Delineation of the preferences and requirements of the human immunodeficiency virus type 1 dimerization initiation signal by using an in vivo cell-based selection approach.
HIV-1 packages two copies of RNA into one particle, and the dimerization initiation signal (DIS) in the viral RNA plays an important role in selecting the copackaged RNA partner. We analyzed the DIS sequences of the circulating HIV-1 isolates in the GenBank database and observed that, in addition to the prevalent GCGCGC, GTGCAC, and GTGCGC sequences, there are many other minor variants. To better understand the requirements for the DIS to carry out its function, we generated a plasmid library containing a subtype B HIV-1 genome with a randomized DIS, infected cells with viruses derived from the library, and monitored the emergence of variants at different time points until 100 days postinfection. We observed rapid loss of viral diversity and found that the selected variants contained palindromes in the DIS. The "wild-type" GCGCGC-containing virus was a major variant, whereas GTGCAC- and GTGCGC-containing viruses were present at low frequencies. Additionally, other 6-nucleotide (nt) palindromic sequences were selected; a major category of the selected variants contained two GC dyads in the center of the palindrome, flanked by a non-GC dyad. Surprisingly, variants with GC-rich 4-nt palindromes were sustained throughout the selection period at significant frequencies ( approximately 12 to 38%); of these, variants containing the CGCGC sequence were observed frequently, suggesting that this sequence has a selection advantage. These results revealed that multiple sequences can fulfill the function of the HIV-1 DIS. A common feature of the selected DIS sequence is a 4- or 6-nt GC-rich palindrome, although not all sequences with these characteristics were selected, suggesting the presence of other unidentified interactions.
Hussein
Islam T M
IT
HIV Drug Resistance Program, NCI-Frederick, Frederick, MD 21702, USA.
Ni
Na
N
Galli
Andrea
A
Chen
Jianbo
J
Moore
Michael D
MD
Hu
Wei-Shau
WS
D002460:Cell Line; D019295:Computational Biology; D016384:Consensus Sequence; D004252:DNA Mutational Analysis; D015497:HIV-1 / Q000502:physiology*; D006801:Humans; D055029:Inverted Repeat Sequences; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D019065:Virus Assembly
D012367:RNA, Viral
Virology. 2004 Aug 15;326(1):103-12
15262499
Nucleic Acids Res. 2006 May 05;34(8):2328-39
16679451
J Virol. 1994 Aug;68(8):5013-8
8035501
J Virol. 2009 Feb;83(4):1635-48
19073717
Nat Med. 2009 Aug;15(8):871-2
19648927
Biochemistry. 1996 Apr 16;35(15):5075-82
8664300
Nature. 2006 Nov 9;444(7116):164
17093443
Virology. 2007 Jul 5;363(2):437-46
17336363
Drug Resist Updat. 2002 Dec;5(6):224-33
12531179
J Virol. 1996 Dec;70(12):8348-54
8970954
Philos Trans R Soc Lond B Biol Sci. 2001 Jun 29;356(1410):867-76
11405934
Bioinformatics. 2007 Nov 1;23(21):2947-8
17846036
J Virol. 1999 Aug;73(8):7014-20
10400801
J Biol Chem. 1995 Apr 7;270(14):8209-16
7713927
Biochemistry. 1997 Aug 5;36(31):9501-8
9235995
J Virol. 1999 Jul;73(7):6147-51
10364374
J Virol. 2004 May;78(9):4907-13
15078972
Biochemistry. 1999 Jan 5;38(1):226-34
9890902
J Virol. 1996 Sep;70(9):5902-8
8709210
Biochemistry. 1994 Nov 15;33(45):13464-74
7947755
Proc Natl Acad Sci U S A. 1996 May 28;93(11):5572-7
8643617
Adv Pharmacol. 2000;48:1-28
10987087
J Virol. 2003 Aug;77(15):8329-35
12857902
Biochemistry. 1996 Feb 6;35(5):1589-98
8634290
Virology. 1997 Jul 7;233(2):271-9
9217051
J Virol. 1998 Aug;72(8):6629-36
9658109
Retrovirology. 2004 Aug 18;1:22
15317659
J Virol. 1975 Aug;16(2):397-411
168408
AIDS Rev. 2009 Apr-Jun;11(2):91-102
19529749
J Virol. 1997 May;71(5):3397-406
9094609
Nucleic Acids Res. 2008 Mar;36(5):1578-88
18216043
Nat Rev Microbiol. 2004 Jun;2(6):461-72
15152202
Proc Natl Acad Sci U S A. 2005 Jun 21;102(25):9002-7
15956186
J Virol. 1996 Oct;70(10):6723-32
8794309
Biochimie. 2007 Oct;89(10):1195-203
17434658
Biochimie. 2002 Sep;84(9):925-44
12458085
J Virol. 1998 Oct;72(10):8073-82
9733847
Proc Natl Acad Sci U S A. 1994 May 24;91(11):4945-9
8197162
J Virol. 2005 Feb;79(3):1666-77
15650192
Retrovirology. 2004 Sep 02;1:23
15345057