Ultrastructure of HIV-1 Genomic RNA

Abstract

The HIV-1 RNA genome is a dimer which consists of two identical strands of RNA linked near their 5' ends by a dimer linkage structure (DLS). We have structurally characterized full-length HIV-1 genomic RNA isolated from HIV-1 virions by electron microscopy. As in other retroviruses, the HIV-1 RNA genome contains a central dimer linkage structure and additional loop structures within each monomer subunit. In contrast to the DLS of other retroviruses, the DLS region of HIV-1 contains a loop of 323 +/- 44 nucleotides. The free 5' ends of the two RNA strands were not visualized, suggesting that the 5' end regions are involved in interstrand complementary base pairing. Computer modeling identified a single stable structure that was consistent with the electron microscopy data. In this model, the two RNA strands are linked at their 5' ends by two contact points derived from "kissing-loop" interactions between r-u5 and SL1 stem-loops and their counterparts on the second strand. These interactions may contribute to the formation of stable HIV-1 RNA dimers in vivo.

HIV-1-based defective lentiviral vectors efficiently transduce human monocytes-derived macrophages and suppress replication of wild-type HIV-1

“…There are several potential mechanisms that may account for this antiviral effect: (a) TAR and RRE decoy effects of the vectors at both the transcriptional and post-transcriptional levels [45]; (b) competition of the vectors for substrates necessary for reverse transcription and RNA encapsidation [44,46]; and (c) co-packaging and/or dimerization of wild-type and DLV genomes, resulting in the generation of defective virus particles [48]. Precedents for some or all of these possibilities exist in the literature, and include the fact that co-packaging of wild-type HIV genome along with a modified HIV genome and subsequent inhibition of HIV-1 replication has been documented using a Moloney retrovirus vector [49].…”

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

“…Similarly, the reactivity of the poly(A) loop was unchanged, although this hairpin has been proposed to participate in the RNA dimerization process (16).…”

“…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).…”

FIV: from lentivirus to lentivector

“…However, an important distinction is that a continuous, discrete, transferable element analogous to that of MLV [71,72] has not been defined for any lentivirus. Mapping experiments suggest additional HIV/SIV encapsidation determinants exist in the 5 end of the mRNA, including R and U5 [79,[85][86][87][88][89][90], extend into gag [75,91], and may include downstream regions [92,93]. Within R, the TAR element has been implicated [86].…”