

[3]  W. Bender,et al.  RD-114, baboon, and woolly monkey viral RNAs compared in size and structure , 1976, Cell.

[4]  C. E. Longfellow,et al.  Improved parameters for prediction of RNA structure. , 1987, Cold Spring Harbor symposia on quantitative biology.

[5]  A. Panganiban,et al.  Ordered interstrand and intrastrand DNA transfer during reverse transcription. , 1988, Science.

[6]  Eric Bieth,et al.  A study of the dimer formation of Rous sarcoma virus RNA and of its effect on viral protein synthesis in vitro , 1990, Nucleic Acids Res..

[7]  R. F. Smith,et al.  Human Retroviruses and AIDS. A compilation and analysis of nucleic acid and amino acid sequences: I--II; III--V , 1993 .

[8]  E. Wagner,et al.  Control of replication of plasmid R1: structures and sequences of the antisense RNA, CopA, required for its binding to the target RNA, CopT. , 1990, The EMBO journal.

[9]  C. Ehresmann,et al.  Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site. , 1994, Nucleic acids research.

[10]  C. Gabus,et al.  Analytical study of avian reticuloendotheliosis virus dimeric RNA generated in vivo and in vitro , 1992, Journal of virology.

[11]  H. Temin.  Sex and recombination in retroviruses. , 1991, Trends in genetics : TIG.

[12]  W. Fu,et al.  Characterization of human immunodeficiency virus type 1 dimeric RNA from wild-type and protease-defective virions , 1994, Journal of virology.

[13]  H. Stuhlmann,et al.  Homologous recombination of copackaged retrovirus RNAs during reverse transcription , 1992, Journal of virology.

[14]  A. Lever,et al.  The human immunodeficiency virus type 1 packaging signal and major splice donor region have a conserved stable secondary structure , 1992, Journal of virology.

[15]  C. Ehresmann,et al.  Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[16]  F. Barré-Sinoussi,et al.  Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1. , 1990, Journal of molecular biology.

[17]  Y. Chien,et al.  High-molecular-weight RNAs of AKR, NZB, and wild mouse viruses and avian reticuloendotheliosis virus all have similar dimer structures , 1978, Journal of virology.

[18]  M. Famulok,et al.  The multimerization state of retroviral RNA is modulated by ammonium ions and affects HIV-1 full-length cDNA synthesis in vitro. , 1993, Nucleic acids research.

[19]  C. Ehresmann,et al.  Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism. , 1991, Nucleic acids research.

[20]  C. Gabus,et al.  cis elements and trans-acting factors involved in dimer formation of murine leukemia virus RNA , 1990, Journal of virology.

[21]  W. Gilbert,et al.  Rous sarcoma virus genome is terminally redundant: the 5' sequence. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[22]  T. Cech,et al.  Monovalent cation-induced structure of telomeric DNA: The G-quartet model , 1989, Cell.

[23]  H. Kim,et al.  A short sequence upstream of the 5' major splice site is important for encapsidation of HIV-1 genomic RNA. , 1994, Virology.

[24]  C. Ehresmann,et al.  An analytical study of the dimerization of in vitro generated RNA of Moloney murine leukemia virus MoMuLV. , 1990, Nucleic acids research.

[25]  W. Sundquist,et al.  Evidence for interstrand quadruplex formation in the dimerization of human immunodeficiency virus 1 genomic RNA. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[26]  B. Berkhout,et al.  In vitro dimerization of HIV‐2 leader RNA in the absence of PuGGAPuA motifs , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[27]  I. Jones,et al.  Recombinant HIV-1 nucleocapsid protein p15 produced as a fusion protein with glutathione S-transferase in Escherichia coli mediates dimerization and enhances reverse transcription of retroviral RNA. , 1992, Gene.

[28]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[29]  T. Yasunaga,et al.  Bovine leukemia virus RNA sequences involved in dimerization and specific gag protein binding: close relation to the packaging sites of avian, murine, and human retroviruses , 1993, Journal of virology.

[30]  D. Sen,et al.  Mode of dimerization of HIV-1 genomic RNA. , 1993, Biochemistry.

[31]  K. Murti,et al.  Secondary structural features in the 70S RNAs of Moloney murine leukemia and Rous sarcoma viruses as observed by electron microscopy , 1981, Journal of virology.

[32]  M Laughrea,et al.  A 19-nucleotide sequence upstream of the 5' major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA. , 1994, Biochemistry.

[33]  A. Gronenborn,et al.  Identification of a binding site for the human immunodeficiency virus type 1 nucleocapsid protein. , 1993, Proceedings of the National Academy of Sciences of the United States of America.