Human Immunodeficiency Virus Type 1 Replication in the Absence of Integrase-Mediated DNA Recombination: Definition of Permissive and Nonpermissive T-Cell Lines

Abstract

Retroviruses carry two enzymes, reverse transcriptase (RT) and integrase (IN), which function early in the viral life cycle. Soon after infection, RT converts genomic RNA into linear double-stranded cDNA. This DNA, which contains a copy of the viral long terminal repeat (LTR) at each end, is the substrate for IN-mediated DNA recombination. IN initially processes the 3Ј ends of the cDNA adjacent to phylogenetically conserved CA dinucleotides and then inserts these cleaved ends into a target DNA site in a cell chromosome. The cisacting end regions important for integration define the viral attachment (att) sites, which are comprised of U3 and U5 sequences in the upstream and downstream LTRs, respectively. (For a recent review of retroviral integration, see reference 6.)In addition to the linear DNA product of reverse transcription, various types of circular DNA form in retroviral-infected cells.

Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection

“…In agreement with earlier reports, the data presented here indicate that gene expression from nonintegrated HIV-1 and HIV vectors is significantly lower than that of their integrated counterparts (6,16) and that episomal HIV vector silencing is promoterindependent. Furthermore, we showed that episomal HIV-1 and HIV-1 vector genomes are organized into nucleosomal structures, enriched in histone modifications typical of silenced chromatin, and thus subjected to layers of gene regulation involved in transcriptional silencing of cellular gene expression.…”

“…Surprisingly, a study by Cara et al described the replication of integrase-deficient HIV-1 in primary macrophages (5). However, this report is in contrast to a large body of studies from several research groups that demonstrated fundamental differences in the level and regulation of gene expression from episomal and integrated HIV-1 genomes (3,6). These studies imply that altered viral gene expression from HIV-1 forms may be involved in the mechanism that renders nonintegrating HIV-1 replication-defective.…”

“…Furthermore, episomal expression has been reported in a cell line-dependent manner (2,6). Importantly, the level of episomal nef expression was sufficient to downregulate CD4 expression on host cell surfaces and to induce T cell activation (2).…”

Lentiviral vectors with a defective integrase allow efficient and sustained transgene expression in vitro and in vivo

“…Although efficient viral replication seems to be associated with integration events, HIV transcription was shown to be supported by circular molecules. Expression of viral proteins, e.g., tat, nef, or reverse transcriptase as well as indicator genes linked to the LTR promoter, have been reported in many assays using virus particles containing class 1 nonpleiotropic IN mutations (13)(14)(15)(16).…”

Integrase-defective lentiviral vectors: progress and applications

“…IDLVs had different expression levels in various T-cell-derived cell lines and primary cells. 77 IDLVs also failed to express in the corpus callosum and expression was reduced in astrocytes as compared with integrating LVs. 22 Although these are limited examples, they raise the possibility that endogenous factors may influence expression from non-integrated episomes.…”