RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs

Simon, Anne; Gehrke, Lee

doi:10.1016/j.bbagrm.2009.05.005

Cited by 50 publications

(47 citation statements)

References 148 publications

(204 reference statements)

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“…13,27,[30][31][32][33][34] These observations highlight the crucial role of complex tertiary interactions that span thousands of nucleotides in viral genomes (reviewed in ref. [35][36][37].…”

Section: Dynamic Rna Structures In the Dengue Virus Genomementioning

confidence: 99%

Dynamic RNA structures in the dengue virus genome

Iglesias¹,

Gamarnik²

2011

RNA Biology

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Section: Dynamic Rna Structures In the Dengue Virus Genomementioning

confidence: 99%

Dynamic RNA structures in the dengue virus genome

Iglesias¹,

Gamarnik²

2011

RNA Biology

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“…The concept of "one RNA, one function" (e.g., for tRNA or mRNA) is increasingly seen as far too simplistic with RNAs known to alter their secondary/tertiary structures in regulated ways to control the appearance of distinct functional states (1). This multifunctionality is also true of the genomes of singlestranded (ss) RNA viruses, where refolding to promote replication, translation and control of gene expression are well known (2). Here we describe additional layers of previously unsuspected functions within the genome of the satellite plant virus, Satellite Tobacco Necrosis Virus (STNV).…”

mentioning

confidence: 99%

Revealing the density of encoded functions in a viral RNA

Patel

Dykeman

Coutts

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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We present direct experimental evidence that assembly of a single-stranded RNA virus occurs via a packaging signal-mediated mechanism. We show that the sequences of coat protein recognition motifs within multiple, dispersed, putative RNA packaging signals, as well as their relative spacing within a genomic fragment, act collectively to influence the fidelity and yield of capsid selfassembly in vitro. These experiments confirm that the selective advantages for viral yield and encapsidation specificity, predicted from previous modeling of packaging signal-mediated assembly, are found in Nature. Regions of the genome that act as packaging signals also function in translational and transcriptional enhancement, as well as directly coding for the coat protein, highlighting the density of encoded functions within the viral RNA. Assembly and gene expression are therefore direct molecular competitors for different functional folds of the same RNA sequence. The strongest packaging signal in the test fragment, encodes a region of the coat protein that undergoes a conformational change upon contact with packaging signals. A similar phenomenon occurs in other RNA viruses for which packaging signals are known. These contacts hint at an even deeper density of encoded functions in viral RNA, which if confirmed, would have profound consequences for the evolution of this class of pathogens.virus assembly | single-molecule fluorescence correlation spectroscopy | satellite tobacco necrosis virus | packaging signal

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“…These structures regulate many stages of the viral replication cycle, including genome replication, genome packaging into new viral particles, and intracellular trafficking (5,6,30,36,42). Studies on recombination in RNA viruses in general and in retroviruses in particular have indicated that RNA secondary structures play a potentially important role in genetic recombination (8,9,12,13,16,21,23,24,41).…”

mentioning

confidence: 99%

RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1

Simon‐Lorière

Martin

Weeks

et al. 2010

J Virol

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Many viruses, including retroviruses, undergo frequent recombination, a process which can increase their rate of adaptive evolution. In the case of HIV, recombination has been responsible for the generation of numerous intersubtype recombinant variants with epidemiological importance in the AIDS pandemic. Although it is known that fragments of genetic material do not combine randomly during the generation of recombinant viruses, the mechanisms that lead to preferential recombination at specific sites are not fully understood. Here we reanalyze recent independent data defining (i) the structure of a complete HIV-1 RNA genome and (ii) favorable sites for recombination. We show that in the absence of selection acting on recombinant genomes, regions harboring RNA structures in the NL4-3 model strain are strongly predictive of recombination breakpoints in the HIV-1 env genes of primary isolates. In addition, we found that breakpoints within recombinant HIV-1 genomes sampled from human populations, which have been acted upon extensively by natural selection, also colocalize with RNA structures. Critically, junctions between genes are enriched in structured RNA elements and are also preferred sites for generating functional recombinant forms. These data suggest that RNA structure-mediated recombination allows the virus to exchange intact genes rather than arbitrary subgene fragments, which is likely to increase the overall viability and replication success of the recombinant HIV progeny.Recombination is a vital source of genetic diversity for many RNA viruses (15,18,37,38,48,49). By combining polymorphisms present in distinct genomes into a new genome in a single round of replication, recombination enables viruses to more rapidly access greater sequence space than is possible by the stepwise accumulation of point mutations. The net effect is to facilitate both the combination of advantageous mutations within individual highly fit genomes and the removal of deleterious mutations from viral populations. In the case of human immunodeficiency virus (HIV), these processes contribute to the dynamic evasion of immune responses and to the evolution of drug resistance (20,27,34,45).In addition to encoding information necessary for protein production, the genomes of RNA viruses, including HIV, convey functional information through their secondary and tertiary structures. These structures regulate many stages of the viral replication cycle, including genome replication, genome packaging into new viral particles, and intracellular trafficking (5,6,30,36,42). Studies on recombination in RNA viruses in general and in retroviruses in particular have indicated that RNA secondary structures play a potentially important role in genetic recombination (8,9,12,13,16,21,23,24,41).In retroviruses, recombination results primarily from template switching during reverse transcription between the two RNA genomes that are present in the same viral particle (22,50). If these two copies are genetically different, as in a heterozygous virus, templat...

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RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs

Cited by 50 publications

References 148 publications

Dynamic RNA structures in the dengue virus genome

Dynamic RNA structures in the dengue virus genome

Revealing the density of encoded functions in a viral RNA

RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1

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