Elsevier

Advances in Genetics

Volume 55, 2005, Pages 147-181
Advances in Genetics

Retroviral DNA Integration—Mechanism and Consequences

https://doi.org/10.1016/S0065-2660(05)55005-3Get rights and content

Abstract

Integration of retroviral cDNA into the host cell chromosome is an essential step in its replication. This process is catalyzed by the retroviral integrase protein, which is conserved among retroviruses and retrotransposons. Integrase binds viral and host DNA in a complex, called the preintegration complex (PIC), with other viral and cellular proteins. While the PIC is capable of directing integration of the viral DNA into any chromosomal location, different retroviruses have clear preferences for integration in or near particular chromosomal features. The determinants of integration site selection are under investigation but may include retrovirus‐specific interactions between integrase and tethering factors bound to the host cell chromosomes. Research into the mechanisms of retroviral integration site selection has shed light on the phenomena of insertional mutagenesis and viral latency.

Introduction

The retroviruses are of utmost significance in biology and medicine. The propensity of some retroviruses to cause cancer in animals has led to the discovery of numerous oncogenes. Human immunodeficiency virus, a member of the retroviral genus Lentivirus, is responsible for one of the most destructive pandemics in human history. Here we discuss how a process central to the retroviral replication cycle (i.e., integration of viral DNA into the host cell chromosome) mediates some of the consequences of retroviral infection.

Section snippets

Retroviral Life Cycle

Following binding of the retroviral envelope glycoprotein to its cellular receptor(s), the viral membrane fuses with the cell membrane, releasing the viral core into the host cell cytoplasm. The viral genomic RNA is then reverse transcribed to form double‐stranded DNA. The viral DNA, in a complex with integrase and other viral and cellular proteins, enters the nucleus. There, the viral integrase protein covalently joins the viral DNA to the host cell DNA. Once integrated, the viral DNA, called

Mechanism of Integration

Integration of viral DNA into the host cell chromosome involves several coordinated steps (i.e., processing of the viral DNA ends, joining of those ends to target DNA, and repairing the gaps). The first two reactions are catalyzed by the viral integrase protein, whereas the last is mediated by as‐yet‐undefined factors.

Integrase Structure

The integrase protein is composed of three separate domains—the N‐terminal zinc‐binding domain, catalytic core, and the C‐terminal DNA‐binding domain. The domain structure was initially suggested by partial proteolysis studies (Engelman et al., 1993). Later the domain structures were solved by NMR and x‐ray crystallography. The crystal and NMR structures of each domain indicate that each dimerizes (Cai 1997, Chen 2000a, Chen 2000b, Eijkelenboom 1999, Goldgur 1998, Goldgur 1999, Lodi 1995,

Composition of Integrase Complexes In Vivo

Integration in vivo is carried out by a nucleoprotein complex that includes the viral DNA and integrase (Bowerman 1989, Brown 1987, Ellison 1990, Farnet 1990, Farnet 1991, Li 2001, Miller 1997). With the development of assays involving PICs purified from virally infected cells (Brown 1987, Ellison 1990, Farnet 1990), it has become possible to study the organization and function of authentic replication intermediates. Preintegration complex preparations have been generated for cells infected

Retroviral Integration Targeting

While most sequences tested in vitro can serve as targets for integration (Bor 1996, Brown 1987, Craigie 1990), all retroviruses tested exhibit nonrandom selection of integration target sites in cells (Mitchell 2004, Schroder 2002, Wu 2003). Explanations for integration target site specificity include the variable accessibility of certain regions of chromosomal DNA or tethering of the PIC to genomic sites through its interaction with specific cellular DNA‐binding proteins.

Consequences of Integration into Host Chromosomes

The fates of the provirus and its host cell are intimately intertwined. The provirus can influence transcription of host genes in its vicinity and the chromosomal environment exerts its effects on proviral transcription. This reciprocal relationship is at least in part responsible for two fascinating phenomena associated with retroviral integration (i.e., insertional mutagenesis and viral latency).

Conclusions

The retroviral integrase protein plays a central role in the retroviral replication cycle, influencing the processes of reverse transcription, assembly, and budding in addition to mediating the covalent attachment of the viral DNA to the host cell chromosome. Integration of retroviral cDNA involves catalysis of terminal cleavage and strand transfer reactions by integrase followed by repair of the gaps at the host–virus DNA junction, probably by cellular DNA repair enzymes. The joining of the

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