Functional Analyses Reveal Extensive RRE Plasticity in Primary HIV-1 Sequences Selected under Selective Pressure

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Functional Analyses Reveal Extensive RRE Plasticity in Primary HIV-1 Sequences Selected under Selective Pressure. / Cunyat, Francesc; Beerens, Nancy; Garcia, Elisabet; Clotet, Bonaventura; Kjems, Jørgen; Cabrera, Cecilia.

In: P L o S One, Vol. 9, No. 8, 106299, 29.08.2014.

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Cunyat, Francesc ; Beerens, Nancy ; Garcia, Elisabet ; Clotet, Bonaventura ; Kjems, Jørgen ; Cabrera, Cecilia. / Functional Analyses Reveal Extensive RRE Plasticity in Primary HIV-1 Sequences Selected under Selective Pressure. In: P L o S One. 2014 ; Vol. 9, No. 8.

Bibtex

@article{e02a9f42d1b14cbc98c249ffbe8888e5,
title = "Functional Analyses Reveal Extensive RRE Plasticity in Primary HIV-1 Sequences Selected under Selective Pressure",
abstract = "Background: HIV-1 Rev response element (RRE) is a functional region of viral RNA lying immediately downstream to the junction of gp120 and gp41 in the env coding sequence. The RRE is essential for HIV replication and binds with the Rev protein to facilitate the export of viral mRNA from nucleus to cytoplasm. It has been suggested that changes in the predicted secondary structure of primary RRE sequences impact the function of the RREs; however, functional assays have not yet been performed. The aim of this study was to characterize the genetic, structural and functional variation in the RRE primary sequences selected in vivo by Enfuvirtide pressure.Results: Multiple RRE variants were obtained from viruses isolated from patients who failed an Enfuvirtide-containing regimen. Different alterations were observed in the predicted RRE secondary structures, with the abrogation of the primary Rev binding site in one of the variants. In spite of this, most of the RRE variants were able to bind Rev and promote the cytoplasmic export of the viral mRNAs with equivalent efficiency in a cell-based assay. Only RRE45 and RRE40-45 showed an impaired ability to bind Rev in a gel-shift binding assay. Unexpectedly, this impairment was not reflected in functional capacity when RNA export was evaluated using a reporter assay, or during virus replication in lymphoid cells, suggesting that in vivo the RRE would be highly malleable.Conclusions: The Rev-RRE functionality is unaffected in RRE variants selected in patients failing an ENF-containing regimen. Our data show that the current understanding of the Rev-RRE complex structure does not suffice and fails to rationally predict the function of naturally occurring RRE mutants. Therefore, this data should be taken into account in the development of antiviral agents that target the RRE-Rev complex.",
keywords = "IMMUNODEFICIENCY-VIRUS TYPE-1, RESPONSIVE ELEMENT RNA, SECONDARY STRUCTURE, TARGET SEQUENCE, GENE-EXPRESSION, ANTIRETROVIRAL THERAPY, TRANS-ACTIVATOR, NUCLEAR EXPORT, REX PROTEINS, BINDING",
author = "Francesc Cunyat and Nancy Beerens and Elisabet Garcia and Bonaventura Clotet and J{\o}rgen Kjems and Cecilia Cabrera",
year = "2014",
month = aug,
day = "29",
doi = "10.1371/journal.pone.0106299",
language = "English",
volume = "9",
journal = "P L o S One",
issn = "1932-6203",
publisher = "public library of science",
number = "8",

}

RIS

TY - JOUR

T1 - Functional Analyses Reveal Extensive RRE Plasticity in Primary HIV-1 Sequences Selected under Selective Pressure

AU - Cunyat, Francesc

AU - Beerens, Nancy

AU - Garcia, Elisabet

AU - Clotet, Bonaventura

AU - Kjems, Jørgen

AU - Cabrera, Cecilia

PY - 2014/8/29

Y1 - 2014/8/29

N2 - Background: HIV-1 Rev response element (RRE) is a functional region of viral RNA lying immediately downstream to the junction of gp120 and gp41 in the env coding sequence. The RRE is essential for HIV replication and binds with the Rev protein to facilitate the export of viral mRNA from nucleus to cytoplasm. It has been suggested that changes in the predicted secondary structure of primary RRE sequences impact the function of the RREs; however, functional assays have not yet been performed. The aim of this study was to characterize the genetic, structural and functional variation in the RRE primary sequences selected in vivo by Enfuvirtide pressure.Results: Multiple RRE variants were obtained from viruses isolated from patients who failed an Enfuvirtide-containing regimen. Different alterations were observed in the predicted RRE secondary structures, with the abrogation of the primary Rev binding site in one of the variants. In spite of this, most of the RRE variants were able to bind Rev and promote the cytoplasmic export of the viral mRNAs with equivalent efficiency in a cell-based assay. Only RRE45 and RRE40-45 showed an impaired ability to bind Rev in a gel-shift binding assay. Unexpectedly, this impairment was not reflected in functional capacity when RNA export was evaluated using a reporter assay, or during virus replication in lymphoid cells, suggesting that in vivo the RRE would be highly malleable.Conclusions: The Rev-RRE functionality is unaffected in RRE variants selected in patients failing an ENF-containing regimen. Our data show that the current understanding of the Rev-RRE complex structure does not suffice and fails to rationally predict the function of naturally occurring RRE mutants. Therefore, this data should be taken into account in the development of antiviral agents that target the RRE-Rev complex.

AB - Background: HIV-1 Rev response element (RRE) is a functional region of viral RNA lying immediately downstream to the junction of gp120 and gp41 in the env coding sequence. The RRE is essential for HIV replication and binds with the Rev protein to facilitate the export of viral mRNA from nucleus to cytoplasm. It has been suggested that changes in the predicted secondary structure of primary RRE sequences impact the function of the RREs; however, functional assays have not yet been performed. The aim of this study was to characterize the genetic, structural and functional variation in the RRE primary sequences selected in vivo by Enfuvirtide pressure.Results: Multiple RRE variants were obtained from viruses isolated from patients who failed an Enfuvirtide-containing regimen. Different alterations were observed in the predicted RRE secondary structures, with the abrogation of the primary Rev binding site in one of the variants. In spite of this, most of the RRE variants were able to bind Rev and promote the cytoplasmic export of the viral mRNAs with equivalent efficiency in a cell-based assay. Only RRE45 and RRE40-45 showed an impaired ability to bind Rev in a gel-shift binding assay. Unexpectedly, this impairment was not reflected in functional capacity when RNA export was evaluated using a reporter assay, or during virus replication in lymphoid cells, suggesting that in vivo the RRE would be highly malleable.Conclusions: The Rev-RRE functionality is unaffected in RRE variants selected in patients failing an ENF-containing regimen. Our data show that the current understanding of the Rev-RRE complex structure does not suffice and fails to rationally predict the function of naturally occurring RRE mutants. Therefore, this data should be taken into account in the development of antiviral agents that target the RRE-Rev complex.

KW - IMMUNODEFICIENCY-VIRUS TYPE-1

KW - RESPONSIVE ELEMENT RNA

KW - SECONDARY STRUCTURE

KW - TARGET SEQUENCE

KW - GENE-EXPRESSION

KW - ANTIRETROVIRAL THERAPY

KW - TRANS-ACTIVATOR

KW - NUCLEAR EXPORT

KW - REX PROTEINS

KW - BINDING

U2 - 10.1371/journal.pone.0106299

DO - 10.1371/journal.pone.0106299

M3 - Journal article

C2 - 25170621

VL - 9

JO - P L o S One

JF - P L o S One

SN - 1932-6203

IS - 8

M1 - 106299

ER -