Evidence map›Paper›PMID 29546662›Full record

ArticleJournal of industrial microbiology & biotechnology2018

An integrated workflow for phenazine-modifying enzyme characterization.

R Cameron Coates, Benjamin P Bowen, Ernst Oberortner, Linda Thomashow, Michalis Hadjithomas, Zhiying Zhao, Jing Ke, Leslie Silva, Katherine Louie, Gaoyan Wang and 13 more

Open access · bronzeAbstract read
PubMed Publisher
In one paragraph

Article in Journal of industrial microbiology & biotechnology, 2018. 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
0.7field-weighted citation impact, top 30% 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

5 citing papers in PubMed, 9 citations in OpenAlex.

  1. Discovery of a phenazine-thiol conjugase from sparse data using genome-informed machine learning.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  2. Article
  3. Review
  4. Whole Genome Sequence ofMarine drugs · 2020
    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

23 authors at 6 institutions in 1 country.

R Cameron CoatesUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Benjamin P BowenUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Ernst OberortnerUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Linda ThomashowUSDA Agricultural Research Service, Wheat Health, Genetics and Quality, Washington State University, Pullman, WA, USA.
Michalis HadjithomasUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Zhiying ZhaoUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Jing KeUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Leslie SilvaUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Katherine LouieUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Gaoyan WangUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
David RobinsonUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Angela TarverUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Matthew HamiltonUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Andrea LubbeEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Meghan FeltcherDepartment of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Jeffery L DanglDepartment of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Amrita PatiUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
David WellerUSDA Agricultural Research Service, Wheat Health, Genetics and Quality, Washington State University, Pullman, WA, USA.
Trent R NorthenUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Jan-Fang ChengUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Nigel J MounceyUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Samuel DeutschUS DOE Joint Genome Institute, Walnut Creek, CA, USA.
Yasuo YoshikuniUS DOE Joint Genome Institute, Walnut Creek, CA, USA. yyoshikuni@lbl.gov.
Joint Genome Institute · USLawrence Berkeley National Laboratory · USAgricultural Research Service · USHoward Hughes Medical Institute · USUniversity of North Carolina at Chapel Hill · USWashington State University · US

Funding

Office of Science DE-AC02-05CH11231
6 · The paper itself

Abstract

Increasing availability of new genomes and putative biosynthetic gene clusters (BGCs) has extended the opportunity to access novel chemical diversity for agriculture, medicine, environmental and industrial purposes. However, functional characterization of BGCs through heterologous expression is limited because expression may require complex regulatory mechanisms, specific folding or activation. We developed an integrated workflow for BGC characterization that integrates pathway identification, modular design, DNA synthesis, assembly and characterization. This workflow was applied to characterize multiple phenazine-modifying enzymes. Phenazine pathways are useful for this workflow because all phenazines are derived from a core scaffold for modification by diverse modifying enzymes (PhzM, PhzS, PhzH, and PhzO) that produce characterized compounds. We expressed refactored synthetic modules of previously uncharacterized phenazine BGCs heterologously in Escherichia coli and were able to identify metabolic intermediates they produced, including a previously unidentified metabolite. These results demonstrate how this approach can accelerate functional characterization of BGCs.

Indexed as

Multigene FamilyBacterial ProteinsBiosynthetic PathwaysEscherichia coliPhenazinesBacterial ProteinsPhenazinesBiosynthesisPathwayPathway designPhenazineRefactoredSynthetic biology

Identifiers

PMID29546662
OpenAlexW2792511454

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.