title: HIV-1 sequences isolated from patients promote expression of shorter isoforms of the Gag polyprotein.
abstract: Human immunodeficiency virus type 1 (HIV-1) unspliced mRNA drives the expression of both Gag and Gag-Pol polyproteins by using both cap- and internal ribosome entry site (IRES)-dependent translation initiation mechanisms. An IRES has been described in the matrix coding region that is involved in the production of shorter isoforms of Gag. However, up to now, this has only been shown with sequences derived from the HIV-1 laboratory strains (NL4.3 and HXB2) and never from clinical HIV-1 isolates. We have isolated ~70 sequences from HIV-1-positive patients that we have sequenced and cloned into an expression vector to monitor their ability to drive translation of Gag p55 and the shorter isoforms both in vitro and ex vivo. The results indicate that (1) the translational efficiency from the AUG-p55 varies significantly among the different isolates; (2) expression initiated at AUG-p40 codon is independent of translation initiation at the AUG-p55 triplet; and (3) all sequences promote expression of shorter Gag isoforms, in particular in Jurkat T cells, in which internal initiation occurs exclusively and directly at the AUG-p40 codon. The composition of the first ~800 nucleotides of the HIV-1 unspliced mRNA modulates the expression initiated both at the AUG-p55 and AUG-p40 codons and may impact viral production and replication. Interestingly, the AUG-p40 codon and its surrounding nucleotide context are conserved amongst clinical isolates and are used as a translation initiation site to produce a shorter Gag isoform.
authors.affiliation: CIRI, International Center for Infectiology Research, Université de Lyon, 46 Allée d'Italie, 69364, Lyon, France.|Inserm, U1111, 46 Allée d'Italie, 69364, Lyon, France.|Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France.|Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69364, Lyon, France.|CNRS, UMR5308, 46 Allée d'Italie, 69364, Lyon, France.|Waking team, Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, Université Claude Bernard, Lyon, France.
authors.forename: Christelle
authors.initials: C
authors.lastname: Daudé
authors.affiliation: CIRI, International Center for Infectiology Research, Université de Lyon, 46 Allée d'Italie, 69364, Lyon, France.|Inserm, U1111, 46 Allée d'Italie, 69364, Lyon, France.|Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France.|Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69364, Lyon, France.|CNRS, UMR5308, 46 Allée d'Italie, 69364, Lyon, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Décimo
authors.affiliation: Hospices Civils de Lyon, Lyon, France.
authors.forename: Mary-Anne
authors.initials: MA
authors.lastname: Trabaud
authors.affiliation: CIRI, International Center for Infectiology Research, Université de Lyon, 46 Allée d'Italie, 69364, Lyon, France.|Inserm, U1111, 46 Allée d'Italie, 69364, Lyon, France.|Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France.|Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69364, Lyon, France.|CNRS, UMR5308, 46 Allée d'Italie, 69364, Lyon, France.|Hospices Civils de Lyon, Lyon, France.
authors.forename: Patrice
authors.initials: P
authors.lastname: André
authors.affiliation: CIRI, International Center for Infectiology Research, Université de Lyon, 46 Allée d'Italie, 69364, Lyon, France. theophile.ohlmann@ens-lyon.fr.|Inserm, U1111, 46 Allée d'Italie, 69364, Lyon, France. theophile.ohlmann@ens-lyon.fr.|Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France. theophile.ohlmann@ens-lyon.fr.|Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69364, Lyon, France. theophile.ohlmann@ens-lyon.fr.|CNRS, UMR5308, 46 Allée d'Italie, 69364, Lyon, France. theophile.ohlmann@ens-lyon.fr.|Hospices Civils de Lyon, Lyon, France. theophile.ohlmann@ens-lyon.fr.
authors.forename: Théophile
authors.initials: T
authors.lastname: Ohlmann
authors.affiliation: CIRI, International Center for Infectiology Research, Université de Lyon, 46 Allée d'Italie, 69364, Lyon, France. sylvain.de.breyne@ens-lyon.fr.|Inserm, U1111, 46 Allée d'Italie, 69364, Lyon, France. sylvain.de.breyne@ens-lyon.fr.|Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France. sylvain.de.breyne@ens-lyon.fr.|Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69364, Lyon, France. sylvain.de.breyne@ens-lyon.fr.|CNRS, UMR5308, 46 Allée d'Italie, 69364, Lyon, France. sylvain.de.breyne@ens-lyon.fr.
authors.forename: Sylvain
authors.identifier: http://orcid.org/0000-0002-1632-3475
authors.initials: S
authors.lastname: de Breyne
mesh_terms: D003001:Cloning, Molecular; D005260:Female; D015870:Gene Expression; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification*; D006801:Humans; D019169:Jurkat Cells; D008297:Male; D014176:Protein Biosynthesis; D020033:Protein Isoforms / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D020033:Protein Isoforms; D012367:RNA, Viral; D054301:gag Gene Products, Human Immunodeficiency Virus