Constructing the metabolic network of wheat kernels based on structure-guided chemical modification and multi-omics data

Zhitao Tian; Jingqi Jia; Bo Yin; Wei Chen

doi:10.1016/j.jgg.2024.02.008

Volume 51 Issue 7

Jul. 2024

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Article Navigation > Journal of Genetics and Genomics > 2024 > 51(7): 714-722

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Constructing the metabolic network of wheat kernels based on structure-guided chemical modification and multi-omics data

doi: 10.1016/j.jgg.2024.02.008

Zhitao Tian^a,b,
Jingqi Jia^a,b,
Bo Yin^a,b,
Wei Chen^a,b

a. National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China;
b. Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China

Funds:

The authors thank the high-performance computing platform and the mass spectrometry platform at the National Key Laboratory of Crop Genetic Improvement at Huazhong Agricultural University. This work was supported by the Young Top-notch Talent Cultivation Program of Hubei Province, the Natural Science Foundation for Distinguished Young Scientists of Hubei Province (2021CFA058), and the First-Class Discipline Construction Funds of College of Plant Science and Technology, Huazhong Agricultural University (2023ZKPY005).

Received Date: 2023-11-08
Accepted Date: 2024-02-27
Rev Recd Date: 2024-02-27

Available Online: 2025-06-06

Publish Date: 2024-03-06

Abstract

Abstract

Metabolic network construction plays a pivotal role in unraveling the regulatory mechanism of biological activities, although it often proves to be challenging and labor-intensive, particularly with non-model organisms. In this study, we develop a computational approach that employs reaction models based on the structure-guided chemical modification and related compounds to construct a metabolic network in wheat. This construction results in a comprehensive structure-guided network, including 625 identified metabolites and additional 333 putative reactions compared with the Kyoto Encyclopedia of Genes and Genomes database. Using a combination of gene annotation, reaction classification, structure similarity, and correlations from transcriptome and metabolome analysis, a total of 229 potential genes related to these reactions are identified within this network. To validate the network, the functionality of a hydroxycinnamoyltransferase (TraesCS3D01G314900) for the synthesis of polyphenols and a rhamnosyltransferase (TraesCS2D01G078700) for the modification of flavonoids are verified through in vitro enzymatic studies and wheat mutant tests, respectively. Our research thus supports the utility of structure-guided chemical modification as an effective tool in identifying causal candidate genes for constructing metabolic networks and further in metabolomic genetic studies.
- Metabolic network,
- Chemical modification,
- Genetic study,
- Wheat kernel,
- Multi-omics

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References(54)

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