Retroviral intasomes search for a target DNA by 1D diffusion which rarely results in integration.
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.
Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, Ohio 43210, USA.|The Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA.
Nathan D
ND
Jones
Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, Ohio 43210, USA.
Miguel A
MA
Lopez
Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, Ohio 43210, USA.
Jeungphill
J
Hanne
Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, Ohio 43210, USA.
Mitchell B
MB
Peake
Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea.|Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Korea.
Jong-Bong
JB
Lee
Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, Ohio 43210, USA.|The Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA.|Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA.
Richard
R
Fishel
Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, Ohio 43210, USA.
Kristine E
http://orcid.org/0000-0002-5598-9018
KE
Yoder
D000818:Animals; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004058:Diffusion; D015870:Gene Expression; D006801:Humans; D019426:Integrases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D000072760:Single Molecule Imaging / Q000379:methods; D016092:Spumavirus / Q000235:genetics* / Q000378:metabolism; D020079:Terminal Repeat Sequences; D059008:Time-Lapse Imaging / Q000379:methods; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016662:Virus Integration
D004277:DNA, Single-Stranded; D014764:Viral Proteins; D004247:DNA; D019426:Integrases