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

作者：Steckelberg Anna Lena; Akiyama Benjamin M; Costantino David A; Sit Tim L; Nix Jay C; Kieft Jeffrey S^*

来源：Proceedings of the National Academy of Sciences, 2018, 115(25): 6404-6409.

DOI：10.1073/pnas.1802429115

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

Folded RNA elements that block processive 5' -> 3' cellular exor-ibonucleases (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 pseudo-knot 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.

• 出版日期2018-6-19