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1.
RNA ; 30(1): 68-88, 2023 Dec 18.
Artículo en Inglés | MEDLINE | ID: mdl-37914398

RESUMEN

The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous regions within the 5' end of the gRNA that assumes a higher order structure harboring several structural motifs. To better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ sequences using genetic, biochemical, and structure-function relationship approaches. Our mutational analysis revealed that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput selective 2' hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences, with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained nucleotides 80-92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA-Pr50Gag interactions. Delineating sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of FIV-based vectors for human gene therapy.


Asunto(s)
Virus de la Inmunodeficiencia Felina , Animales , Gatos , Humanos , Virus de la Inmunodeficiencia Felina/genética , Virus de la Inmunodeficiencia Felina/metabolismo , ARN Guía de Sistemas CRISPR-Cas , ARN Viral/química , Sitios de Unión , Genómica , Ensamble de Virus/genética
2.
Nucleic Acids Res ; 49(8): 4668-4688, 2021 05 07.
Artículo en Inglés | MEDLINE | ID: mdl-33836091

RESUMEN

Retroviral RNA genome (gRNA) harbors cis-acting sequences that facilitate its specific packaging from a pool of other viral and cellular RNAs by binding with high-affinity to the viral Gag protein during virus assembly. However, the molecular intricacies involved during selective gRNA packaging are poorly understood. Binding and footprinting assays on mouse mammary tumor virus (MMTV) gRNA with purified Pr77Gag along with in cell gRNA packaging study identified two Pr77Gag binding sites constituting critical, non-redundant packaging signals. These included: a purine loop in a bifurcated stem-loop containing the gRNA dimerization initiation site, and the primer binding site (PBS). Despite these sites being present on both unspliced and spliced RNAs, Pr77Gag specifically bound to unspliced RNA, since only that could adopt the native bifurcated stem-loop structure containing looped purines. These results map minimum structural elements required to initiate MMTV gRNA packaging, distinguishing features that are conserved amongst divergent retroviruses from those perhaps unique to MMTV. Unlike purine-rich motifs frequently associated with packaging signals, direct involvement of PBS in gRNA packaging has not been documented in retroviruses. These results enhance our understanding of retroviral gRNA packaging/assembly, making it not only a target for novel therapeutic interventions, but also development of safer gene therapy vectors.


Asunto(s)
Productos del Gen gag/metabolismo , Virus del Tumor Mamario del Ratón/metabolismo , Empalme del ARN , ARN Viral/metabolismo , Ensamble de Virus/genética , Animales , Sitios de Unión/genética , Cartilla de ADN , Dispersión Dinámica de Luz , Productos del Gen gag/genética , Genoma Viral , Virus del Tumor Mamario del Ratón/genética , Ratones , Conformación de Ácido Nucleico , Purinas , ARN Viral/genética , Reacción en Cadena en Tiempo Real de la Polimerasa
3.
Int J Mol Sci ; 22(6)2021 Mar 11.
Artículo en Inglés | MEDLINE | ID: mdl-33799890

RESUMEN

Protein post-translational modifications (PTMs) play key roles in eukaryotes since they finely regulate numerous mechanisms used to diversify the protein functions and to modulate their signaling networks. Besides, these chemical modifications also take part in the viral hijacking of the host, and also contribute to the cellular response to viral infections. All domains of the human immunodeficiency virus type 1 (HIV-1) Gag precursor of 55-kDa (Pr55Gag), which is the central actor for viral RNA specific recruitment and genome packaging, are post-translationally modified. In this review, we summarize the current knowledge about HIV-1 Pr55Gag PTMs such as myristoylation, phosphorylation, ubiquitination, sumoylation, methylation, and ISGylation in order to figure out how these modifications affect the precursor functions and viral replication. Indeed, in HIV-1, PTMs regulate the precursor trafficking between cell compartments and its anchoring at the plasma membrane, where viral assembly occurs. Interestingly, PTMs also allow Pr55Gag to hijack the cell machinery to achieve viral budding as they drive recognition between viral proteins or cellular components such as the ESCRT machinery. Finally, we will describe and compare PTMs of several other retroviral Gag proteins to give a global overview of their role in the retroviral life cycle.


Asunto(s)
VIH-1/metabolismo , Precursores de Proteínas/metabolismo , Procesamiento Proteico-Postraduccional , ARN Viral/metabolismo , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/metabolismo , Membrana Celular/metabolismo , Membrana Celular/virología , Complejos de Clasificación Endosomal Requeridos para el Transporte/genética , VIH-1/genética , Humanos , Precursores de Proteínas/genética , ARN Viral/genética , Ensamble de Virus/genética , Replicación Viral/genética , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/genética
4.
Biophys J ; 119(2): 419-433, 2020 07 21.
Artículo en Inglés | MEDLINE | ID: mdl-32574557

RESUMEN

The human immunodeficiency virus type 1 Gag precursor specifically selects the unspliced viral genomic RNA (gRNA) from the bulk of cellular and spliced viral RNAs via its nucleocapsid (NC) domain and drives gRNA encapsidation at the plasma membrane (PM). To further identify the determinants governing the intracellular trafficking of Gag-gRNA complexes and their accumulation at the PM, we compared, in living and fixed cells, the interactions between gRNA and wild-type Gag or Gag mutants carrying deletions in NC zinc fingers (ZFs) or a nonmyristoylated version of Gag. Our data showed that the deletion of both ZFs simultaneously or the complete NC domain completely abolished intracytoplasmic Gag-gRNA interactions. Deletion of either ZF delayed the delivery of gRNA to the PM but did not prevent Gag-gRNA interactions in the cytoplasm, indicating that the two ZFs display redundant roles in this respect. However, ZF2 played a more prominent role than ZF1 in the accumulation of the ribonucleoprotein complexes at the PM. Finally, the myristate group, which is mandatory for anchoring the complexes at the PM, was found to be dispensable for the association of Gag with the gRNA in the cytosol.


Asunto(s)
VIH-1 , Membrana Celular , Genómica , VIH-1/genética , Humanos , ARN Guía de Kinetoplastida , ARN Viral , Ensamble de Virus , Dedos de Zinc
5.
Nat Methods ; 12(9): 866-72, 2015 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-26237229

RESUMEN

RNA regulates many biological processes; however, identifying functional RNA sequences and structures is complex and time-consuming. We introduce a method, mutational interference mapping experiment (MIME), to identify, at single-nucleotide resolution, the primary sequence and secondary structures of an RNA molecule that are crucial for its function. MIME is based on random mutagenesis of the RNA target followed by functional selection and next-generation sequencing. Our analytical approach allows the recovery of quantitative binding parameters and permits the identification of base-pairing partners directly from the sequencing data. We used this method to map the binding site of the human immunodeficiency virus-1 (HIV-1) Pr55(Gag) protein on the viral genomic RNA in vitro, and showed that, by analyzing permitted base-pairing patterns, we could model RNA structure motifs that are crucial for protein binding.


Asunto(s)
Mutagénesis Sitio-Dirigida/métodos , Precursores de Proteínas/química , Precursores de Proteínas/genética , ARN Viral/química , ARN Viral/genética , Análisis de Secuencia de ARN/métodos , Secuencia de Bases , Datos de Secuencia Molecular , Mutación/genética , Relación Estructura-Actividad
6.
RNA Biol ; 15(7): 923-936, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29954247

RESUMEN

The Pr55Gag precursor specifically selects the HIV-1 genomic RNA (gRNA) from a large excess of cellular and partially or fully spliced viral RNAs and drives the virus assembly at the plasma membrane. During these processes, the NC domain of Pr55Gag interacts with the gRNA, while its C-terminal p6 domain binds cellular and viral factors and orchestrates viral particle release. Gag∆p6 is a truncated form of Pr55Gag lacking the p6 domain usually used as a default surrogate for wild type Pr55Gag for in vitro analysis. With recent advance in production of full-length recombinant Pr55Gag, here, we tested whether the p6 domain also contributes to the RNA binding specificity of Pr55Gag by systematically comparing binding of Pr55Gag and Gag∆p6 to a panel of viral and cellular RNAs. Unexpectedly, our fluorescence data reveal that the p6 domain is absolutely required for specific binding of Pr55Gag to the HIV-1 gRNA. Its deletion resulted not only in a decreased affinity for gRNA, but also in an increased affinity for spliced viral and cellular RNAs. In contrast Gag∆p6 displayed a similar affinity for all tested RNAs. Removal of the C-terminal His-tag from Pr55Gag and Gag∆p6 uniformly increased the Kd values of the RNA-protein complexes by ~ 2.5 fold but did not affect the binding specificities of these proteins. Altogether, our results demonstrate a novel role of the p6 domain in the specificity of Pr55Gag-RNA interactions, and strongly suggest that the p6 domain contributes to the discrimination of HIV-1 gRNA from cellular and spliced viral mRNAs, which is necessary for its selective encapsidation.


Asunto(s)
Genoma Viral/genética , VIH-1/fisiología , Precursores de Proteínas/metabolismo , ARN Viral/metabolismo , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/metabolismo , Sitios de Unión , Colorantes Fluorescentes/química , Colorantes Fluorescentes/metabolismo , VIH-1/genética , Humanos , Mutación , Plásmidos , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Precursores de Proteínas/genética , ARN Viral/genética , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/química , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/genética
7.
RNA Biol ; 14(1): 90-103, 2017 01 02.
Artículo en Inglés | MEDLINE | ID: mdl-27841704

RESUMEN

The HIV-1 Pr55Gag precursor specifically selects genomic RNA (gRNA) from a large variety of cellular and spliced viral RNAs (svRNAs), however the molecular mechanisms of this selective recognition remains poorly understood. To gain better understanding of this process, we analyzed the interactions between Pr55Gag and a large panel of viral RNA (vRNA) fragments encompassing the main packaging signal (Psi) and its flanking regions by fluorescence spectroscopy. We showed that the gRNA harbors a high affinity binding site which is absent from svRNA species, suggesting that this site might be crucial for selecting the HIV-1 genome. Our stoichiometry analysis of protein/RNA complexes revealed that few copies of Pr55Gag specifically associate with the 5' region of the gRNA. Besides, we found that gRNA dimerization significantly impacts Pr55Gag binding, and we confirmed that the internal loop of stem-loop 1 (SL1) in Psi is crucial for specific interaction with Pr55Gag. Our analysis of gRNA fragments of different length supports the existence of a long-range tertiary interaction involving sequences upstream and downstream of the Psi region. This long-range interaction might promote optimal exposure of SL1 for efficient Pr55Gag recognition. Altogether, our results shed light on the molecular mechanisms allowing the specific selection of gRNA by Pr55Gag among a variety of svRNAs, all harboring SL1 in their first common exon.


Asunto(s)
Genoma Viral , VIH-1/genética , VIH-1/metabolismo , Precursores de Proteínas/metabolismo , Empalme del ARN , ARN Viral/genética , ARN Viral/metabolismo , Sitios de Unión , Humanos , Secuencias Invertidas Repetidas , Cinética , Mutación , Conformación de Ácido Nucleico , ARN Viral/química , Proteínas de Unión al ARN/metabolismo
8.
J Virol ; 87(11): 6492-506, 2013 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-23576497

RESUMEN

The HIV-1 viral infectivity factor (Vif) is a small basic protein essential for viral fitness and pathogenicity. Vif allows productive infection in nonpermissive cells, including most natural HIV-1 target cells, by counteracting the cellular cytosine deaminases APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G [A3G]) and A3F. Vif is also associated with the viral assembly complex and packaged into viral particles through interactions with the viral genomic RNA and the nucleocapsid domain of Pr55(Gag). Recently, we showed that oligomerization of Vif into high-molecular-mass complexes induces Vif folding and influences its binding to high-affinity RNA binding sites present in the HIV genomic RNA. To get further insight into the role of Vif multimerization in viral assembly and A3G repression, we used fluorescence lifetime imaging microscopy (FLIM)- and fluorescence resonance energy transfer (FRET)-based assays to investigate Vif-Vif interactions in living cells. By using two N-terminally tagged Vif proteins, we show that Vif-Vif interactions occur in living cells. This oligomerization is strongly reduced when the putative Vif multimerization domain ((161)PPLP(164)) is mutated, indicating that this domain is crucial, but that regions outside this motif also participate in Vif oligomerization. When coexpressed together with Pr55(Gag), Vif is largely relocated to the cell membrane, where Vif oligomerization also occurs. Interestingly, wild-type A3G strongly interferes with Vif multimerization, contrary to an A3G mutant that does not bind to Vif. These findings confirm that Vif oligomerization occurs in living cells partly through its C-terminal motif and suggest that A3G may target and perturb the Vif oligomerization state to limit its functions in the cell.


Asunto(s)
Citidina Desaminasa/metabolismo , Infecciones por VIH/enzimología , VIH-1/metabolismo , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/química , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/metabolismo , Desaminasa APOBEC-3G , Secuencias de Aminoácidos , Citidina Desaminasa/genética , Infecciones por VIH/genética , Infecciones por VIH/virología , VIH-1/química , VIH-1/genética , Humanos , Multimerización de Proteína , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/genética
9.
RNA Biol ; 11(7): 906-20, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25144404

RESUMEN

The viral infectivity factor (Vif) is essential for the productive infection and dissemination of HIV-1 in non-permissive cells, containing the cellular anti-HIV defense cytosine deaminases APOBEC3 (A3G and A3F). Vif neutralizes the antiviral activities of the APOBEC3G/F by diverse mechanisms including their degradation through the ubiquitin/proteasome pathway and their translational inhibition. In addition, Vif appears to be an active partner of the late steps of viral replication by interacting with Pr55(Gag), reverse transcriptase and genomic RNA. Here, we expressed and purified full-length and truncated Vif proteins, and analyzed their RNA binding and chaperone properties. First, we showed by CD and NMR spectroscopies that the N-terminal domain of Vif is highly structured in solution, whereas the C-terminal domain remains mainly unfolded. Both domains exhibited substantial RNA binding capacities with dissociation constants in the nanomolar range, whereas the basic unfolded C-terminal domain of Vif was responsible in part for its RNA chaperone activity. Second, we showed by NMR chemical shift mapping that Vif and NCp7 share the same binding sites on tRNA(Lys) 3, the primer of HIV-1 reverse transcriptase. Finally, our results indicate that Vif has potent RNA chaperone activity and provide direct evidence for an important role of the unstructured C-terminal domain of Vif in this capacity.


Asunto(s)
VIH-1/metabolismo , Chaperonas Moleculares/metabolismo , ARN de Transferencia/metabolismo , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/química , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/metabolismo , Sitios de Unión , Dicroismo Circular , Resonancia Magnética Nuclear Biomolecular , Unión Proteica , Estructura Secundaria de Proteína , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/química , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/metabolismo
10.
Bioconjug Chem ; 24(11): 1813-23, 2013 Nov 20.
Artículo en Inglés | MEDLINE | ID: mdl-24134734

RESUMEN

Mannoside glycolipid conjugates are able to inhibit human immunodeficiency virus type 1 (HIV-1) trans-infection mediated by human dendritic cells (DCs). The conjugates are formed by three building blocks: a linear or branched mannose head, a hydrophilic linker, and a 24-carbon lipid chain. We have shown that, even as single molecules, these compounds efficiently target mannose-binding lectins, such as DC-specific ICAM-3-grabbing nonintegrin (DC-SIGN) important for HIV-1 transmission. With the goal to optimize their inhibitory activity by supramolecular structure formation, we have compared saturated and unsaturated conjugates, as single molecules, self-assemblies of dynamic micelles, and photopolymerized cross-linked polymers. Surface plasmon resonance showed that, unexpectedly, polymers of trivalent conjugates did not display a higher binding affinity for DC-SIGN than single molecules. Interactions on a chip or in solution were independent of calcium; however, binding to DCs was inhibited by a calcium chelator. Moreover, HIV-1 trans-infection was mostly inhibited by dynamic micelles and not by rigid polymers. The inhibition data revealed a clear correlation between the structure and molecular assembly of a conjugate and its biological antiviral activity. We present an interaction model between DC-SIGN and conjugates-either single molecules, micelles, or polymers-that highlights that the most effective interactions by dynamic micelles involve both mannose heads and lipid chains. Our data reveal that trivalent glycolipid conjugates display the highest microbicide potential for HIV prophylaxis, as dynamic micelles conjugates and not as rigid polymers.


Asunto(s)
Fármacos Anti-VIH/farmacología , Glucolípidos/farmacología , Infecciones por VIH/tratamiento farmacológico , Infecciones por VIH/transmisión , VIH-1/efectos de los fármacos , Manósidos/farmacología , Micelas , Polímeros/farmacología , Fármacos Anti-VIH/química , Células Cultivadas , Células Dendríticas/efectos de los fármacos , Células Dendríticas/inmunología , Células Dendríticas/virología , Relación Dosis-Respuesta a Droga , Glucolípidos/química , Infecciones por VIH/inmunología , VIH-1/fisiología , Humanos , Manósidos/química , Pruebas de Sensibilidad Microbiana , Microscopía Electrónica de Transmisión , Modelos Moleculares , Estructura Molecular , Polímeros/química , Espectrometría de Fluorescencia , Relación Estructura-Actividad , Resonancia por Plasmón de Superficie , Termodinámica
11.
Nucleic Acids Res ; 39(6): 2404-15, 2011 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-21076154

RESUMEN

The HIV-1 viral infectivity factor (Vif) is required for productive infection of non-permissive cells, including most natural HIV-1 targets, where it counteracts the antiviral activities of the cellular cytosine deaminases APOBEC-3G (A3G) and A3F. Vif is a multimeric protein and the conserved proline-rich domain (161)PPLP(164) regulating Vif oligomerization is crucial for its function and viral infectivity. Here, we expressed and purified wild-type Vif and a mutant protein in which alanines were substituted for the proline residues of the (161)PPLP(164) domain. Using dynamic light scattering, circular dichroism and fluorescence spectroscopy, we established the impact of these mutations on Vif oligomerization, secondary structure content and nucleic acids binding properties. In vitro, wild-type Vif formed oligomers of five to nine proteins, while Vif AALA formed dimers and/or trimers. Up to 40% of the unbound wild-type Vif protein appeared to be unfolded, but binding to the HIV-1 TAR apical loop promoted formation of ß-sheets. Interestingly, alanine substitutions did not significantly affect the secondary structure of Vif, but they diminished its binding affinity and specificity for nucleic acids. Dynamic light scattering showed that Vif oligomerization, and interaction with folding-promoting nucleic acids, favor formation of high molecular mass complexes. These properties could be important for Vif functions involving RNAs.


Asunto(s)
Proteínas de Unión al ARN/química , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/química , Secuencias de Aminoácidos , Sustitución de Aminoácidos , Fluorescencia , VIH-1/genética , Mutación , Prolina/genética , Unión Proteica , Pliegue de Proteína , Multimerización de Proteína , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , ARN Viral/metabolismo , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/genética , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/metabolismo
12.
Nucleic Acids Res ; 38(2): 633-46, 2010 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-19910370

RESUMEN

The HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells (including most natural HIV-1 targets) by counteracting the cellular cytosine deaminases APOBEC-3G (hA3G) and hA3F. The Vif-induced degradation of these restriction factors by the proteasome has been extensively studied, but little is known about the translational repression of hA3G and hA3F by Vif, which has also been proposed to participate in Vif function. Here, we studied Vif binding to hA3G mRNA and its role in translational repression. Filter binding assays and fluorescence titration curves revealed that Vif tightly binds to hA3G mRNA. Vif overall binding affinity was higher for the 3'UTR than for the 5'UTR, even though this region contained at least one high affinity Vif binding site (apparent K(d) = 27 +/- 6 nM). Several Vif binding sites were identified in 5' and 3'UTRs using RNase footprinting. In vitro translation evidenced that Vif inhibited hA3G translation by two mechanisms: a main time-independent process requiring the 5'UTR and an additional time-dependent, UTR-independent process. Results using a Vif protein mutated in the multimerization domain suggested that the molecular mechanism of translational control is more complicated than a simple physical blockage of scanning ribosomes.


Asunto(s)
Citidina Desaminasa/genética , Biosíntesis de Proteínas , ARN Mensajero/metabolismo , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/metabolismo , Regiones no Traducidas 3' , Regiones no Traducidas 5' , Desaminasa APOBEC-3G , Sitios de Unión , Citidina Desaminasa/metabolismo , Humanos , Mutación , Huella de Proteína , Espectrometría de Fluorescencia , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/genética
13.
Viruses ; 14(2)2022 02 05.
Artículo en Inglés | MEDLINE | ID: mdl-35215917

RESUMEN

Retroviruses must selectively recognize their unspliced RNA genome (gRNA) among abundant cellular and spliced viral RNAs to assemble into newly formed viral particles. Retroviral gRNA packaging is governed by Gag precursors that also orchestrate all the aspects of viral assembly. Retroviral life cycles, and especially the HIV-1 one, have been previously extensively analyzed by several methods, most of them based on molecular biology and biochemistry approaches. Despite these efforts, the spatio-temporal mechanisms leading to gRNA packaging and viral assembly are only partially understood. Nevertheless, in these last decades, progress in novel bioimaging microscopic approaches (as FFS, FRAP, TIRF, and wide-field microscopy) have allowed for the tracking of retroviral Gag and gRNA in living cells, thus providing important insights at high spatial and temporal resolution of the events regulating the late phases of the retroviral life cycle. Here, the implementation of these recent bioimaging tools based on highly performing strategies to label fluorescent macromolecules is described. This report also summarizes recent gains in the current understanding of the mechanisms employed by retroviral Gag polyproteins to regulate molecular mechanisms enabling gRNA packaging and the formation of retroviral particles, highlighting variations and similarities among the different retroviruses.


Asunto(s)
Cápside/metabolismo , Productos del Gen gag/metabolismo , Infecciones por Retroviridae/virología , Retroviridae/fisiología , Ensamble de Virus , Animales , Productos del Gen gag/genética , Genoma Viral , Humanos , Retroviridae/genética , Virión/genética , Virión/fisiología
14.
Viruses ; 13(8)2021 08 06.
Artículo en Inglés | MEDLINE | ID: mdl-34452424

RESUMEN

Late assembly (L) domains are conserved sequences that are necessary for the late steps of viral replication, acting like cellular adaptors to engage the ESCRT membrane fission machinery that promote virion release. These short sequences, whose mutation or deletion produce the accumulation of immature virions at the plasma membrane, were firstly identified within retroviral Gag precursors, and in a further step, also in structural proteins of many other enveloped RNA viruses including arenaviruses, filoviruses, rhabdoviruses, reoviruses, and paramyxoviruses. Three classes of L domains have been identified thus far (PT/SAP, YPXnL/LXXLF, and PPxY), even if it has recently been suggested that other motifs could act as L domains. Here, we summarize the current state of knowledge of the different types of L domains and their cellular partners in the budding events of RNA viruses, with a particular focus on retroviruses.


Asunto(s)
Virus ARN/genética , Virus ARN/fisiología , Ensamble de Virus/genética , Liberación del Virus , Complejos de Clasificación Endosomal Requeridos para el Transporte/metabolismo , Humanos , Unión Proteica , Ubiquitinación , Virión/fisiología , Ensamble de Virus/fisiología , Replicación Viral
15.
J Mol Biol ; 433(10): 166923, 2021 05 14.
Artículo en Inglés | MEDLINE | ID: mdl-33713677

RESUMEN

How retroviral Gag proteins recognize the packaging signals (Psi) on their genomic RNA (gRNA) is a key question that we addressed here using Mason-Pfizer monkey virus (MPMV) as a model system by combining band-shift assays and footprinting experiments. Our data show that Pr78Gag selects gRNA against spliced viral RNA by simultaneously binding to two single stranded loops on the MPMV Psi RNA: (1) a large purine loop (ssPurines), and (2) a loop which partially overlaps with a mostly base-paired purine repeat (bpPurines) and extends into a GU-rich binding motif. Importantly, this second Gag binding site is located immediately downstream of the major splice donor (mSD) and is thus absent from the spliced viral RNAs. Identifying elements crucial for MPMV gRNA packaging should help in understanding not only the mechanism of virion assembly by retroviruses, but also facilitate construction of safer retroviral vectors for human gene therapy.


Asunto(s)
Productos del Gen gag/química , Guanina/química , Virus del Mono Mason-Pfizer/química , ARN Viral/química , Uracilo/química , Animales , Emparejamiento Base , Secuencia de Bases , Sitios de Unión , Ensayo de Cambio de Movilidad Electroforética , Regulación Viral de la Expresión Génica , Productos del Gen gag/genética , Productos del Gen gag/metabolismo , Guanina/metabolismo , Interacciones Huésped-Patógeno , Virus del Mono Mason-Pfizer/genética , Virus del Mono Mason-Pfizer/metabolismo , Conformación de Ácido Nucleico , Papio , Unión Proteica , Conformación Proteica , Huella de Proteína , ARN Viral/genética , ARN Viral/metabolismo , Transducción de Señal , Uracilo/metabolismo
16.
Viruses ; 12(12)2020 11 26.
Artículo en Inglés | MEDLINE | ID: mdl-33256140

RESUMEN

RNA viruses are extraordinary evolution machines that efficiently ensure their replication by taking advantage of the association with viral and cellular components to form ribonucleic complexes (vRNPs) [...].


Asunto(s)
Complejos Multiproteicos/metabolismo , Ribonucleoproteínas/metabolismo , Proteínas Virales/metabolismo , Fenómenos Fisiológicos de los Virus , Animales , Regulación Viral de la Expresión Génica , Humanos , Unión Proteica , Ribonucleoproteínas/genética , Proteínas Virales/genética , Replicación Viral
17.
Methods Mol Biol ; 2113: 31-39, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32006306

RESUMEN

Dynamic light scattering represents an accurate, robust, and reliable technique to analyze molecule size in solution and monitor their interactions in real time. Here, we describe how to analyze by DLS an RNA-protein interaction. In our frame, we studied complexes formed between RNA fragments derived from the genome of HIV-1 in association with the viral precursor Pr55Gag. These interactions are crucial for the specific selection of the viral genomic RNA (gRNA) from the bulk of the viral spliced and cellular RNAs. This chapter displays how DLS allows to characterize the interactions that regulate the early steps of viral assembly.


Asunto(s)
VIH-1/fisiología , Precursores de Proteínas/metabolismo , ARN Viral/metabolismo , Dispersión Dinámica de Luz , VIH-1/metabolismo , Hidrodinámica , Ensamble de Virus
18.
Methods Mol Biol ; 2113: 237-250, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32006318

RESUMEN

Isothermal titration calorimetry (ITC) provides a sensitive, powerful, and accurate tool to suitably analyze the thermodynamic of RNA binding events. This approach does not require any modification or labeling of the system under analysis and is performed in solution. ITC is a very convenient technique that provides an accurate determination of binding parameters, as well as a complete thermodynamic profile of the molecular interactions. Here we show how this approach can be used to characterize the interactions between the dimerization initiation site (DIS) RNA localized within the HIV-1 viral genome and aminoglycoside antibiotics. Our ITC study showed that the 4,5-disubstituted 2-desoxystreptamine (2-DOS) aminoglycosides can bind the DIS with a nanomolar affinity and a high specificity.


Asunto(s)
Aminoglicósidos/metabolismo , Antibacterianos/metabolismo , VIH-1/genética , ARN Viral/química , ARN Viral/metabolismo , Calorimetría , Dimerización , VIH-1/química , Modelos Moleculares , Conformación de Ácido Nucleico , Termodinámica
19.
Nucleic Acids Res ; 35(21): 7128-39, 2007.
Artículo en Inglés | MEDLINE | ID: mdl-17942426

RESUMEN

Owing to a striking, and most likely fortuitous, structural and sequence similarity with the bacterial 16 S ribosomal A site, the RNA kissing-loop complex formed by the HIV-1 genomic RNA dimerization initiation site (DIS) specifically binds 4,5-disubstituted 2-deoxystreptamine (2-DOS) aminoglycoside antibiotics. We used chemical probing, molecular modeling, isothermal titration calorimetry (ITC) and UV melting to investigate aminoglycoside binding to the DIS loop-loop complex. We showed that apramycin, an aminoglycoside containing a bicyclic moiety, also binds the DIS, but in a different way than 4,5-disubstituted 2-DOS aminoglycosides. The determination of thermodynamic parameters for various aminoglycosides revealed the role of the different rings in the drug-RNA interaction. Surprisingly, we found that the affinity of lividomycin and neomycin for the DIS (K(d) approximately 30 nM) is significantly higher than that obtained in the same experimental conditions for their natural target, the bacterial A site (K(d) approximately 1.6 microM). In good agreement with their respective affinity, aminoglycoside increase the melting temperature of the loop-loop interaction and also block the conversion from kissing-loop complex to extended duplex. Taken together, our data might be useful for selecting new molecules with improved specificity and affinity toward the HIV-1 DIS RNA.


Asunto(s)
Regiones no Traducidas 5'/química , Aminoglicósidos/química , Antivirales/química , VIH-1/genética , ARN Viral/química , Antibacterianos/química , Sitios de Unión , Calorimetría , Cinamatos/química , Dimerización , Higromicina B/análogos & derivados , Higromicina B/química , Modelos Moleculares , Nebramicina/análogos & derivados , Nebramicina/química , Conformación de Ácido Nucleico , Paromomicina/análogos & derivados , Paromomicina/química , Termodinámica
20.
Front Microbiol ; 9: 527, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29623074

RESUMEN

The genome of the retroviruses is a dimer composed by two homologous copies of genomic RNA (gRNA) molecules of positive polarity. The dimerization process allows two gRNA molecules to be non-covalently linked together through intermolecular base-pairing. This step is critical for the viral life cycle and is highly conserved among retroviruses with the exception of spumaretroviruses. Furthermore, packaging of two gRNA copies into viral particles presents an important evolutionary advantage for immune system evasion and drug resistance. Recent studies reported RNA switches models regulating not only gRNA dimerization, but also translation and packaging, and a spatio-temporal characterization of viral gRNA dimerization within cells are now at hand. This review summarizes our current understanding on the structural features of the dimerization signals for a variety of retroviruses (HIVs, MLV, RSV, BLV, MMTV, MPMV…), the mechanisms of RNA dimer formation and functional implications in the retroviral cycle.

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