A 19-Nucleotide Sequence Upstream of the 5' Major Splice Donor Is Part of the Dimerization Domain of Human Immunodeficiency Virus 1 Genomic RNA

Laughrea, Michael; Jetté, Louis

doi:10.1021/bi00249a035

Cited by 232 publications

(287 citation statements)

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“…The structure and the location of this element are homologous to those of the HIV-1 SL1, which is the element that mediates dimerization of HIV-1 RNA fragments in vitro (5)(6)(7)13,14,33,34). However the HIV-2 SL1 sequence does not mediate the formation of loose dimers in vitro, either as an isolated structure (9) or as a structural element in the 1-561 RNA (17).…”

Section: Discussionmentioning

confidence: 99%

“…These tight dimers are defined by their resistance to dissociation during electrophoresis at room temperature and in the presence of EDTA. The tight dimer behavior of small HIV-1 or HIV-2 RNAs is thought to be caused by an extended base pairing arrangement of SL1 (first proposed in (6,33,34) and further analyzed in (10,11,15)). The 1-444 RNA is well suited to forming a tight dimer probably because the SL1 dimer-inducing element is located at the very 3′ end of this fragment ( Figure 1).…”

Section: Discussionmentioning

confidence: 99%

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Elements Located Upstream and Downstream of the Major Splice Donor Site Influence the Ability of HIV-2 Leader RNA To Dimerize in Vitro

et al. 2003

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An essential step in the replication cycle of all retroviruses is the dimerization of genomic RNA prior to or during budding and maturation of the viral particle. In HIV-1 a 5′ leader region site referred to as stem-loop1 (SL1) promotes RNA dimerization in vitro and influences dimerization in vivo. In HIV-2, two sequences promote dimerization of RNA fragments in vitro: the 5′-end of the primerbinding site (PBS) and a stem loop homologous to the HIV-1 SL1 sequence. Because HIV-2 RNA constructs of different lengths use these two dimerization signals disproportionately, we hypothesized that other sequences could modulate their relative utilization. Here, we characterized the influence of sequences upstream and downstream of the major splice donor site on the formation of HIV-2 RNA dimers in vitro using a variety of RNA constructs and dimerization/electrophoresis protocols. We first assayed the formation of loose or tight dimers for 1-444 and 1-561 model RNAs. Although both RNAs could form PBS-dependent loose dimers, the 1-561 RNA was unable to make SL1-dependent tight dimers. Using RNAs truncated at their 5′ and/or 3′ ends and by making compensatory base substitutions we found that two elements interfere with the formation of SL1-dependent tight dimers. The cores of these elements are located at nucleotides 189-196 and 543-550. Our results suggest that base pairing between these sequences prevents the formation of SL1- † This research was supported by the National Institutes of Health grant number AI45388 to J.S.L.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Elements Located Upstream and Downstream of the Major Splice Donor Site Influence the Ability of HIV-2 Leader RNA To Dimerize in Vitro

et al. 2003

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“…Beside these intramolecular interactions, symmetric intermolecular interactions take place in vitro at the DIS (12)(13)(14) and could also occur at TAR (15) and poly(A) hairpin (16). In addition, tRNA 3 Lys , the reverse transcription primer, is selectively encapsidated into virions and is annealed to the PBS during or after budding (17,18).…”

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confidence: 99%

First Snapshots of the HIV-1 RNA Structure in Infected Cells and in Virions

Paillart

Dettenhofer

et al. 2004

Journal of Biological Chemistry

128

143

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With the increasing interest of RNAs in regulating a range of cell biological processes, very little is known about the structure of RNAs in tissue culture cells. We focused on the 5 -untranslated region of the human immunodeficiency virus type 1 RNA genome, a highly conserved RNA region, which contains structural domains that regulate key steps in the viral replication cycle. Up until now, structural information only came from in vitro studies. Here, we developed chemical modification assays to test nucleotide accessibility directly in infected cells and viral particles, thus circumventing possible biases and artifacts linked to in vitro assays. The secondary structure of the 5 -untranslated region in infected cells points to the existence of the various stemloop motifs associated to distinct functions, proposed from in vitro probing, mutagenesis, and phylogeny. However, compared with in vitro data, subtle differences were observed in the dimerization initiation site hairpin, and none of the proposed long range interactions were observed between the functional domains. Moreover, no global RNA rearrangement was observed; structural differences between infected cells and viral particles were limited to the primer binding site, which became protected against chemical modification upon tRNA 3 Lys annealing in virions and to the main packaging signal. In addition, our data suggested that the genomic RNA could already dimerize in the cytoplasm of infected cells. Taken together, our results provided the first analysis of the dynamic of RNA structure of the human immunodeficiency virus type 1 RNA genome during virus assembly ex vivo.

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“…The dimer linkage structure is located within the ∼350-nt 5′-leader of the HIV gRNA, which contains several highly structured and conserved stem-loops that play essential roles at distinct steps during viral replication (9). Among these stem-loops, the dimerization initiation site (DIS) was identified early on as important for dimerization (10)(11)(12). Isolated DIS stem-loops spontaneously form "kissing" dimers through self-pairing of the palindromic apical loop.…”

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confidence: 99%