Evidence map›Paper›PMID 30327558›Full record

ArticleNature chemical biology2018

Metabolic repair through emergence of new pathways in Escherichia coli.

Sammy Pontrelli, Riley C B Fricke, Shao Thing Teoh, Walter A Laviña, Sastia Prama Putri, Sorel Fitz-Gibbon, Matthew Chung, Matteo Pellegrini, Eiichiro Fukusaki, James C Liao

Abstract read
PubMed Publisher
In one paragraph

Article in Nature chemical biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
1.3field-weighted citation impact, top 19% 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

13 citing papers in PubMed, 37 citations in OpenAlex.

  1. Article
  2. Review
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  4. Article
  5. New-to-nature CONature communications · 2024
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  6. Article
  7. Review
  8. Article
  9. Article
  10. Metabolic Dynamics inACS synthetic biology · 2021
    Article
  11. Article
  12. Review
  13. 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

10 authors at 4 institutions in 4 countries.

Sammy PontrelliDepartment of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-6265-8842
Riley C B FrickeDepartment of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-9463-6314
Shao Thing TeohDepartment of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.ORCID http://orcid.org/0000-0002-5938-258X
Walter A LaviñaDepartment of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.
Sastia Prama PutriDepartment of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.
Sorel Fitz-GibbonInstitute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-7090-5719
Matthew ChungDepartment of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-4623-4828
Matteo PellegriniInstitute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.
Eiichiro FukusakiDepartment of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.
James C LiaoInstitute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. Liaoj@gate.sinica.edu.tw.ORCID http://orcid.org/0000-0002-4580-7276
University of California, Los Angeles · USThe University of Osaka · JPInstitute of Biological Chemistry, Academia Sinica · TWUniversity of the Philippines Los Baños · PH

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Escherichia coli can derive all essential metabolites and cofactors through a highly evolved metabolic system. Damage of pathways may affect cell growth and physiology, but the strategies by which damaged metabolic pathways can be circumvented remain intriguing. Here, we use a ΔpanD (encoding for aspartate 1-decarboxylase) strain of E. coli that is unable to produce the β-alanine required for CoA biosynthesis to demonstrate that metabolic systems can overcome pathway damage by extensively rerouting metabolic pathways and modifying existing enzymes for unnatural functions. Using directed cell evolution, rewiring and repurposing of uracil metabolism allowed formation of an alternative β-alanine biosynthetic pathway. After this pathway was deleted, a second was evolved that used a gain-of-function mutation on ornithine decarboxylase (SpeC) to alter reaction and substrate specificity toward an oxidative decarboxylation-deamination reaction. After deletion of both pathways, yet another independent pathway emerged using polyamine biosynthesis, demonstrating the vast capacity of metabolic repair.

Indexed as

beta-AlanineBiosynthetic PathwaysCarboxy-LyasesEscherichia coliEscherichia coli ProteinsGene Expression Regulation, BacterialGlutamate DecarboxylaseMalondialdehydeMutationOrnithine DecarboxylasePhenotypePoint MutationPolyaminesSpectrophotometrySubstrate SpecificityUracilaspartate-alpha-decarboxylasebeta-AlanineCarboxy-LyasesEscherichia coli ProteinsGlutamate DecarboxylaseMalondialdehydemalonic semialdehydeOrnithine DecarboxylasePanD protein, E coliPolyaminesUracil

Identifiers

PMID30327558
OpenAlexW2897847356

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.