Targeted enzyme gene re-positioning: A computational approach for discovering alternative bacterial enzymes for the synthesis of plant-specific secondary metabolites.

Yuya Nakamura, Shuichi Hirose, Yuko Taniguchi, Yuki Moriya, Takuji Yamada

Open access · goldAbstract read

In one paragraph

Article in Metabolic engineering communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

0.3field-weighted citation impact, top 43% 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

1 citing paper in PubMed, 4 citations in OpenAlex.

Lignans of Sesame (Molecules (Basel, Switzerland) · 2021
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4 · The record

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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

5 authors at 4 institutions in 1 country.

Yuya NakamuraSchool of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo, 152-8550, Japan.

Shuichi HiroseNAGASE R&D Center, Nagase & Co., Ltd, Kobe High Tech Park 2-2-3 Murotani, Nishi- ku, Kobe, Hyogo, 651-2241, Japan.

Yuko TaniguchiNAGASE R&D Center, Nagase & Co., Ltd, Kobe High Tech Park 2-2-3 Murotani, Nishi- ku, Kobe, Hyogo, 651-2241, Japan.

Yuki MoriyaDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa, 277-0871, Japan.

Takuji YamadaSchool of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo, 152-8550, Japan.

Nagase (Japan) · JPJapan Science and Technology Agency · JPResearch Organization of Information and Systems · JPTokyo Institute of Technology · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Plant-biosynthesised secondary metabolites are unique sources of pharmaceuticals, food additives, and flavourings, among other industrial uses. However, industrial production of these metabolites is difficult because of their structural complexity, dangerousness and unfriendliness to natural environment, so the development of new methods to synthesise them is required. In this study, we developed a novel approach to identifying alternative bacterial enzyme to produce plant-biosynthesised secondary metabolites. Based on the similarity of enzymatic reactions, we searched for candidate bacterial genes encoding enzymes that could potentially replace the enzymes in plant-specific secondary metabolism reactions that are contained in the KEGG database (enzyme re-positioning). As a result, we discovered candidate bacterial alternative enzyme genes for 447 plant-specific secondary metabolic reaction. To validate our approach, we focused on the ability of an enzyme from

Indexed as

Enzyme repositioningGenomicsNootkatonePlant secondary metabolismReaction similarity

Identifiers

PMID31720217

DOI10.1016/j.mec.2019.e00102

PMCPMC6838473

OpenAlexW2972420742

What OpenQuestion holds

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LicenceCC BY

Read underepoch 390

Registered trials

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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.