{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T11:03:34Z","timestamp":1785927814246,"version":"3.56.0"},"reference-count":21,"publisher":"American Society for Microbiology","issue":"23","license":[{"start":{"date-parts":[[2017,12,1]],"date-time":"2017-12-01T00:00:00Z","timestamp":1512086400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"UCI Center for Virus Research","award":["777"],"award-info":[{"award-number":["777"]}]},{"name":"UCI Cancer Research Institute","award":["888"],"award-info":[{"award-number":["888"]}]},{"DOI":"10.13039\/100000057","name":"HHS | NIH | National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["T32-GM08620"],"award-info":[{"award-number":["T32-GM08620"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005192","name":"California HIV\/AIDS Research Program","doi-asserted-by":"publisher","award":["ID07-I-124"],"award-info":[{"award-number":["ID07-I-124"]}],"id":[{"id":"10.13039\/100005192","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009819","name":"UC | UCI | Chao Family Comprehensive Cancer Center","doi-asserted-by":"publisher","award":["999"],"award-info":[{"award-number":["999"]}],"id":[{"id":"10.13039\/100009819","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Virol"],"published-print":{"date-parts":[[2017,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Previous studies in our laboratory showed that the RNA debranching enzyme (DBR1) is not required for early steps in HIV cDNA formation but is necessary for synthesis of intermediate and late cDNA products. To further characterize this effect, we evaluated the topology of the 5\u2032 end of the HIV-1 RNA genome during early infection with and without inhibition of DBR1 synthesis. Cells were transfected with DBR1 short hairpin RNA (shRNA) followed 48 h later by infection with an HIV-1-derived vector containing an RNase H-deficient reverse transcriptase (RT). RNA was isolated at several times postinfection and treated with various RNA-modifying enzymes prior to rapid amplification of 5\u2032 cDNA ends (5\u2032 RACE) for HIV-1 RNA and quantitative reverse transcriptase PCR (qRT-PCR). In infected cells, DBR1 knockdown inhibited detection of free HIV-1 RNA 5\u2032 ends at all time points. The difference in detection of free HIV-1 RNA 5\u2032 ends in infected DBR1 knockdown versus control cells was eliminated by\n            <jats:italic>in vitro<\/jats:italic>\n            incubation of infected cell RNAs with yeast or human DBR1 enzyme prior to 5\u2032 RACE and qRT-PCR. This was dependent on the 2\u2032-5\u2032 phosphatase activity of DBR1, since it did not occur when we used the catalytically inactive DBR1(N85A) mutant. Finally, HIV-1 RNA from infected DBR1 knockdown cells was resistant to RNase R that degrades linear RNAs but not RNAs in circular or lariat-like conformations. These results provide evidence for formation of a lariat-like structure involving the 5\u2032 end of HIV-1 RNA during an early step in infection and the involvement of DBR1 in resolving it.\n          <\/jats:p>\n          <jats:p>\n            <jats:bold>IMPORTANCE<\/jats:bold>\n            Our findings support a new view of the early steps in HIV genome replication. We show that the HIV genomic RNA is rapidly decapped and forms a lariat-like structure after entering a cell. The lariat-like structure is subsequently resolved by the cellular enzyme DBR1, leaving a 5\u2032 phosphate. This pathway is similar to the formation and resolution of pre-mRNA intron lariats and therefore suggests that similar mechanisms may be used by HIV. Our work therefore opens a new area of investigation in HIV replication and may ultimately uncover new targets for inhibiting HIV replication and for preventing the development of AIDS.\n          <\/jats:p>","DOI":"10.1128\/jvi.01377-17","type":"journal-article","created":{"date-parts":[[2017,9,21]],"date-time":"2017-09-21T00:30:27Z","timestamp":1505953827000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":16,"title":["Conformational Changes in the 5\u2032 End of the HIV-1 Genome Dependent on the Debranching Enzyme DBR1 during Early Stages of Infection"],"prefix":"10.1128","volume":"91","author":[{"given":"Alvaro E.","family":"Galvis","sequence":"first","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA"},{"name":"Division of Infectious Diseases, University of California, Irvine, California, USA"},{"name":"Cancer Research Institute, University of California, Irvine, California, USA"},{"name":"Center for Virus Research, University of California, Irvine, California, USA"},{"name":"Institute for Immunology, University of California, Irvine, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hugh E.","family":"Fisher","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, University of California, Irvine, California, USA"},{"name":"Cancer Research Institute, University of California, Irvine, California, USA"},{"name":"Center for Virus Research, University of California, Irvine, California, USA"},{"name":"Institute for Immunology, University of California, Irvine, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hung","family":"Fan","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA"},{"name":"Cancer Research Institute, University of California, 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