Evidence map›Paper›PMID 40444637›Full record

ArticleNucleic acids research2025

Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.

Disha-Gajanan Hiregange, Sarit Samiya, Danuta Mizgalska, Efrat Ben-Zeev, Miriam Waghalter, Andre Rivalta, K Shanmugha Rajan, Yehuda Halfon, Elinor Breiner-Goldstein, Igor Kaczmarczyk and 9 more

Abstract read
In one paragraph

Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. The Ascent of Miniproteins.Biochemistry · 2026
    Review
  3. Article
  4. Review
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

19 authors.

Disha-Gajanan HiregangeDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
Sarit SamiyaDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
Danuta MizgalskaDepartment of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow 30-387, Poland.
Efrat Ben-ZeevNancy and Stephen Grand Israel National Center for Personalized Medicine, Mantoux Institute for Bioinformatics, Weizmann Institute of Science, Rehovot 7610001, Israel.
Miriam WaghalterDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
Andre RivaltaDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
K Shanmugha RajanDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
Yehuda HalfonDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
Elinor Breiner-GoldsteinDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
Igor KaczmarczykDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.ORCID 0000-0002-5607-7416
Aneta SrokaDepartment of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow 30-387, Poland.
Masato TaokaDepartment of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.ORCID 0000-0001-5554-4951
Yuko NobeDepartment of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
Toshiaki IsobeDepartment of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
Susanne PauknerNabriva Therapeutics GmbH, Vienna 1110, Austria.
Ella ZimmermanDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
Anat BashanDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.ORCID 0000-0002-7705-0466
Jan PotempaDepartment of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow 30-387, Poland.
Ada YonathDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.

Funding

Fumagillin Derivatives as Novel Antigiardiasis and Antiamebiasis DrugsR33AI119788 · NIAID · UNIV OF MARYLAND, COLLEGE PARK · PI HERZBERG, OSNAT · 2017 to 2019
$1.3M
Fumagillin Derivatives as Novel Antigiardiasis and Antiamebiasis DrugsR21AI119788 · NIAID · UNIV OF MARYLAND, COLLEGE PARK · PI HERZBERG, OSNAT · 2015 to 2016
$418k
Kimmelman Center for Macromolecular AssembliesNIAID NIH HHS R21 AI119788NIAID NIH HHS R33 AI119788NIH HHS AI119788Strategic Programme Excellence Initiative
6 · The paper itself

Abstract

Porphyromonas gingivalis, an anaerobic pathogen in chronic periodontitis, belongs to the Bacteroidota phylum and is associated with various virulence factors. Its antibiotic-resistant strains and its propensity to form biofilms pose a challenge to effective treatment. To explore therapeutic avenues, we studied the high-resolution cryogenic electron microscope structures of ribosomes from the wild-type P. gingivalis W83 and the macrolide-resistant mutant strain ermΔporN. The structural analysis revealed unique features primarily at the ribosome periphery. Together with the distinctive distribution of ribosomal RNA modifications, these findings offer insights into the therapeutical potential, such as creation of novel therapeutic compounds inhibiting the specific cellular functions of the P. gingivalis ribosomes. Moreover, the high-resolution structure of the ermΔporN ribosome in its complex with the approved antibiotic lefamulin suggests its repurposing against P. gingivalis. Furthermore, we provide a foundation for additional effective strategies to treat periodontitis and associated systemic diseases.

Indexed as

Porphyromonas gingivalisRibosomesAnti-Bacterial AgentsCryoelectron MicroscopyDrug Resistance, BacterialHumansRNA, RibosomalAnti-Bacterial AgentsRNA, Ribosomal

Identifiers

PMID40444637
PMCPMC12123416

What Socratic holds

Textmetadata
LicenceCC BY-NC
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 Socratic graph.