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Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA.

ABSTRACT: While G/U pairs are present in many RNAs, the lack of molecular studies to characterize the roles of multiple G/U pairs within a single RNA limits our understanding of their biological significance. From known RNA 3D structures, we observed that the probability a G/U will form a Watson-Crick (WC) base pair depends on sequence context. We analyzed 17 G/U pairs in the 359-nucleotide genome of Potato spindle tuber viroid (PSTVd), a circular non-coding RNA that replicates and spreads systemically in host plants. Most putative G/U base pairs were experimentally supported by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). Deep sequencing PSTVd genomes from plants inoculated with a cloned master sequence revealed naturally occurring variants, and showed that G/U pairs are maintained to the same extent as canonical WC base pairs. Comprehensive mutational analysis demonstrated that nearly all G/U pairs are critical for replication and/or systemic spread. Two selected G/U pairs were found to be required for PSTVd entry into, but not for exit from, the host vascular system. This study identifies critical roles for G/U pairs in the survival of an infectious RNA, and increases understanding of structure-based regulation of replication and trafficking of pathogen and cellular RNAs.

SUBMITTER: Wu J

PROVIDER: S-EPMC7102988 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA.

Wu Jian J Zhou Cuiji C Li James J Li Chun C Tao Xiaorong X Leontis Neocles B NB Zirbel Craig L CL Bisaro David M DM Ding Biao B

Nucleic acids research 20200401 6

While G/U pairs are present in many RNAs, the lack of molecular studies to characterize the roles of multiple G/U pairs within a single RNA limits our understanding of their biological significance. From known RNA 3D structures, we observed that the probability a G/U will form a Watson-Crick (WC) base pair depends on sequence context. We analyzed 17 G/U pairs in the 359-nucleotide genome of Potato spindle tuber viroid (PSTVd), a circular non-coding RNA that replicates and spreads systemically in ...[more]

PMID: 32083649

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Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA.

Publications

Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA.

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