Evidence map›Paper›PMID 27713529›Full record

ArticleScientific reports2016

A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network.

Yuan-Nong Ye, Bin-Guang Ma, Chuan Dong, Hong Zhang, Ling-Ling Chen, Feng-Biao Guo

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

Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
1.2field-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

3 citing papers in PubMed, 11 citations in OpenAlex.

  1. Article
  2. Comparative genomics ofMicrobial genomics · 2025
    Article
  3. 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

6 authors at 2 institutions in 1 country.

Yuan-Nong YeCenter of Bioinformatics, Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.
Bin-Guang MaCollege of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
Chuan DongCenter of Bioinformatics, Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.
Hong ZhangCollege of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
Ling-Ling ChenCollege of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
Feng-Biao GuoCenter of Bioinformatics, Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.
Huazhong Agricultural University · CNUniversity of Electronic Science and Technology of China · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

A minimal gene set (MGS) is critical for the assembly of a minimal artificial cell. We have developed a proposal of simplifying bacterial gene set to approximate a bacterial MGS by the following procedure. First, we base our simplified bacterial gene set (SBGS) on experimentally determined essential genes to ensure that the genes included in the SBGS are critical. Second, we introduced a half-retaining strategy to extract persistent essential genes to ensure stability. Third, we constructed a viable metabolic network to supplement SBGS. The proposed SBGS includes 327 genes and required 431 reactions. This report describes an SBGS that preserves both self-replication and self-maintenance systems. In the minimized metabolic network, we identified five novel hub metabolites and confirmed 20 known hubs. Highly essential genes were found to distribute the connecting metabolites into more reactions. Based on our SBGS, we expanded the pool of targets for designing broad-spectrum antibacterial drugs to reduce pathogen resistance. We also suggested a rough semi-de novo strategy to synthesize an artificial cell, with potential applications in industry.

Indexed as

Artificial CellsBacterial ProteinsEscherichia coliGene Expression Regulation, BacterialGenes, BacterialGenes, EssentialGenomicsHaemophilus influenzaeMetabolic Networks and PathwaysMycoplasma genitaliumBacterial Proteins

Identifiers

PMID27713529
PMCPMC5054358
OpenAlexW2528608125

What OpenQuestion holds

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LicenceCC BY
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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.