{"doi":"10.1016/j.jbc.2021.100550","title":"Retroviral prototype foamy virus intasome binding to a nucleosome target does not determine integration efficiency","abstract":"Retroviral integrases must navigate host DNA packaged as chromatin during integration of the viral genome. Prototype foamy virus (PFV) integrase (IN) forms a tetramer bound to two viral DNA (vDNA) ends in a complex termed an intasome. PFV IN consists of four domains: the amino terminal extension domain (NED), amino terminal domain (NTD), catalytic core domain (CCD), and carboxyl terminal domain (CTD). The domains of the two inner IN protomers have been visualized, as well as the CCDs of the two outer IN protomers. However, the roles of the amino and carboxyl terminal domains of the PFV intasome outer subunits during integration to a nucleosome target substrate are not clear. We used the well-characterized 601 nucleosome to assay integration activity as well as intasome binding. PFV intasome integration to 601 nucleosomes occurs in clusters at four independent sites. We find that the outer protomer NED and NTD domains have no significant effects on integration efficiency, site selection, or binding. The CTDs of the outer PFV intasome subunits dramatically affect nucleosome binding but have little effect on total integration efficiency. The outer PFV IN CTDs did significantly alter the integration efficiency at one site. Histone tails also significantly affect intasome binding, but have little impact on PFV integration efficiency or site selection. These results indicate that binding to nucleosomes does not correlate with integration efficiency and suggests most intasome-binding events are unproductive. Retroviral integrases must navigate host DNA packaged as chromatin during integration of the viral genome. Prototype foamy virus (PFV) integrase (IN) forms a tetramer bound to two viral DNA (vDNA) ends in a complex termed an intasome. PFV IN consists of four domains: the amino terminal extension domain (NED), amino terminal domain (NTD), catalytic core domain (CCD), and carboxyl terminal domain (CTD). The domains of the two inner IN protomers have been visualized, as well as the CCDs of the two outer IN protomers. However, the roles of the amino and carboxyl terminal domains of the PFV intasome outer subunits during integration to a nucleosome target substrate are not clear. We used the well-characterized 601 nucleosome to assay integration activity as well as intasome binding. PFV intasome integration to 601 nucleosomes occurs in clusters at four independent sites. We find that the outer protomer NED and NTD domains have no significant effects on integration efficiency, site selection, or binding. The CTDs of the outer PFV intasome subunits dramatically affect nucleosome binding but have little effect on total integration efficiency. The outer PFV IN CTDs did significantly alter the integration efficiency at one site. Histone tails also significantly affect intasome binding, but have little impact on PFV integration efficiency or site selection. These results indicate that binding to nucleosomes does not correlate with integration efficiency and suggests most intasome-binding events are unproductive. Following entry to a cell, the retroviral enzyme reverse transcriptase copies the viral genomic RNA to a linear double-stranded cDNA (1Coffin J.M. Hughes S.H. Varmus H.E. Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY1997Google Scholar). Then retroviral integrase (IN) covalently joins the cDNA 3′ ends to host DNA. The integration reaction is faithfully recapitulated in vitro by complexes assembled from recombinant IN and oligomers mimicking the viral DNA ends (vDNA), termed intasomes (2Maertens G.N. Hare S. Cherepanov P. The mechanism of retroviral integration from X-ray structures of its key intermediates.Nature. 2010; 468: 326-329Crossref PubMed Scopus (250) Google Scholar). The IN of prototype foamy virus (PFV) has four domains: an amino terminal extension domain (NED), an amino terminal domain (NTD), a catalytic core domain (CCD), and a carboxyl terminal domain (CTD) (3Valkov E. Gupta S.S. Hare S. Hela","journal":"Journal of Biological Chemistry","year":2021,"id":201031,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9609,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":779331,"name":"Nathan D. Jones","orcid":"0000-0002-2159-1394","position":1,"is_corresponding":false},{"id":779332,"name":"Gayan Senavirathne","orcid":"0000-0002-9113-4201","position":2,"is_corresponding":false},{"id":515000,"name":"Anne M. Gardner","orcid":"0000-0001-7095-772X","position":3,"is_corresponding":false},{"id":779333,"name":"Ryan K. Messer","orcid":"0000-0002-9961-8171","position":4,"is_corresponding":false},{"id":779833,"name":"Yow Yong Tan","orcid":null,"position":5,"is_corresponding":false},{"id":694674,"name":"Anthony J. Rabe","orcid":null,"position":6,"is_corresponding":false},{"id":77388,"name":"Richard Fishel","orcid":"0000-0001-8753-2269","position":7,"is_corresponding":false},{"id":411452,"name":"Kristine E. Yoder","orcid":"0000-0002-5598-9018","position":8,"is_corresponding":false},{"id":779330,"name":"Randi M. Kotlar","orcid":"0000-0002-2513-6479","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":null,"created_at":"2026-07-18T23:50:52.535403Z","pmid":"33744295","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}