A Viral Noncoding RNA Complements a Weakened Viral RNA Silencing Suppressor and Promotes Efficient Systemic Host Infection

Flobinus, Alyssa; Hleibieh, Kamal; Klein, Elodie; Ratti, Claudio; Bouzoubaa, S.; Gilmer, David

doi:10.3390/v8100272

Cited by 29 publications

(33 citation statements)

References 33 publications

(80 reference statements)

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“…The mechanisms by which other RNA viruses maintain the stability of their transcripts during infection have not been wellcharacterized. Interestingly, XRN1 stalling at specific sites in viral RNAs has also been noted for several segmented plant RNA viruses (19,20). Thus, we hypothesized that segmented RNA viruses infecting mammalian systems might have also evolved RNA structure-based strategies to stall XRN1 as part of their approach for effective host interaction.…”

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confidence: 90%

Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1

Charley

Wilusz

2018

Journal of Biological Chemistry

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Regulated mRNA decay plays a vital role in determining both the level and quality of cellular gene expression. Viral RNAs must successfully evade this host RNA decay machinery to establish a productive infection. One way for RNA viruses to accomplish this is to target the cellular exoribonuclease XRN1, because this enzyme is accessible in the cytoplasm and plays a major role in mRNA decay. Members of the Flaviviridae use RNA structures in their 5'- or 3'-untranslated regions to stall and repress XRN1, effectively stabilizing viral RNAs while also causing significant dysregulation of host cell mRNA stability. Here, we use a series of biochemical assays to demonstrate that the 3'-terminal portion of the nucleocapsid (N) mRNA of Rift Valley fever virus, a phlebovirus of the Bunyaviridae family, also can effectively stall and repress XRN1. The region responsible for impeding XRN1 includes a G-rich portion that likely forms a G-quadruplex structure. The 3'-terminal portions of ambisense-derived transcripts of multiple arenaviruses also stalled XRN1. Therefore, we conclude that RNAs from two additional families of mammalian RNA viruses stall and repress XRN1. This observation. emphasizes the importance and commonality of this viral strategy to interfere with the 5'-to-3'-exoribonuclease component of the cytoplasmic RNA decay machinery.

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confidence: 90%

Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1

Charley

Wilusz

2018

Journal of Biological Chemistry

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“…Exoribonuclease resistance as a means to generate non-coding RNA from larger precursors is an emerging theme in virology (21)(22)(23)(24)26). We have found that exoribonuclease-blocking sequences from plant-infecting dianthoviruses are authentic xrRNAs, generating viral non-coding RNAs in a process dependent on a specific but dynamic threedimensional RNA fold.…”

Section: Discussionmentioning

confidence: 99%

“…Exoribonuclease resistance conferred by RNA structure may be a more common mechanism than hitherto anticipated, and recent studies have identified putative xrRNAs in several virus families. A conserved sequence that blocks 5¢à3¢ exoribonucleolytic decay was recently found in the 3¢UTR of plant-infecting benyviruses and cucumoviruses; both have multipartite positive-sense RNA genomes (23,24,31). Moreover, Xrn1 is confounded by RNA elements in the 5¢UTRs of hepaci-and pestiviruses (21), as well as by a G-rich sequence structure in the N mRNA of Rift Valley fever virus, and multiple RNA structures in ambisense-derived transcripts of arenaviruses (22).…”

Section: Discussionmentioning

confidence: 99%

“…The three-dimensional structure of a class 2 flavivirus RNA has not been solved, thus for simplicity we will use the term 'flavivirus xrRNA' here to refer to the well-characterized class 1 flavivirus xrRNAs, unless otherwise specified. In addition, RNA sequences that appear to resist 5¢à3¢ exoribonuclease degradation have been identified in a few other virus families (21)(22)(23)(24), However, nothing is known about the molecular processes or structures of putative xrRNAs outside the flavivirus family. We do not know if other candidate exoribonuclease-resistant RNAs operate with the help of protein factors or if they are stably structured elements sufficient to block processive degradation.…”

Section: Introductionmentioning

confidence: 99%

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A folded viral noncoding RNA blocks host cell exoribonucleases through programmed remodeling of RNA structure

Steckelberg

et al. 2018

Preprint

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Folded RNA elements that block processive 5¢à3¢ cellular exoribonucleases (xrRNAs) to produce biologically active viral non-coding RNAs were discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, it was unknown if this RNA structure-dependent mechanism exists elsewhere and if so, whether a singular RNA fold is required. Here, we demonstrate the existence of authentic RNA structure-dependent xrRNAs in dianthoviruses, plant-infecting viruses unrelated to animal-infecting flaviviruses. These novel xrRNAs have no sequence similarity to known xrRNAs, thus we used a combination of biochemistry and virology to characterize their sequence requirements and mechanism of stopping exoribonucleases. By solving the structure of a dianthovirus xrRNAs by x-ray crystallography, we reveal a complex fold that is very different from the flavivirus xrRNAs. However, both versions of xrRNAs contain a unique topological feature that is created by a different set of intramolecular contacts; this may be a defining structural feature of xrRNAs. Remarkably, the dianthovirus xrRNA can use 'co-degradational remodeling,' exploiting the exoribonuclease's degradation-linked helicase activity to help form their resistant structure; such a mechanism has not previously been reported. Convergent evolution has created RNA structure-dependent exoribonuclease resistance in different contexts, which establishes it as a general RNA maturation mechanism and defines xrRNAs as an authentic functional class of RNAs.peer-reviewed)

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“…During infection of Beta macrocarpa by Beet necrotic yellow vein virus (BNYVV), a member of the Benyviridae family and Benyvirus genus 22 , a non-coding RNA is produced from BNYVV RNA3 23 . This RNA, and in particular the "core" sequence it carries, has been shown to be necessary for long-distance movement by the virus and can be produced by action of either yeast Xrn1 or plant XRN4 [24][25][26] . A highly conserved 20 nucleotide (nt) sequence within the core, termed "coremin", plays an important role in allowing for systematic infection by BNYVV RNA3 in Beta macrocarpa 23 .…”

Section: Introductionmentioning

confidence: 99%

A widespread Xrn1-resistant RNA motif composed of two short hairpins

2019

Preprint

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Xrn1 is a major 5'-3' exoribonuclease involved in the RNA metabolism of many eukaryotic species.RNA viruses have evolved ways to thwart Xrn1 in order to produce subgenomic non-coding RNA that affects the hosts RNA metabolism. The 3' untranslated region of several beny-and cucumovirus RNAs harbors a so-called 'coremin' motif that is required for Xrn1 stalling. The structural features of this motif have not been studied in detail yet. Here, by using in vitro Xrn1 degradation assays, we tested over 50 different RNA constructs based on the Beet necrotic yellow vein virus sequence, to deduce putative structural features responsible for Xrn1-stalling. We demonstrated that the minimal benyvirus stalling site consists of two hairpins of 3 and 4 base pairs respectively. The 5' proximal hairpin requires a YGAD (Y = U/C, D = G/A/U) consensus loop sequence, whereas the 3' proximal hairpin loop sequence is variable. The sequence of the 9-nucleotide spacer that separates the hairpins is highly conserved and potentially involved in tertiary interactions. Similar coremin motifs were identified in plant virus isolates from other families including Betaflexiviridae, Virgaviridae and Secoviridae (order of the Picornavirales). We conclude that Xrn-stalling motifs are more widespread among RNA viruses than previously realized.

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A Viral Noncoding RNA Complements a Weakened Viral RNA Silencing Suppressor and Promotes Efficient Systemic Host Infection

Cited by 29 publications

References 33 publications

Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1

Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1

A folded viral noncoding RNA blocks host cell exoribonucleases through programmed remodeling of RNA structure

A widespread Xrn1-resistant RNA motif composed of two short hairpins

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