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: London Nature Publishing Group UK 25.04.2016; Nature Publishing Group; Nature Portfolio
• Subjects: 14/35; 631/326/596/2148; 631/45/147; 631/57/2272; 82/16; 82/83; 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; Humanities and Social Sciences; Humans; Integrase; Integrases - chemistry; Integrases - genetics; Integrases - metabolism; Integration; Long terminal repeat; multidisciplinary; Nucleotides; Science; Science (multidisciplinary); 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. Retroviral Integration into the host DNA is a rare event with evidence suggesting that it relies on DNA topology and sequence. Here the authors present single molecule evidence that shows the retroviral integration machinery vigorously scans the target DNA by 1D-diffusion but infrequently integrates.