Structure of the HIV-1 5′ Untranslated Region Dimer Alone and in Complex with Gold Nanocolloids: Support of a TAR–TAR-Containing 5′ Dimer Linkage Site (DLS) and a 3′ DIS–DIS-Containing DLS

Biochemistry ◽  
2011 ◽  
Vol 50 (28) ◽  
pp. 6170-6177 ◽  
Author(s):  
Jesper Pallesen
Keyword(s):  
Untranslated Region ◽  
Dimer Linkage ◽  
Hiv 1

Does HIV-1 mRNA 5'-untranslated region bear an internal ribosome entry site?

Biochimie ◽  
2016 ◽  
Vol 121 ◽  
pp. 228-237 ◽  
Author(s):  
Victoria V. Smirnova ◽  
Ilya M. Terenin ◽  
Anastasia A. Khutornenko ◽  
Dmitri E. Andreev ◽  
Sergey E. Dmitriev ◽  
...  
Keyword(s):  
Internal Ribosome Entry Site ◽  
Untranslated Region ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Hiv 1

scholarly journals Dimerization and Template Switching in the 5′ Untranslated Region between Various Subtypes of Human Immunodeficiency Virus Type 1

2003 ◽  
Vol 77 (5) ◽  
pp. 3020-3030 ◽  
Author(s):  
Ebbe Sloth Andersen ◽  
Rienk E. Jeeninga ◽  
Christian Kroun Damgaard ◽  
Ben Berkhout ◽  
Jørgen Kjems
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Reverse Transcription ◽  
Untranslated Region ◽  
Template Switching ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT The human immunodeficiency virus type 1 (HIV-1) particle contains two identical RNA strands, each corresponding to the entire genome. The 5′ untranslated region (UTR) of each RNA strand contains extensive secondary and tertiary structures that are instrumental in different steps of the viral replication cycle. We have characterized the 5′ UTRs of nine different HIV-1 isolates representing subtypes A through G and, by comparing their homodimerization and heterodimerization potentials, found that complementarity between the palindromic sequences in the dimerization initiation site (DIS) hairpins is necessary and sufficient for in vitro dimerization of two subtype RNAs. The 5′ UTR sequences were used to design donor and acceptor templates for a coupled in vitro dimerization-reverse transcription assay. We showed that template switching during reverse transcription is increased with a matching DIS palindrome and further stimulated proportional to the level of homology between the templates. The presence of the HIV-1 nucleocapsid protein NCp7 increased the template-switching efficiency for matching DIS palindromes twofold, whereas the recombination efficiency was increased sevenfold with a nonmatching palindrome. Since NCp7 did not effect the dimerization of nonmatching palindromes, we concluded that the protein most likely stimulates the strand transfer reaction. An analysis of the distribution of template-switching events revealed that it occurs throughout the 5′ UTR. Together, these results demonstrate that the template switching of HIV-1 reverse transcriptase occurs frequently in vitro and that this process is facilitated mainly by template proximity and the level of homology.

scholarly journals Reconstitution of selective HIV-1 RNA packaging in vitro by membrane-bound Gag assemblies

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Lars-Anders Carlson ◽  
Yun Bai ◽  
Sarah C Keane ◽  
Jennifer A Doudna ◽  
James H Hurley
Keyword(s):  
Self Assembly ◽  
Untranslated Region ◽  
Minimal System ◽  
The Self ◽  
Viral Rna ◽  
Large Excess ◽  
Rna Packaging ◽  
Membrane Bound ◽  
Hiv 1

HIV-1 Gag selects and packages a dimeric, unspliced viral RNA in the context of a large excess of cytosolic human RNAs. As Gag assembles on the plasma membrane, the HIV-1 genome is enriched relative to cellular RNAs by an unknown mechanism. We used a minimal system consisting of purified RNAs, recombinant HIV-1 Gag and giant unilamellar vesicles to recapitulate the selective packaging of the 5’ untranslated region of the HIV-1 genome in the presence of excess competitor RNA. Mutations in the CA-CTD domain of Gag which subtly affect the self-assembly of Gag abrogated RNA selectivity. We further found that tRNA suppresses Gag membrane binding less when Gag has bound viral RNA. The ability of HIV-1 Gag to selectively package its RNA genome and its self-assembly on membranes are thus interdependent on one another.

scholarly journals Intrinsic conformational dynamics of the HIV-1 genomic RNA 5′UTR

2019 ◽  
Vol 116 (21) ◽  
pp. 10372-10381 ◽  
Author(s):  
Benjamin S. Brigham ◽  
Jonathan P. Kitzrow ◽  
Joshua-Paolo C. Reyes ◽  
Karin Musier-Forsyth ◽  
James B. Munro
Keyword(s):  
Single Molecule ◽  
Untranslated Region ◽  
Conformational Dynamics ◽  
Initiation Site ◽  
Conformational Switch ◽  
Virion Assembly ◽  
Primer Annealing ◽  
Genome Dimerization ◽  
Hiv 1 ◽  
Dimerization Initiation Site

The highly conserved 5′ untranslated region (5′UTR) of the HIV-1 RNA genome is central to the regulation of virus replication. NMR and biochemical experiments support a model in which the 5′UTR can transition between at least two conformational states. In one state the genome remains a monomer, as the palindromic dimerization initiation site (DIS) is sequestered via base pairing to upstream sequences. In the second state, the DIS is exposed, and the genome is competent for kissing loop dimerization and packaging into assembling virions where an extended dimer is formed. According to this model the conformation of the 5′UTR determines the fate of the genome. In this work, the dynamics of this proposed conformational switch and the factors that regulate it were probed using multiple single-molecule and in-gel ensemble FRET assays. Our results show that the HIV-1 5′UTR intrinsically samples conformations that are stabilized by both viral and host factor binding. Annealing of tRNALys3, the primer for initiation of reverse transcription, can promote the kissing dimer but not the extended dimer. In contrast, HIV-1 nucleocapsid (NC) promotes formation of the extended dimer in both the absence and presence of tRNALys3. Our data are consistent with an ordered series of events that involves primer annealing, genome dimerization, and virion assembly.

scholarly journals Conservation of tRNA mimicry in the 5′-untranslated region of distinct HIV-1 subtypes

RNA ◽  
2017 ◽  
Vol 23 (12) ◽  
pp. 1850-1859 ◽  
Author(s):  
Roopa Comandur ◽  
Erik D. Olson ◽  
Karin Musier-Forsyth
Keyword(s):  
Untranslated Region ◽  
Hiv 1

scholarly journals Unpaired Guanosines in the 5′ Untranslated Region of HIV-1 RNA Act Synergistically To Mediate Genome Packaging

2020 ◽  
Vol 94 (21) ◽  
Author(s):  
Olga A. Nikolaitchik ◽  
Xayathed Somoulay ◽  
Jonathan M. O. Rawson ◽  
Jennifer A. Yoo ◽  
Vinay K. Pathak ◽  
...  
Keyword(s):  
Binding Sites ◽  
Untranslated Region ◽  
Virus Assembly ◽  
Viral Rna ◽  
Rna Packaging ◽  
Genome Packaging ◽  
Stem Loop ◽  
Rna Genome ◽  
Genome Encapsidation ◽  
Hiv 1

ABSTRACT The viral protein Gag selects full-length HIV-1 RNA from a large pool of mRNAs as virion genome during virus assembly. Currently, the precise mechanism that mediates the genome selection is not understood. Previous studies have identified several sites in the 5′ untranslated region (5′ UTR) of HIV-1 RNA that are bound by nucleocapsid (NC) protein, which is derived from Gag during virus maturation. However, whether these NC binding sites direct HIV-1 RNA genome packaging has not been fully investigated. In this report, we examined the roles of single-stranded exposed guanosines at NC binding sites in RNA genome packaging using stable cell lines expressing competing wild-type and mutant HIV-1 RNAs. Mutant RNA packaging efficiencies were determined by comparing their prevalences in cytoplasmic RNA and in virion RNA. We observed that multiple NC binding sites affected RNA packaging; of the sites tested, those located within stem-loop 1 of the 5′ UTR had the most significant effects. These sites were previously reported as the primary NC binding sites by using a chemical probe reverse-footprinting assay and as the major Gag binding sites by using an in vitro assay. Of the mutants tested in this report, substituting 3 to 4 guanosines resulted in <2-fold defects in packaging. However, when mutations at different NC binding sites were combined, severe defects were observed. Furthermore, combining the mutations resulted in synergistic defects in RNA packaging, suggesting redundancy in Gag-RNA interactions and a requirement for multiple Gag binding on viral RNA during HIV-1 genome encapsidation. IMPORTANCE HIV-1 must package its RNA genome during virus assembly to generate infectious viruses. To better understand how HIV-1 packages its RNA genome, we examined the roles of RNA elements identified as binding sites for NC, a Gag-derived RNA-binding protein. Our results demonstrate that binding sites within stem-loop 1 of the 5′ untranslated region play important roles in genome packaging. Although mutating one or two NC-binding sites caused only mild defects in packaging, mutating multiple sites resulted in severe defects in genome encapsidation, indicating that unpaired guanosines act synergistically to promote packaging. Our results suggest that Gag-RNA interactions occur at multiple RNA sites during genome packaging; furthermore, there are functionally redundant binding sites in viral RNA.

scholarly journals HLA-G 3′ Untranslated Region 14–Base Pair Deletion: Association With Poor Survival in an HIV-1–Infected Zimbabwean Population

2012 ◽  
Vol 207 (6) ◽  
pp. 903-906 ◽  
Author(s):  
Margit Hørup Larsen ◽  
Rutendo Zinyama ◽  
Per Kallestrup ◽  
Jan Gerstoft ◽  
Exnevia Gomo ◽  
...  
Keyword(s):  
Base Pair ◽  
Untranslated Region ◽  
Poor Survival ◽  
Base Pair Deletion ◽  
Hiv 1

Characterization of the 3' Untranslated Region of HLA-G in HIV-1 Infected Black South African Mothers and their Infants

2014 ◽  
Vol 30 (S1) ◽  
pp. A218-A219
Author(s):  
Heather A. Hong ◽  
Maria Paximadis ◽  
Glenda E. Gray ◽  
Louise Kuhn ◽  
Caroline T. Tiemessen
Keyword(s):  
South African ◽  
Untranslated Region ◽  
Black South African ◽  
Hiv 1
Sign in / Sign up

Export Citation Format

Share Document