Evidence map›Paper›PMID 32083649›Full record

ArticleNucleic acids research2020

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

Jian Wu, Cuiji Zhou, James Li, Chun Li, Xiaorong Tao, Neocles B Leontis, Craig L Zirbel, David M Bisaro, Biao Ding

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

16 citing papers in PubMed.

  1. Article
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  5. Article
  6. Review
  7. Article
  8. Article
  9. Review
  10. Article
  11. Article
  12. Article
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  14. Progress in 50 years of viroid research-Molecular structure, pathogenicity, and host adaptation.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2021
    Article
  15. Article
  16. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Jian WuDepartment of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.
Cuiji ZhouDepartment of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.
James LiDepartment of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.
Chun LiDepartment of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China.
Xiaorong TaoDepartment of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China.
Neocles B LeontisDepartment of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA.
Craig L ZirbelDepartment of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA.
David M BisaroDepartment of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.
Biao DingDepartment of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.

Funding

RNA 3D Motif Search, Atlas, and Prediction from SequenceR01GM085328 · NIGMS · BOWLING GREEN STATE UNIVERSITY · PI ZIRBEL, CRAIG L · 2010 to 2023
$4.0M
NIGMS NIH HHS R01 GM085328
6 · The paper itself

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.

Indexed as

Genome, ViralMutationNucleic Acid ConformationPlant VirusesRNA, UntranslatedRNA, ViralSolanum tuberosumViroidsVirus DiseasesVirus ReplicationRNA, UntranslatedRNA, Viral

Identifiers

PMID32083649
PMCPMC7102988

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.