Evidence map›Paper›PMID 38994432›Full record

ArticleChemical science2024

Structural-model-based genome mining can efficiently discover novel non-canonical terpene synthases hidden in genomes of diverse species.

Tohru Abe, Haruna Shiratori, Kosuke Kashiwazaki, Kazuma Hiasa, Daijiro Ueda, Tohru Taniguchi, Hajime Sato, Takashi Abe, Tsutomu Sato

Abstract read
In one paragraph

Article in Chemical science, 2024. 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
–field-weighted citation impact
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.

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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

9 authors.

Tohru AbeDepartment of Life and Food Sciences, Graduate School of Science and Technology, Niigata University Ikarashi 2-8050, Nishi-ku Niigata 950-2181 Japan satot@agr.niigata-u.ac.jp.ORCID https://orcid.org/0000-0003-4868-3237
Haruna ShiratoriDepartment of Life and Food Sciences, Graduate School of Science and Technology, Niigata University Ikarashi 2-8050, Nishi-ku Niigata 950-2181 Japan satot@agr.niigata-u.ac.jp.
Kosuke KashiwazakiDepartment of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University Ikarashi 2-8050, Nishi-ku Niigata 950-2181 Japan takaabe@ie.niigata-u.ac.jp.
Kazuma HiasaInterdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi 4-4-37 Takeda Kofu Yamanashi 400-8510 Japan hsato@yamanashi.ac.jp.
Daijiro UedaDepartment of Life and Food Sciences, Graduate School of Science and Technology, Niigata University Ikarashi 2-8050, Nishi-ku Niigata 950-2181 Japan satot@agr.niigata-u.ac.jp.ORCID https://orcid.org/0000-0002-9870-7690
Tohru TaniguchiFrontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University North 21 West 11 Sapporo 001-0021 Japan.ORCID https://orcid.org/0000-0002-4965-7383
Hajime SatoInterdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi 4-4-37 Takeda Kofu Yamanashi 400-8510 Japan hsato@yamanashi.ac.jp.ORCID https://orcid.org/0000-0001-5185-096X
Takashi AbeDepartment of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University Ikarashi 2-8050, Nishi-ku Niigata 950-2181 Japan takaabe@ie.niigata-u.ac.jp.
Tsutomu SatoDepartment of Life and Food Sciences, Graduate School of Science and Technology, Niigata University Ikarashi 2-8050, Nishi-ku Niigata 950-2181 Japan satot@agr.niigata-u.ac.jp.ORCID https://orcid.org/0000-0002-1130-9025

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Non-canonical terpene synthases (TPSs) with primary sequences that are unrecognizable as canonical TPSs have evaded detection by conventional genome mining. This study aimed to prove that novel non-canonical TPSs can be efficiently discovered from proteins, hidden in genome databases, predicted to have 3D structures similar to those of class I TPSs. Six types of non-canonical TPS candidates were detected using this search strategy from 268 genome sequences from actinomycetes. Functional analyses of these candidates revealed that at least three types were novel non-canonical TPSs. We propose classifying the non-canonical TPSs as classes ID, IE, and IF. A hypothetical protein MBB6373681 from

Identifiers

PMID38994432
PMCPMC11234867

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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.