2020
DOI: 10.1261/rna.077065.120
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Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA

Abstract: During infection by a flavivirus (FV), cells accumulate noncoding subgenomic flavivirus RNAs (sfRNAs) that interfere with several antiviral pathways. These sfRNAs are formed by structured RNA elements in the 3′ untranslated region (UTR) of the viral genomic RNA, which block the progression of host cell exoribonucleases that have targeted the viral RNA for destruction. Previous work on these exoribonuclease-resistant RNAs (xrRNAs) from mosquito-borne FVs revealed a specific 3-dimensional fold with a unique topo… Show more

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Cited by 32 publications
(57 citation statements)
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“…68 Choice of RNA structure datasets: RNA molecules often display large conformational variations, and hence variations in their inter-nucleotide interaction patterns, in response to changes in the local environment as well as to even small sequence variations. 69,70 Hence, a conventional nonredundant dataset is not expected to provide a comprehensive repertoire of different instances of base triples present in RNA. On the other hand, the statistical biases inherent in redundant datasets are expected to skew their respective occurrence frequency data, leading to misleading inferences regarding their significance.…”
Section: Methodsmentioning
confidence: 99%
“…68 Choice of RNA structure datasets: RNA molecules often display large conformational variations, and hence variations in their inter-nucleotide interaction patterns, in response to changes in the local environment as well as to even small sequence variations. 69,70 Hence, a conventional nonredundant dataset is not expected to provide a comprehensive repertoire of different instances of base triples present in RNA. On the other hand, the statistical biases inherent in redundant datasets are expected to skew their respective occurrence frequency data, leading to misleading inferences regarding their significance.…”
Section: Methodsmentioning
confidence: 99%
“…A clear example of how different primary and secondary structures can lead to the same 3D xrRNA has been reported in the divergent flavivirus Tamana bat virus (TABV) [ 30 , 107 , 109 , 110 ]. X-ray crystallization studies have shown that while the ring-like structure of the xrRNA is preserved across TABV and other flaviviruses, significant variations occur in the corresponding nucleotide sequences and secondary structural elements [ 107 , 110 ]. One major difference resides in the shortening of the stems that form the ring-like structure.…”
Section: Subgenomic Flavivirus Rnasmentioning
confidence: 99%
“…Consequently, in TABV, the xrRNA is more compact and rigid. In addition, the region encircling the 5′ end of the xrRNA lacks Watson–Crick pairs, requiring the interplay of Mg 2+ ions and water molecules to stabilize the final structure [ 110 ]. These differences support the idea that the TABV represents a phylogenetically distinct lineage within flaviviruses and mark the path for understanding the mechanisms that drive the generation of subgenomic RNAs in other virus families (see below).…”
Section: Subgenomic Flavivirus Rnasmentioning
confidence: 99%
“…This unique fold determines the resistance of xrRNAs to XRN1 as the RNA ring creates a roadblock for the progression of the enzyme 22 (Supplementary figure 1A). To date, secondary structures have been experimentally determined for xrRNAs of MBFs 9,23,24 , TBFs 19 , NKVFs 19,25 and cISF CFAV 19 .…”
Section: Introductionmentioning
confidence: 99%
“…In addition, crystal structures have been solved for three MBF xrRNAs 20,21 and xrRNA of NKVF Tamana Bat virus 25 . Based on the conserved structural elements, xrRNAs are classified into two classes -class 1 xrRNAs occur in MBF, while class 2 xrRNAs occur in TBFs and NKVFs 19 .…”
Section: Introductionmentioning
confidence: 99%