Evidence map›Paper›PMID 38175233›Full record

ArticleApplied microbiology and biotechnology2024

Mining and rational design of psychrophilic catalases using metagenomics and deep learning models.

Shuning Wu, Guoshun Xu, Yongping Su, Huoqing Huang, Xinxin Xu, Yuhong Zhang, Jian Tian, Wei Zhang, Zhiwei Zhang, Bo Liu

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

Article in Applied microbiology and biotechnology, 2024. 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
0.5field-weighted citation impact, top 39% 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, 2 citations in OpenAlex.

  1. 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

10 authors at 2 institutions in 2 countries.

Shuning Wu *Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China.
Guoshun Xu *Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
Yongping SuBiotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China.
Huoqing HuangInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
Xinxin XuBiotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China.
Yuhong ZhangBiotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China.
Jian TianBiotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China.
Wei ZhangBiotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China.
Zhiwei ZhangCollege of Forestry, Shanxi Agricultural University, No.81 Longcheng Street, Taiyuan, 030031, Shanxi, China. zhiweizhang2012@163.com.
Bo LiuBiotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian District, Beijing, 100081, China. liubo01@caas.cn.ORCID http://orcid.org/0009-0008-8013-0644
Chinese Academy of Agricultural Sciences · CNShanxi Agricultural University · CN

Funding

Agricultural Science and Technology Innovation Program CAAS-ZDRW202305National Key Research and Development Program of China 2021YFA0910602National Key Research and Development Program of China 2022YFA0912301the China Agriculture Research System of MOF and MARA CARS-41
6 · The paper itself

Abstract

A complete catalase-encoding gene, designated soiCat1, was obtained from soil samples via metagenomic sequencing, assembly, and gene prediction. soiCat1 showed 73% identity to a catalase-encoding gene of Mucilaginibacter rubeus strain P1, and the amino acid sequence of soiCAT1 showed 99% similarity to the catalase of a psychrophilic bacterium, Pedobacter cryoconitis. soiCAT1 was identified as a psychrophilic enzyme due to the low optimum temperature predicted by the deep learning model Preoptem, which was subsequently validated through analysis of enzymatic properties. Experimental results showed that soiCAT1 has a very narrow range of optimum temperature, with maximal specific activity occurring at the lowest test temperature (4 °C) and decreasing with increasing reaction temperature from 4 to 50 °C. To rationally design soiCAT1 with an improved temperature range, soiCAT1 was engineered through site-directed mutagenesis based on molecular evolution data analyzed through position-specific amino acid possibility calculation. Compared with the wild type, one mutant, soiCAT1

Indexed as

Deep LearningAmino AcidsAmino Acid SequenceCatalaseSoilAmino AcidsCatalaseSoilCatalaseDeep learning modelMetagenomicsOptimum temperatureRational design

Identifiers

PMID38175233
PMCPMC13498043
OpenAlexW4390586236

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.