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Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6404-6409. doi: 10.1073/pnas.1802429115. Epub 2018 Jun 4.

A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.

Author information

1
Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045.
2
Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606.
3
Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
4
Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045; Jeffrey.Kieft@ucdenver.edu.
5
RNA BioScience Initiative, School of Medicine, University of Colorado, Aurora, CO 80045.

Abstract

Folded RNA elements that block processive 5' → 3' cellular exoribonucleases (xrRNAs) to produce biologically active viral noncoding RNAs have been discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, whether this RNA structure-dependent mechanism exists elsewhere and, if so, whether a singular RNA fold is required, have been unclear. Here we demonstrate the existence of authentic RNA structure-dependent xrRNAs in dianthoviruses, plant-infecting viruses unrelated to animal-infecting flaviviruses. These 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 xrRNA by X-ray crystallography, we reveal a complex fold that is very different from that of the flavivirus xrRNAs. However, both versions of xrRNAs contain a unique topological feature, a pseudoknot that creates a protective ring around the 5' end of the RNA structure; this may be a defining structural feature of xrRNAs. Single-molecule FRET experiments reveal that the dianthovirus xrRNAs undergo conformational changes and can use "codegradational remodeling," exploiting the exoribonucleases' 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.

KEYWORDS:

RNA dynamics; RNA structure; exoribonuclease resistance; noncoding RNA maturation; single-molecule FRET

PMID:
29866852
PMCID:
PMC6016793
DOI:
10.1073/pnas.1802429115
[Indexed for MEDLINE]
Free PMC Article

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