Evidence map›Paper›PMID 39948061›Full record

ArticleNature communications2025

Structural insights into transcription regulation of the global OmpR/PhoB family regulator PhoP from Mycobacterium tuberculosis.

Jing Shi, Zhenzhen Feng, Qian Song, Aijia Wen, Tianyu Liu, Liqiao Xu, Zonghang Ye, Simin Xu, Fei Gao, Liuxiang Xiao and 6 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Vitamin BCommunications biology · 2025
    Article
  5. 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

16 authors.

Jing Shi *School of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China. shijing301@njucm.edu.cn.ORCID http://orcid.org/0000-0001-9389-4055
Zhenzhen Feng *School of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China.
Qian Song *School of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China.
Aijia Wen *Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
Tianyu LiuSchool of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China.
Liqiao XuDepartment of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
Zonghang YeSchool of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China.
Simin XuSchool of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China.
Fei GaoSchool of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China.
Liuxiang XiaoSchool of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China.
Jiapeng ZhuSchool of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China.ORCID http://orcid.org/0000-0002-9165-0126
Kalyan DasRega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.ORCID http://orcid.org/0000-0002-8897-324X
Guoping ZhaoKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.ORCID http://orcid.org/0000-0002-7621-6620
Jie LiSchool of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China. lijier@nju.edu.cn.ORCID http://orcid.org/0000-0003-0973-8645
Yu FengDepartment of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China. yufengjay@zju.edu.cn.ORCID http://orcid.org/0000-0003-4239-8320
Wei LinSchool of Medicine, Nanjing University of Chinese Medicine, Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing, China. weilin@njucm.edu.cn.ORCID http://orcid.org/0000-0002-2940-6966

Funding

National Natural Science Foundation of China (National Science Foundation of China) 82311530689, 32270037, 32270192, 82072240, 32000025
6 · The paper itself

Abstract

As a global transcription activator or repressor, the representative OmpR/PhoB family response regulator PhoP plays a crucial role in regulating bacterial pathogenicity and stress adaptation. However, the molecular mechanisms underlying the transcriptional regulation that define its differential functions remain largely unclear. In the present study, we determine three cryo-EM structures of Mycobacterium tuberculosis (Mtb) PhoP-dependent transcription activation complexes (PhoP-TACs) and build one preliminary cryo-EM structure model of Mtb PhoP-dependent transcription repression complex (PhoP-TRC). In PhoP-TACs, tandem PhoP dimers cooperatively recognize various types of promoters through conserved PhoP-PHO box interactions, which displace the canonical interactions between the -35 element and σ

Indexed as

Bacterial ProteinsGene Expression Regulation, BacterialMycobacterium tuberculosisTrans-ActivatorsCryoelectron MicroscopyDNA-Directed RNA PolymerasesModels, MolecularPromoter Regions, GeneticProtein BindingProtein MultimerizationTranscription, GeneticBacterial ProteinsDNA-Directed RNA PolymerasesPhoB protein, BacteriaPhoP protein, BacteriaTrans-Activators

Identifiers

PMID39948061
PMCPMC11825685

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.