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Discovery of novel glycoside hydrolases from C-glycoside-degrading bacteria using sequence similarity network analysis

  • Microbial Genetics, Genomics and Molecular Biology
  • Published:
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ab]Abstract

C-Glycosides are an important type of natural product with significant bioactivities, and the C-glycosidic bonds of C-glycosides can be cleaved by several intestinal bacteria, as exemplified by the human faeces-derived puerarin-degrading bacterium Dorea strain PUE. However, glycoside hydrolases in these bacteria, which may be involved in the C-glycosidic bond cleavage of C-glycosides, remain largely unknown. In this study, the genomes of the closest phylogenetic neighbours of five puerarin-degrading intestinal bacteria (including Dorea strain PUE) were retrieved, and the protein-coding genes in the genomes were subjected to sequence similarity network (SSN) analysis. Only four clusters of genes were annotated as glycoside hydrolases and observed in the genome of D. longicatena DSM 13814T (the closest phylogenetic neighbour of Dorea strain PUE); therefore, genes from D. longicatena DSM 13814T belonging to these clusters were selected to overexpress recombinant proteins (CG1, CG2, CG3, and CG4) in Escherichia coli BL21(DE3). In vitro assays indicated that CG4 efficiently cleaved the O-glycosidic bond of daidzin and showed moderate β-D-glucosidase and β-D-xylosidase activity. CG2 showed weak activity in hydrolyzing daidzin and pNP-β-D-fucopyranoside, while CG3 was identified as a highly selective and efficient α-glycosidase. Interestingly, CG3 and CG4 could be selectively inhibited by daidzein, explaining their different performance in kinetic studies. Molecular docking studies predicted the molecular determinants of CG2, CG3, and CG4 in substrate selectivity and inhibition propensity. The present study identified three novel and distinctive glycoside hydrolases, highlighting the potential of SSN in the discovery of novel enzymes from genomic data.

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Acknowledgements

This work was financially supported by the National Key Research and Development Program (2017YFE0103100), the programs of the National Natural Science Foundation of China (No. 81903534, No. 81773628, and No. 81741165), the High-Level Talent Special Support Plan of Zhejiang Province (No. 2019R52009) and the Scientific Research Fund of Second Institute of Oceanography, State Oceanic Administration (JB2002).

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  1. These authors contributed equally to this work.

Authors and Affiliations

  1. College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, P. R. China

    Bin Wei, Ya-Kun Wang, Jin-Biao Yu, Si-Jia Wang, Yan-Lei Yu & Hong Wang

  2. Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, 310014, P. R. China

    Bin Wei & Hong Wang

  3. Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, P. R. China

    Bin Wei & Xue-Wei Xu

  4. Center for Human Nutrition, David Geffen School of Medicine, University of California, Los Angeles, California, 90024, USA

    Si-Jia Wang

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  1. Bin Wei
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Contributions

HW and XX conceived and designed the study. BW and YW conducted experiments and wrote the manuscript. JY and SW contributed analytical tools and analyzed data. YY revised the manuscript. All the authors read and approved the manuscript.

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Correspondence to Xue-Wei Xu or Hong Wang.

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All authors declare no conflicts of interest. This article does not contain any studies with human participants performed by any of the authors.

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Wei, B., Wang, YK., Yu, JB. et al. Discovery of novel glycoside hydrolases from C-glycoside-degrading bacteria using sequence similarity network analysis. J Microbiol. 59, 931–940 (2021). https://doi.org/10.1007/s12275-021-1292-4

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  • DOI: https://doi.org/10.1007/s12275-021-1292-4

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