Precision enzyme discovery through targeted mining of metagenomic data

Shohreh Ariaeenejad, Javad Gharechahi, Mehdi Foroozandeh Shahraki, Fereshteh Fallah Atanaki, Jian Lin Han, Xue Zhi Ding, Falk Hildebrand, Mohammad Bahram, Kaveh Kavousi*, Ghasem Hosseini Salekdeh*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

2 Citations (Scopus)
1 Downloads (Pure)

Abstract

Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.

Original languageEnglish
Article number7
Pages (from-to)1-17
Number of pages17
JournalNatural Products and Bioprospecting
Volume14
Issue number1
Early online date1 Nov 2024
DOIs
Publication statusAccepted/In press - 19 Dec 2023

Bibliographical note

Copyright the Author(s) 2024. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

  • Enzyme bioprospecting
  • Functional-based screening
  • Metagenomics
  • Natural products
  • Protein structure prediction
  • Sequence-based screening

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