Retroviral intasomes search for a target DNA by 1D diffusion which rarely results in integration

• Published in: Nature communications Vol. 7; no. 1; p. 11409
• Main Authors: Jones, Nathan D, Lopez, Jr, Miguel A, Hanne, Jeungphill, Peake, Mitchell B, Lee, Jong-Bong, Fishel, Richard, Yoder, Kristine E
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 25.04.2016; Nature Portfolio
• Subjects: Animals; Deoxyribonucleic acid; Diffusion; DNA; DNA - chemistry; DNA - genetics; DNA - metabolism; DNA repair; DNA, Single-Stranded - chemistry; DNA, Single-Stranded - genetics; DNA, Single-Stranded - metabolism; Gene Expression; Gene therapy; Genomes; Humans; Integrase; Integrases - chemistry; Integrases - genetics; Integrases - metabolism; Integration; Long terminal repeat; Nucleotides; Single Molecule Imaging - methods; Single-stranded DNA; Spumavirus - genetics; Spumavirus - metabolism; Target recognition; Terminal Repeat Sequences; Time-Lapse Imaging - methods; Viral Proteins - chemistry; Viral Proteins - genetics; Viral Proteins - metabolism; Virus Integration; Viruses
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms11409

Retroviruses must integrate their linear viral cDNA into the host genome for a productive infection. Integration is catalysed by the retrovirus-encoded integrase (IN), which forms a tetramer or octamer complex with the viral cDNA long terminal repeat (LTR) ends termed an intasome. IN removes two 3'-nucleotides from both LTR ends and catalyses strand transfer of the recessed 3'-hydroxyls into the target DNA separated by 4-6 bp. Host DNA repair restores the resulting 5'-Flap and single-stranded DNA (ssDNA) gap. Here we have used multiple single molecule imaging tools to determine that the prototype foamy virus (PFV) retroviral intasome searches for an integration site by one-dimensional (1D) rotation-coupled diffusion along DNA. Once a target site is identified, the time between PFV strand transfer events is 470 ms. The majority of PFV intasome search events were non-productive. These observations identify new dynamic IN functions and suggest that target site-selection limits retroviral integration.