Evidence map›Paper›PMID 30655545›Full record

ArticleScientific reports2019

Crystal structure of the multidrug resistance regulator RamR complexed with bile acids.

Suguru Yamasaki, Ryosuke Nakashima, Keisuke Sakurai, Sylvie Baucheron, Etienne Giraud, Benoît Doublet, Axel Cloeckaert, Kunihiko Nishino

Abstract read
In one paragraph

Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.

0numbers the graph read from it
0cells of the map it votes in
27citing 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

27 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Investigating the Chemical-Biological Link inFood science & nutrition · 2025
    Article
  6. Article
  7. Review
  8. Article
  9. Article
  10. Major primary bile salts repressFrontiers in microbiology · 2024
    Article
  11. Review
  12. Article
  13. Article
  14. Review
  15. Article
  16. Review
  17. Article
  18. Article
  19. Review
  20. 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

8 authors.

Suguru YamasakiGraduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, 565-0871, Osaka, Japan.ORCID 0000-0003-3370-5851
Ryosuke NakashimaInstitute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.
Keisuke SakuraiInstitute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.ORCID 0000-0002-6948-1899
Sylvie BaucheronINRA, UMR1282 Infectiologie et Santé Publique, F-37380, Nouzilly, France.
Etienne GiraudINRA, UMR1282 Infectiologie et Santé Publique, F-37380, Nouzilly, France.ORCID 0000-0002-2534-4040
Benoît DoubletINRA, UMR1282 Infectiologie et Santé Publique, F-37380, Nouzilly, France.ORCID 0000-0003-0531-0967
Axel CloeckaertINRA, UMR1282 Infectiologie et Santé Publique, F-37380, Nouzilly, France.
Kunihiko NishinoGraduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, 565-0871, Osaka, Japan. nishino@sanken.osaka-u.ac.jp.ORCID 0000-0003-3349-1769

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

During infection, Salmonella senses and responds to harsh environments within the host. Persistence in a bile-rich environment is important for Salmonella to infect the small intestine or gallbladder and the multidrug efflux system AcrAB-TolC is required for bile resistance. The genes encoding this system are mainly regulated by the ramRA locus, which is composed of the divergently transcribed ramA and ramR genes. The acrAB and tolC genes are transcriptionally activated by RamA, whose encoding gene is itself transcriptionally repressed by RamR. RamR recognizes multiple drugs; however, the identity of the environmental signals to which it responds is unclear. Here, we describe the crystal structures of RamR in complexes with bile components, including cholic acid and chenodeoxycholic acid, determined at resolutions of 2.0 and 1.8 Å, respectively. Both cholic and chenodeoxycholic acids form four hydrogen bonds with Tyr59, Thr85, Ser137 and Asp152 of RamR, instead of π-π interactions with Phe155, a residue that is important for the recognition of multiple compounds including berberine, crystal violet, dequalinium, ethidium bromide and rhodamine 6 G. Binding of these compounds to RamR reduces its DNA-binding affinity, resulting in the increased transcription of ramA and acrAB-tolC. Our results reveal that Salmonella senses bile acid components through RamR and then upregulates the expression of RamA, which can lead to induction of acrAB-tolC expression with resulting tolerance to bile-rich environments.

Indexed as

ATP-Binding Cassette, Sub-Family C ProteinsBacterial ProteinsBile Acids and SaltsCarrier ProteinsChenodeoxycholic AcidCholic AcidCrystallography, X-RayDrug Resistance, MultipleDrug ToleranceMolecular StructureProtein BindingTrans-ActivatorsUp-RegulationAcrAB-TolC protein, Salmonella entericaATP-Binding Cassette, Sub-Family C ProteinsBacterial ProteinsBile Acids and SaltsCarrier ProteinsChenodeoxycholic AcidCholic AcidRamA protein, Salmonella typhimuriumRamR protein, Salmonella typhimuriumTrans-Activators

Identifiers

PMID30655545
PMCPMC6336783

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Registered trials

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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.