Evidence map›Paper›PMID 39763890›Full record

ArticlebioRxiv : the preprint server for biology2024

The pseudoknot structure of a viral RNA reveals a conserved mechanism for programmed exoribonuclease resistance.

Jeanine G Gezelle, Sophie M Korn, Jayden T McDonald, Zhen Gong, Anna Erickson, Chih-Hung Huang, Feiyue Yang, Matt Cronin, Yen-Wen Kuo, Brian T Wimberly and 1 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Jeanine G GezelleDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.ORCID 0000-0003-3664-6199
Sophie M KornDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.ORCID 0000-0003-3798-3277
Jayden T McDonaldDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Zhen GongDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.ORCID 0000-0003-0760-1493
Anna EricksonDepartment of Plant Pathology, University of California, Davis, CA, USA.
Chih-Hung HuangDepartment of Plant Pathology, University of California, Davis, CA, USA.
Feiyue YangDepartment of Systems Biology, Columbia University, New York, NY, USA.ORCID 0009-0009-1860-288X
Matt CroninDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Yen-Wen KuoDepartment of Plant Pathology, University of California, Davis, CA, USA.ORCID 0000-0003-2746-2953
Brian T WimberlyNew York Structural Biology Center, New York, NY, USA.ORCID 0000-0003-3928-8358
Anna-Lena SteckelbergDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.ORCID 0000-0001-7988-9946

Funding

X-ray Scattering Technology CoreP30GM133893 · NIGMS · BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB · PI Vivian Stojanoff · 2019 to 2026
$38.6M
Mechanisms of viral RNA maturation by co-opting cellular exonucleasesR01AI133348 · NIAID · UNIVERSITY OF COLORADO DENVER · PI KIEFT, JEFFREY S · 2017 to 2025
$4.5M
An Eiger2 XE 9M detector for the NYSBC-operated NYX beamline at NSLS-IIS10OD030394 · OD · NEW YORK STRUCTURAL BIOLOGY CENTER · PI BATTAILE, KEVIN P · 2021 to 2021
$1.8M
Understanding the antiviral roles of acellular RNA quality control pathwayR35GM150778 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Anna-Lena Steckelberg · 2023 to 2026
$1.6M
Combination CD-Fluorescence Polarization Spectrophotometer for the Columbia Precision Biomolecular Characterization FacilityS10OD025102 · OD · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI HUNT, JOHN FRANCIS · 2018 to 2018
$138k
NIAID NIH HHS R01 AI133348NIGMS NIH HHS P30 GM133893NIGMS NIH HHS R35 GM150778NIH HHS S10 OD025102NIH HHS S10 OD030394
6 · The paper itself

Abstract

Exoribonuclease-resistant RNAs (xrRNAs) are viral RNA structures that block degradation by cellular 5'-3' exoribonucleases to produce subgenomic viral RNAs during infection. Initially discovered in flaviviruses, xrRNAs have since been identified in wide range of RNA viruses, including those that infect plants. High sequence variability among viral xrRNAs raises questions about the shared molecular features that characterize this functional RNA class. Here, we present the first structure of a plant-virus xrRNA in its active exoribonuclease-resistant conformation. The xrRNA forms a 9 base pair pseudoknot that creates a knot-like topology similar to that of flavivirus xrRNAs, despite lacking sequence similarity. Biophysical assays confirm a compact pseudoknot structure in solution, and functional studies validate its relevance both

Identifiers

PMID39763890
PMCPMC11702639

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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.