Evidence map›Paper›PMID 25897118›Full record

ArticleNucleic acids research2015

A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin.

Milya Davlieva, Yiwen Shi, Paul G Leonard, Troy A Johnson, Michael R Zianni, Cesar A Arias, John E Ladbury, Yousif Shamoo

Open access · goldAbstract read
In one paragraph

Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.

0numbers the graph read from it
0cells of the map it votes in
30citing papers in PubMed
3.7field-weighted citation impact, top 6% 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

30 citing papers in PubMed, 41 citations in OpenAlex.

  1. Review
  2. Article
  3. LiaS-dependent activation of the MadR regulon enables cross-talk betweenbioRxiv : the preprint server for biology · 2025
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  4. Review
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  7. Two Distinct Regulatory Systems Control Pulcherrimin Biosynthesis inbioRxiv : the preprint server for biology · 2024
    Article
  8. Article
  9. Article
  10. Article
  11. Resistance in Vancomycin-Resistant Enterococci.Infectious disease clinics of North America · 2020
    Review
  12. Review
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Proceedings of the National Academy of Sciences of the United States of America · 2018
    Article
  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

8 authors at 4 institutions in 2 countries.

Milya DavlievaDepartment of BioSciences, Rice University, Houston, TX 77005, USA.
Yiwen ShiDepartment of BioSciences, Rice University, Houston, TX 77005, USA.
Paul G LeonardDepartment of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Center for Biomolecular Structure and Function, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Troy A JohnsonDepartment of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Center for Biomolecular Structure and Function, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Michael R ZianniPlant-Microbe Genomics Facility, The Ohio State University, Columbus, OH 43210, USA.
Cesar A AriasDivision of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, 110121, Colombia.
John E LadburyCenter for Biomolecular Structure and Function, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Yousif ShamooDepartment of BioSciences, Rice University, Houston, TX 77005, USA shamoo@rice.edu.
Rice University · USThe University of Texas MD Anderson Cancer Center · USThe Ohio State University · USUniversidad El Bosque · CO

Funding

Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Scott Kopetz · 1985 to 2026
$290.8M
Defining Evolutionary Trajectories: Molecular adaptation to antibiotic resistanceR01AI080714 · NIAID · RICE UNIVERSITY · PI SHAMOO, YOUSIF · 2009 to 2023
$4.3M
Molecular Mechanisms Of Daptomycin Resistance In EnterococciR01AI093749 · NIAID · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI ARIAS, CESAR AUGUSTO · 2011 to 2015
$1.9M
Characterization of LiaR from multidrug-resistant E. faeciumR21AI114961 · NIAID · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI ARIAS, CESAR AUGUSTO · 2015 to 2016
$438k
Targeting Cell Membrane Adaptation in Multidrug-Resistant Enterococcus faeciumR21AI121519 · NIAID · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI ARIAS, CESAR AUGUSTO · 2016 to 2017
$226k
NIAID NIH HHS R01 AI080714NIAID NIH HHS R01AI080714NIAID NIH HHS R01 AI093749NIAID NIH HHS R21 AI114961NIAID NIH HHS R21 AI121519
6 · The paper itself

Abstract

LiaR is a 'master regulator' of the cell envelope stress response in enterococci and many other Gram-positive organisms. Mutations to liaR can lead to antibiotic resistance to a variety of antibiotics including the cyclic lipopeptide daptomycin. LiaR is phosphorylated in response to membrane stress to regulate downstream target operons. Using DNA footprinting of the regions upstream of the liaXYZ and liaFSR operons we show that LiaR binds an extended stretch of DNA that extends beyond the proposed canonical consensus sequence suggesting a more complex level of regulatory control of target operons. We go on to determine the biochemical and structural basis for increased resistance to daptomycin by the adaptive mutation to LiaR (D191N) first identified from the pathogen Enterococcus faecalis S613. LiaR(D191N) increases oligomerization of LiaR to form a constitutively activated tetramer that has high affinity for DNA even in the absence of phosphorylation leading to increased resistance. Crystal structures of the LiaR DNA binding domain complexed to the putative consensus sequence as well as an adjoining secondary sequence show that upon binding, LiaR induces DNA bending that is consistent with increased recruitment of RNA polymerase to the transcription start site and upregulation of target operons.

Indexed as

Anti-Bacterial AgentsBacterial ProteinsBase SequenceConsensus SequenceDaptomycinDNA, BacterialDNA-Binding ProteinsDrug Resistance, BacterialEnterococcus faecalisModels, MolecularMutationOperonProtein BindingProtein MultimerizationProtein Structure, TertiaryAnti-Bacterial AgentsBacterial ProteinsDaptomycinDNA, BacterialDNA-Binding Proteins

Identifiers

PMID25897118
PMCPMC4482077
OpenAlexW2100448562

What OpenQuestion holds

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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.