Evidence map›Paper›PMID 27536006›Full record

ArticleNucleic acids research2016

A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor.

Ramesh K Jha, Theresa L Kern, Youngchang Kim, Christine Tesar, Robert Jedrzejczak, Andrzej Joachimiak, Charlie E M Strauss

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
1.7field-weighted citation impact, top 15% 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

14 citing papers in PubMed, 41 citations in OpenAlex.

  1. Review
  2. Review
  3. Review
  4. Article
  5. Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. A protocatechuate biosensor forMetabolic engineering communications · 2018
    Article
  14. Tailor-made transcriptional biosensors for optimizing microbial cell factories.Journal of industrial microbiology & biotechnology · 2017
    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

7 authors at 2 institutions in 1 country.

Ramesh K JhaBioscience Division, PO Box 1663, Los Alamos National Laboratory, Los Alamos NM 87545, USA cems@lanl.gov.
Theresa L KernBioscience Division, PO Box 1663, Los Alamos National Laboratory, Los Alamos NM 87545, USA.
Youngchang KimThe Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA.
Christine TesarThe Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA.
Robert JedrzejczakThe Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA.
Andrzej JoachimiakThe Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA.
Charlie E M StraussBioscience Division, PO Box 1663, Los Alamos National Laboratory, Los Alamos NM 87545, USA rjha@lanl.gov.
Argonne National Laboratory · USLos Alamos National Laboratory · US

Funding

Midwest Center for Structural GenomicsU54GM094585 · NIGMS · UNIVERSITY OF CHICAGO · PI OTWINOWSKI, ZBYSZEK · 2010 to 2014
$33.7M
The Midwest Center for Structural Genomics - Community ResourceR24GM115586 · NIGMS · UNIVERSITY OF CHICAGO · PI JOACHIMIAK, ANDRZEJ · 2015 to 2017
$2.8M
NIGMS NIH HHS R24 GM115586NIGMS NIH HHS U54 GM094585
6 · The paper itself

Abstract

A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of TFs. Using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to 'sense' a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 10(7) variants of PobR, four were active when dosed with pNP, with two mutants showing a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production from hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show the fluorescence of the cells correlated with the catalytic efficiency of the PTE variant expressed in each cell. High selectivity between similar molecules (4HB versus pNP), high sensitivity for pNP detection (∼2 μM) and agreement of apo- and holo-structures of PobR scaffold with predetermined computational models are other significant results presented in this work.

Indexed as

Biosensing TechniquesProtein EngineeringBacterial ProteinsCrystallography, X-RayFlow CytometryHydrolysisLigandsMolecular Docking SimulationNitrophenolsOrganophosphatesParaoxonPlasmidsStructural Homology, ProteinTranscription Factors4-nitrophenolBacterial ProteinsLigandsNitrophenolsOrganophosphatesParaoxonTranscription Factors

Identifiers

PMID27536006
PMCPMC5041483
OpenAlexW2507402876

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.