scholarly journals Splicing affects presentation of RNA dimerization signals in HIV-2 in vitro

2004 ◽  
Vol 32 (15) ◽  
pp. 4585-4595 ◽  
Author(s):  
J.-M. Lanchy
Keyword(s):  
Rna Dimerization

scholarly journals Monitoring Retroviral RNA Dimerization In Vivo via Hammerhead Ribozyme Cleavage

1998 ◽  
Vol 72 (10) ◽  
pp. 8349-8353 ◽  
Author(s):  
Bijay K. Pal ◽  
Lisa Scherer ◽  
Laurie Zelby ◽  
Edouard Bertrand ◽  
John J. Rossi
Keyword(s):  
Hammerhead Ribozyme ◽  
Specific Interaction ◽  
Genetic Analyses ◽  
Rna Dimerization ◽  
Domain Interactions

ABSTRACT We have used a strategy for colocalization of Psi (Ψ)-tethered ribozymes and targets to demonstrate that Ψ sequences are capable of specific interaction in the cytoplasm of both packaging and nonpackaging cells. These results indicate that current in vitro dimerization models may have in vivo counterparts. The methodology used may be applied to further genetic analyses on Ψ domain interactions in vivo.

scholarly journals RNA Binding Properties of the Ty1 LTR-Retrotransposon Gag Protein

2021 ◽  
Vol 22 (16) ◽  
pp. 9103
Author(s):  
Julita Gumna ◽  
Angelika Andrzejewska-Romanowska ◽  
David J. Garfinkel ◽  
Katarzyna Pachulska-Wieczorek
Keyword(s):  
Rna Structure ◽  
Rna Binding ◽  
Rna Packaging ◽  
Packaging Signal ◽  
Mobility Shift ◽  
Gag Protein ◽  
Rna Dimerization ◽  
Electrophoretic Mobility Shift Assays

A universal feature of retroelement propagation is the formation of distinct nucleoprotein complexes mediated by the Gag capsid protein. The Ty1 retrotransposon Gag protein from Saccharomyces cerevisiae lacks sequence homology with retroviral Gag, but is functionally related. In addition to capsid assembly functions, Ty1 Gag promotes Ty1 RNA dimerization and cyclization and initiation of reverse transcription. Direct interactions between Gag and retrotransposon genomic RNA (gRNA) are needed for Ty1 replication, and mutations in the RNA-binding domain disrupt nucleation of retrosomes and assembly of functional virus-like particles (VLPs). Unlike retroviral Gag, the specificity of Ty1 Gag-RNA interactions remain poorly understood. Here we use microscale thermophoresis (MST) and electrophoretic mobility shift assays (EMSA) to analyze interactions of immature and mature Ty1 Gag with RNAs. The salt-dependent experiments showed that Ty1 Gag binds with high and similar affinity to different RNAs. However, we observed a preferential interaction between Ty1 Gag and Ty1 RNA containing a packaging signal (Psi) in RNA competition analyses. We also uncover a relationship between Ty1 RNA structure and Gag binding involving the pseudoknot present on Ty1 gRNA. In all likelihood, the differences in Gag binding affinity detected in vitro only partially explain selective Ty1 RNA packaging into VLPs in vivo.

scholarly journals A Riboswitch Regulates RNA Dimerization and Packaging in Human Immunodeficiency Virus Type 1 Virions

2004 ◽  
Vol 78 (19) ◽  
pp. 10814-10819 ◽  
Author(s):  
Marcel Ooms ◽  
Hendrik Huthoff ◽  
Rodney Russell ◽  
Chen Liang ◽  
Ben Berkhout
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Large Set ◽  
Rna Packaging ◽  
Rna Dimerization ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT The genome of retroviruses, including human immunodeficiency virus type 1 (HIV-1), consists of two identical RNA strands that are packaged as noncovalently linked dimers. The core packaging and dimerization signals are located in the downstream part of the untranslated leader of HIV-1 RNA—the Ψ and the dimerization initiation site (DIS) hairpins. The HIV-1 leader can adopt two alternative conformations that differ in the presentation of the DIS hairpin and consequently in their ability to dimerize in vitro. The branched multiple-hairpin (BMH) structure folds the poly(A) and DIS hairpins, but these domains are base paired in a long distance interaction (LDI) in the most stable LDI conformation. This LDI-BMH riboswitch regulates RNA dimerization in vitro. It was recently shown that the Ψ hairpin structure is also presented differently in the LDI and BMH structures. Several detailed in vivo studies have indicated that sequences throughout the leader RNA contribute to RNA packaging, but how these diverse mutations affect the packaging mechanism is not known. We reasoned that these effects may be due to a change in the LDI-BMH equilibrium, and we therefore reanalyzed the structural effects of a large set of leader RNA mutations that were presented in three previous studies (J. L. Clever, D. Mirandar, Jr., and T. G. Parslow, J. Virol. 76:12381-12387, 2002; C. Helga-Maria, M. L. Hammarskjold, and D. Rekosh, J. Virol. 73:4127-4135, 1999; R. S. Russell, J. Hu, V. Beriault, A. J. Mouland, M. Laughrea, L. Kleiman, M. A. Wainberg, and C. Liang, J. Virol. 77:84-96, 2003). This analysis revealed a strict correlation between the status of the LDI-BMH equilibrium and RNA packaging. Furthermore, a correlation is apparent between RNA dimerization and RNA packaging, and these processes may be coordinated by the same LDI-BMH riboswitch mechanism.

scholarly journals Bipartite Signal for Genomic RNA Dimerization in Moloney Murine Leukemia Virus

2002 ◽  
Vol 76 (7) ◽  
pp. 3135-3144 ◽  
Author(s):  
Hinh Ly ◽  
Tristram G. Parslow
Keyword(s):  
Thermal Stability ◽  
Murine Leukemia Virus ◽  
Leukemia Virus ◽  
Point Mutations ◽  
Moloney Murine Leukemia Virus ◽  
Genomic Rna ◽  
Rna Dimerization ◽  
Thermal Stability Of ◽  
Murine Leukemia

ABSTRACT Retroviral virions each contain two identical genomic RNA strands that are stably but noncovalently joined in parallel near their 5′ ends. For certain viruses, this dimerization has been shown to depend on a unique RNA stem-loop locus, called the dimer initiation site (DIS), that efficiently homodimerizes through a palindromic base sequence in its loop. Previous studies with Moloney murine leukemia virus (Mo-MuLV) identified two alternative DIS loci that can each independently support RNA dimerization in vitro but whose relative contributions are unknown. We now report that both of these loci contribute to the assembly of the Mo-MuLV dimer. Using targeted deletions, point mutagenesis, and antisense oligonucleotides, we found that each of the two stem-loops forms as predicted and contributes independently to dimerization in vitro through a mechanism involving autocomplementary interactions of its loop. Disruption of either DIS locus individually reduced both the yield and the thermal stability of the in vitro dimers, whereas disruption of both eliminated dimerization altogether. Similarly, the thermal stability of virion-derived dimers was impaired by deletion of both DIS elements, and point mutations in either element produced defects in viral replication that correlated with their effects on in vitro RNA dimerization. These findings support the view that in some retroviruses, dimer initiation and stability involve two or more closely linked DIS loci which together align the nascent dimer strands in parallel and in register.

scholarly journals Moloney Murine Sarcoma Virus Genomic RNAs Dimerize via a Two-Step Process: a Concentration-Dependent Kissing-Loop Interaction Is Driven by Initial Contact between Consecutive Guanines

1999 ◽  
Vol 73 (9) ◽  
pp. 7255-7261 ◽  
Author(s):  
Hinh Ly ◽  
Donald P. Nierlich ◽  
John C. Olsen ◽  
Andrew H. Kaplan
Keyword(s):  
Viral Replication ◽  
Genomic Rnas ◽  
Rna Dimerization ◽  
Murine Sarcoma Virus ◽  
Sarcoma Virus ◽  
Moloney Murine Sarcoma Virus ◽  
Murine Sarcoma ◽  
Palindromic Sequences ◽  
Kissing Loop

ABSTRACT Retroviruses contain two plus-strand genomic RNAs, which are stably but noncovalently joined in their 5′ regions by a dimer linkage structure (DLS). Two models have been put forward to explain the mechanisms by which the RNAs dimerize; each model emphasizes the role of specific molecular determinants. The kissing-loop model implicates interactions between palindromic sequences in the DLS region. The second model proposes that purine-rich stretches in the region form purine quartet structures. Here, we present an examination of the in vitro dimerization of Moloney murine sarcoma virus (MuSV) RNA in the context of these two models. Dimers were found to form spontaneously in a temperature-, time-, concentration-, and salt-dependent manner. In contrast to earlier reports, we found that deletion of neither the palindrome nor the consensus purine motifs (PuGGAPuA) affected the level of dimer formation at low concentrations of RNA. Rather, different purine-rich sequences, i.e., consecutive stretches of guanines, were found to enhance both in vitro RNA dimerization and in vivo viral replication. Biochemical evidence further suggests that these guanine-rich (G-rich) stretches form guanine quartet structures. We also found that the palindromic sequences could support dimerization at significantly higher RNA concentrations. In addition, the G-rich stretches were as important as the palindromic sequence for maintaining efficient viral replication. Overall, our data support a model that entails contributions from both of the previously proposed mechanisms of retroviral RNA dimerization.

scholarly journals RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

2012 ◽  
Vol 41 (4) ◽  
pp. 2594-2608 ◽  
Author(s):  
Daniella Ishimaru ◽  
Ewan P. Plant ◽  
Amy C. Sims ◽  
Boyd L. Yount ◽  
Braden M. Roth ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Palindromic Sequence ◽  
Sars Coronavirus ◽  
Stem Loop ◽  
Ribosomal Frameshifting ◽  
Rna Dimerization ◽  
Cellular Environment ◽  
Vitro Analysis ◽  
And Function

Abstract Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis.

scholarly journals HIV-2 RNA dimerization is regulated by intramolecular interactions in vitro

RNA ◽  
2007 ◽  
Vol 13 (8) ◽  
pp. 1341-1354 ◽  
Author(s):  
T. T. Baig ◽  
J.-M. Lanchy ◽  
J. S. Lodmell
Keyword(s):  
Intramolecular Interactions ◽  
Rna Dimerization

scholarly journals A Human Immunodeficiency Virus Type 1-Infected Individual with Low Viral Load Harbors a Virus Variant That Exhibits an In Vitro RNA Dimerization Defect

2004 ◽  
Vol 78 (9) ◽  
pp. 4907-4913 ◽  
Author(s):  
Hendrik Huthoff ◽  
Atze T. Das ◽  
Monique Vink ◽  
Bep Klaver ◽  
Fokla Zorgdrager ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Viral Load ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Infected Individual ◽  
Initiation Site ◽  
Rna Dimerization ◽  
Immunodeficiency Virus

ABSTRACT We investigated the in vitro RNA dimerization properties of the untranslated leader RNA derived from human immunodeficiency virus type 1 variants circulating in an individual with a low viral load and slow disease progression. The leader sequences of these viruses contain highly unusual polymorphisms within the dimerization initiation site (DIS): an insert that abolishes dimerization and a compensatory substitution. The dimerization of leader RNA from late stages of infection is further improved by additional mutations outside the DIS motif that facilitate a secondary structure switch from a dimerization-incompetent to a dimerization-competent RNA conformation.

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