HIV-1 integrase binding to genomic RNA 5′-UTR induces local structural changes in vitro and in virio

Abstract Background During HIV-1 maturation, Gag and Gag-Pol polyproteins are proteolytically cleaved and the capsid protein polymerizes to form the honeycomb capsid lattice. HIV-1 integrase (IN) binds the viral genomic RNA (gRNA) and impairment of IN-gRNA binding leads to mis-localization of the nu...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Shuohui Liu, Pratibha C. Koneru, Wen Li, Chathuri Pathirage, Alan N. Engelman, Mamuka Kvaratskhelia, Karin Musier-Forsyth
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	HIV-1 Nucleocapsid Integrase XL-SHAPE 5′-UTR RNA binding Immunologic diseases. Allergy RC581-607
Acceso en línea:	https://doaj.org/article/b25da067a5a5468487406fa1f1cc362a
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:b25da067a5a5468487406fa1f1cc362a
record_format	dspace
spelling	oai:doaj.org-article:b25da067a5a5468487406fa1f1cc362a2021-11-28T12:38:05ZHIV-1 integrase binding to genomic RNA 5′-UTR induces local structural changes in vitro and in virio10.1186/s12977-021-00582-01742-4690https://doaj.org/article/b25da067a5a5468487406fa1f1cc362a2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12977-021-00582-0https://doaj.org/toc/1742-4690Abstract Background During HIV-1 maturation, Gag and Gag-Pol polyproteins are proteolytically cleaved and the capsid protein polymerizes to form the honeycomb capsid lattice. HIV-1 integrase (IN) binds the viral genomic RNA (gRNA) and impairment of IN-gRNA binding leads to mis-localization of the nucleocapsid protein (NC)-condensed viral ribonucleoprotein complex outside the capsid core. IN and NC were previously demonstrated to bind to the gRNA in an orthogonal manner in virio; however, the effect of IN binding alone or simultaneous binding of both proteins on gRNA structure is not yet well understood. Results Using crosslinking-coupled selective 2′-hydroxyl acylation analyzed by primer extension (XL-SHAPE), we characterized the interaction of IN and NC with the HIV-1 gRNA 5′-untranslated region (5′-UTR). NC preferentially bound to the packaging signal (Psi) and a UG-rich region in U5, irrespective of the presence of IN. IN alone also bound to Psi but pre-incubation with NC largely abolished this interaction. In contrast, IN specifically bound to and affected the nucleotide (nt) dynamics of the apical loop of the transactivation response element (TAR) and the polyA hairpin even in the presence of NC. SHAPE probing of the 5′-UTR RNA in virions produced from allosteric IN inhibitor (ALLINI)-treated cells revealed that while the global secondary structure of the 5′-UTR remained unaltered, the inhibitor treatment induced local reactivity differences, including changes in the apical loop of TAR that are consistent with the in vitro results. Conclusions Overall, the binding interactions of NC and IN with the 5′-UTR are largely orthogonal in vitro. This study, together with previous probing experiments, suggests that IN and NC binding in vitro and in virio lead to only local structural changes in the regions of the 5′-UTR probed here. Accordingly, disruption of IN-gRNA binding by ALLINI treatment results in local rather than global secondary structure changes of the 5′-UTR in eccentric virus particles. Graphical AbstractShuohui LiuPratibha C. KoneruWen LiChathuri PathirageAlan N. EngelmanMamuka KvaratskheliaKarin Musier-ForsythBMCarticleHIV-1NucleocapsidIntegraseXL-SHAPE5′-UTRRNA bindingImmunologic diseases. AllergyRC581-607ENRetrovirology, Vol 18, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	HIV-1 Nucleocapsid Integrase XL-SHAPE 5′-UTR RNA binding Immunologic diseases. Allergy RC581-607
spellingShingle	HIV-1 Nucleocapsid Integrase XL-SHAPE 5′-UTR RNA binding Immunologic diseases. Allergy RC581-607 Shuohui Liu Pratibha C. Koneru Wen Li Chathuri Pathirage Alan N. Engelman Mamuka Kvaratskhelia Karin Musier-Forsyth HIV-1 integrase binding to genomic RNA 5′-UTR induces local structural changes in vitro and in virio
description	Abstract Background During HIV-1 maturation, Gag and Gag-Pol polyproteins are proteolytically cleaved and the capsid protein polymerizes to form the honeycomb capsid lattice. HIV-1 integrase (IN) binds the viral genomic RNA (gRNA) and impairment of IN-gRNA binding leads to mis-localization of the nucleocapsid protein (NC)-condensed viral ribonucleoprotein complex outside the capsid core. IN and NC were previously demonstrated to bind to the gRNA in an orthogonal manner in virio; however, the effect of IN binding alone or simultaneous binding of both proteins on gRNA structure is not yet well understood. Results Using crosslinking-coupled selective 2′-hydroxyl acylation analyzed by primer extension (XL-SHAPE), we characterized the interaction of IN and NC with the HIV-1 gRNA 5′-untranslated region (5′-UTR). NC preferentially bound to the packaging signal (Psi) and a UG-rich region in U5, irrespective of the presence of IN. IN alone also bound to Psi but pre-incubation with NC largely abolished this interaction. In contrast, IN specifically bound to and affected the nucleotide (nt) dynamics of the apical loop of the transactivation response element (TAR) and the polyA hairpin even in the presence of NC. SHAPE probing of the 5′-UTR RNA in virions produced from allosteric IN inhibitor (ALLINI)-treated cells revealed that while the global secondary structure of the 5′-UTR remained unaltered, the inhibitor treatment induced local reactivity differences, including changes in the apical loop of TAR that are consistent with the in vitro results. Conclusions Overall, the binding interactions of NC and IN with the 5′-UTR are largely orthogonal in vitro. This study, together with previous probing experiments, suggests that IN and NC binding in vitro and in virio lead to only local structural changes in the regions of the 5′-UTR probed here. Accordingly, disruption of IN-gRNA binding by ALLINI treatment results in local rather than global secondary structure changes of the 5′-UTR in eccentric virus particles. Graphical Abstract
format	article
author	Shuohui Liu Pratibha C. Koneru Wen Li Chathuri Pathirage Alan N. Engelman Mamuka Kvaratskhelia Karin Musier-Forsyth
author_facet	Shuohui Liu Pratibha C. Koneru Wen Li Chathuri Pathirage Alan N. Engelman Mamuka Kvaratskhelia Karin Musier-Forsyth
author_sort	Shuohui Liu
title	HIV-1 integrase binding to genomic RNA 5′-UTR induces local structural changes in vitro and in virio
title_short	HIV-1 integrase binding to genomic RNA 5′-UTR induces local structural changes in vitro and in virio
title_full	HIV-1 integrase binding to genomic RNA 5′-UTR induces local structural changes in vitro and in virio
title_fullStr	HIV-1 integrase binding to genomic RNA 5′-UTR induces local structural changes in vitro and in virio
title_full_unstemmed	HIV-1 integrase binding to genomic RNA 5′-UTR induces local structural changes in vitro and in virio
title_sort	hiv-1 integrase binding to genomic rna 5′-utr induces local structural changes in vitro and in virio
publisher	BMC
publishDate	2021
url	https://doaj.org/article/b25da067a5a5468487406fa1f1cc362a
work_keys_str_mv	AT shuohuiliu hiv1integrasebindingtogenomicrna5utrinduceslocalstructuralchangesinvitroandinvirio AT pratibhackoneru hiv1integrasebindingtogenomicrna5utrinduceslocalstructuralchangesinvitroandinvirio AT wenli hiv1integrasebindingtogenomicrna5utrinduceslocalstructuralchangesinvitroandinvirio AT chathuripathirage hiv1integrasebindingtogenomicrna5utrinduceslocalstructuralchangesinvitroandinvirio AT alannengelman hiv1integrasebindingtogenomicrna5utrinduceslocalstructuralchangesinvitroandinvirio AT mamukakvaratskhelia hiv1integrasebindingtogenomicrna5utrinduceslocalstructuralchangesinvitroandinvirio AT karinmusierforsyth hiv1integrasebindingtogenomicrna5utrinduceslocalstructuralchangesinvitroandinvirio
_version_	1718407914119495680

HIV-1 integrase binding to genomic RNA 5′-UTR induces local structural changes in vitro and in virio

Ejemplares similares