A 19-nucleotide sequence upstream of the 5' major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA
- PMID: 7947755
- DOI: 10.1021/bi00249a035
A 19-nucleotide sequence upstream of the 5' major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA
Abstract
The genome of all retroviruses, including human immunodeficiency virus type 1 (HIV-1), consists of two identical RNAs noncovalently linked near their 5' end. Dimerization of genomic RNA is thought to modulate several steps in the retroviral life cycle, such as recombination, translation, and encapsidation. We report the results of experiments designed to identify the 5' and 3' boundaries of the dimerization domain of the HIV-1 genome: (1) An HIV-1 RNA starting at nucleotide 252 or at other downstream positions (four tested) does not dimerize despite the inclusion of the whole of a previously proposed dimerization domain (nucleotides 295-401); (2) an RNA starting between nucleotides 242 and 249 (five positions tested) dimerizes to a variable extent depending on the starting position; (3) an RNA starting at nucleotide 233 or at other upstream positions (five tested) is fully or > 80% dimeric; (4) an RNA starting at nucleotide 1 but lacking the 233-251 or the 242-251 region is, respectively, fully monomeric or about 50% monomeric; (5) the 343-401 region contains two strings of G's (GGGGG367 and GGG384) that had been postulated to promote genome dimerization through the formation of guanine quartets. We have deleted the 379-401, 358-401, and 343-401 regions from otherwise dimeric RNAs without changing their ability to dimerize. We reach three conclusions: (1) a dimerization signal exists upstream of the major 5' splice donor (nucleotide 290); (2) the previously proposed downstream dimerization domain is insufficient to promote dimerization and has a 3' half that is not necessary to obtain fully dimeric RNAs; (3) the 5' boundary of the HIV-1 dimerization domain is located somewhere between nucleotides 233 and 242, and the 3' boundary is located no farther than at nucleotide 342, making it possible that the 5' and 3' boundaries of the HIV-1 dimerization domain are both located within the leader sequence. We speculate that the 248-270 or 233-285 region forms a hairpin that is the core dimerization domain of HIV-1 RNA.
Similar articles
-
Kissing-loop model of HIV-1 genome dimerization: HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensable for dimer formation.Biochemistry. 1996 Feb 6;35(5):1589-98. doi: 10.1021/bi951838f. Biochemistry. 1996. PMID: 8634290
-
HIV-1 genome dimerization: kissing-loop hairpin dictates whether nucleotides downstream of the 5' splice junction contribute to loose and tight dimerization of human immunodeficiency virus RNA.Biochemistry. 1997 Aug 5;36(31):9501-8. doi: 10.1021/bi970862l. Biochemistry. 1997. PMID: 9235995
-
Elements located upstream and downstream of the major splice donor site influence the ability of HIV-2 leader RNA to dimerize in vitro.Biochemistry. 2003 Mar 11;42(9):2634-42. doi: 10.1021/bi0271190. Biochemistry. 2003. PMID: 12614158 Free PMC article.
-
Dimerization of retroviral genomic RNAs: structural and functional implications.Biochimie. 1996;78(7):639-53. doi: 10.1016/s0300-9084(96)80010-1. Biochimie. 1996. PMID: 8955907 Review.
-
HIV-1 RNA dimerization: It takes two to tango.AIDS Rev. 2009 Apr-Jun;11(2):91-102. AIDS Rev. 2009. PMID: 19529749 Free PMC article. Review.
Cited by
-
Moloney murine sarcoma virus genomic RNAs dimerize via a two-step process: a concentration-dependent kissing-loop interaction is driven by initial contact between consecutive guanines.J Virol. 1999 Sep;73(9):7255-61. doi: 10.1128/JVI.73.9.7255-7261.1999. J Virol. 1999. PMID: 10438813 Free PMC article.
-
Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding.RNA. 1999 Sep;5(9):1222-34. doi: 10.1017/s1355838299990982. RNA. 1999. PMID: 10496223 Free PMC article.
-
Functional characterization of the dimer linkage structure RNA of Moloney murine sarcoma virus.J Virol. 2000 Nov;74(21):9937-45. doi: 10.1128/jvi.74.21.9937-9945.2000. J Virol. 2000. PMID: 11024121 Free PMC article.
-
Modeling the dynamics of a mutated stem-loop in the SL1 domain of HIV-1Lai genomic RNA by 1H-NOESY spectra.J Biomol NMR. 2001 Aug;20(4):333-49. doi: 10.1023/a:1011251308365. J Biomol NMR. 2001. PMID: 11563557
-
Impaired RNA incorporation and dimerization in live attenuated leader-variants of SIVmac239.Retrovirology. 2006 Dec 21;3:96. doi: 10.1186/1742-4690-3-96. Retrovirology. 2006. PMID: 17184529 Free PMC article.