Evidence map›Paper›PMID 25092327›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2014

Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1.

Kazuhiro Ishibashi, Yuichiro Kezuka, Chihoko Kobayashi, Masahiko Kato, Tsuyoshi Inoue, Takamasa Nonaka, Masayuki Ishikawa, Hiroyoshi Matsumura, Etsuko Katoh

Open access · bronzeAbstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed
3.7field-weighted citation impact, top 8% of its field
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

25 citing papers in PubMed, 48 citations in OpenAlex.

  1. Article
  2. Review
  3. BreedingFrontiers in plant science · 2026
    Article
  4. Article
  5. Tm-1 back in business: an allele from Solanum pennellii accessions plays a major role in ToBRFV resistance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025
    Article
  6. Article
  7. Review
  8. Article
  9. Advances in understanding the interaction betweenPlant signaling & behavior · 2024
    Review
  10. Review
  11. Review
  12. Article
  13. Advances and Prospects of Virus-Resistant Breeding in Tomatoes.International journal of molecular sciences · 2023
    Review
  14. Review
  15. Article
  16. Article
  17. Resistance to Turnip Mosaic Virus in the FamilyThe plant pathology journal · 2021
    Review
  18. Review
  19. Article
  20. 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

9 authors at 4 institutions in 2 countries.

Kazuhiro IshibashiPlant-Microbe Interactions Research Unit and.
Yuichiro KezukaDepartment of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 020-0023, Japan; and.
Chihoko KobayashiBiomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
Masahiko KatoBiomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
Tsuyoshi InoueGraduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.
Takamasa NonakaDepartment of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 020-0023, Japan; and.ORCID http://orcid.org/0000-0002-5353-0289
Masayuki IshikawaPlant-Microbe Interactions Research Unit and.
Hiroyoshi MatsumuraGraduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan matsumura@chem.eng.osaka-u.ac.jp ekatoh@nias.affrc.go.jp.
Etsuko KatohBiomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan; matsumura@chem.eng.osaka-u.ac.jp ekatoh@nias.affrc.go.jp.
Institute of Agrobiological Sciences · JPIwate Medical University · JPLaboratoire des Interactions Plantes Micro-Organismes · FROsaka University · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The tomato mosaic virus (ToMV) resistance gene Tm-1 encodes a protein that shows no sequence homology to functionally characterized proteins. Tm-1 binds ToMV replication proteins and thereby inhibits replication complex formation. ToMV mutants that overcome this resistance have amino acid substitutions in the helicase domain of the replication proteins (ToMV-Hel). A small region of Tm-1 in the genome of the wild tomato Solanum habrochaites has been under positive selection during its antagonistic coevolution with ToMV. Here we report crystal structures for the N-terminal inhibitory domains of Tm-1 and a natural Tm-1 variant with an I91-to-T substitution that has a greater ability to inhibit ToMV RNA replication and their complexes with ToMV-Hel. Each complex contains a Tm-1 dimer and two ToMV-Hel monomers with the interfaces between Tm-1 and ToMV-Hel bridged by ATP. Residues in ToMV-Hel and Tm-1 involved in antagonistic coevolution are found at the interface. The structural differences between ToMV-Hel in its free form and in complex with Tm-1 suggest that Tm-1 affects nucleoside triphosphatase activity of ToMV-Hel, and this effect was confirmed experimentally. Molecular dynamics simulations of complexes formed by Tm-1 with ToMV-Hel variants showed how the amino acid changes in ToMV-Hel impair the interaction with Tm-1 to overcome the resistance. With these findings, together with the biochemical properties of the interactions between ToMV-Hel and Tm-1 variants and effects of the mutations in the polymorphic residues of Tm-1, an atomic view of a step-by-step coevolutionary arms race between a plant resistance protein and a viral protein emerges.

Indexed as

Genes, ViralAllelesImmune EvasionMolecular Dynamics SimulationMosaic VirusesSolanum lycopersicumVirus Replicationprotein complexvirus resistance

Identifiers

PMID25092327
PMCPMC4143053
OpenAlexW2032836628

What OpenQuestion holds

Textmetadata
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.