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Metabologenomics-Inspired Discovery and Combinatorial Biosynthesis-Based Diversification of Fungal O-Glycosylated Depsides

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Download Hi-Res ImageDownload to MS-PowerPointCite This:Org. Lett. 2024, 26, 39, 8317-8322
    Letter

    Metabologenomics-Inspired Discovery and Combinatorial Biosynthesis-Based Diversification of Fungal O-Glycosylated Depsides
    Click to copy article linkArticle link copied!

    • Hu Yang
      Hu Yang
      Key Laboratory of Chemical Biology (Ministry of Education), Shandong Basic Science Research Center (Pharmacy), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
      More by Hu Yang
    • Zhuo Shang
      Zhuo Shang
      Key Laboratory of Chemical Biology (Ministry of Education), Shandong Basic Science Research Center (Pharmacy), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
      More by Zhuo Shang
      Orcidhttps://orcid.org/0000-0002-5755-2629
    • Yingying Chen
      Yingying Chen
      CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
      More by Yingying Chen
    • Feng Li
      Feng Li
      Key Laboratory of Chemical Biology (Ministry of Education), Shandong Basic Science Research Center (Pharmacy), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
      More by Feng Li
    • Kunlong Li
      Kunlong Li
      Key Laboratory of Chemical Biology (Ministry of Education), Shandong Basic Science Research Center (Pharmacy), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
      More by Kunlong Li
    • Hongjie Zhu
      Hongjie Zhu
      Key Laboratory of Chemical Biology (Ministry of Education), Shandong Basic Science Research Center (Pharmacy), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
      More by Hongjie Zhu
    • Ming Peng
      Ming Peng
      Key Laboratory of Chemical Biology (Ministry of Education), Shandong Basic Science Research Center (Pharmacy), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
      More by Ming Peng
    • Jiafan Yang
      Jiafan Yang
      CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
      More by Jiafan Yang
    • Cunlei Cai
      Cunlei Cai
      CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
      More by Cunlei Cai
    • Jianhua Ju*
      Jianhua Ju
      Key Laboratory of Chemical Biology (Ministry of Education), Shandong Basic Science Research Center (Pharmacy), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
      CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
      *Email: jju@sdu.edu.cn
      More by Jianhua Ju
      Orcidhttps://orcid.org/0000-0001-7712-8027
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    Organic Letters

    Cite this: Org. Lett. 2024, 26, 39, 8317–8322
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    https://doi.org/10.1021/acs.orglett.4c03024
    Published September 20, 2024
    Copyright © 2024 American Chemical Society
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    Abstract

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    Through metabologenomics mining, we prioritized Exophiala xenobiotica SDU 039, a deep-sea sediment-derived fungus producing O-glycosylated depsides (1–9), including seven new species with varying aliphatic chains. Heterologous expression validated the exo gene cluster, and in vitro enzyme assays elucidated the function of glycosyltransferase ExoC. The chemical diversity of O-glycosylated depsides is expanded by combinatorial biosynthesis using homologues depside biosynthetic genes and in vitro transformation with ExoC and different sugars as substrate.

    Copyright © 2024 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.orglett.4c03024.

    • General experimental procedures, structural analysis, in vivo/in vitro data mentioned in the text, and spectroscopic/chromatographic data (PDF)

    Metabologenomics-Inspired Discovery and Combinatorial Biosynthesis-Based Diversification of Fungal O‑Glycosylated Depsides

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    1
    Supporting Information
    M
    etabologenomics
    -
    I
    nspired
    D
    iscovery
    and
    Combinatorial Biosynthesis
    -
    Based
    Diversification
    of
    Fungal
    O
    -
    Glycosylated
    D
    epsides
    Hu Yang
    †
    ,
    Zhuo Shang
    †
    ,
    Yingying Chen
    ‡
    ,
    Feng Li
    †
    ,
    Kunlong Li
    †
    , Hongjie Zhu
    †
    ,
    Ming Peng
    †
    ,
    Jiafan Yang
    ‡
    , Cunlei Cai
    ‡
    , and Jianhua Ju
    †
    ‡
    *
    †
    Key Laboratory of Chemical Biology (Ministry of Education), Shandong Basic Science Research Center
    (Pharmacy), School of Pharmaceutical Sciences,
    Cheeloo College of Medicine,
    Shandong University,
    Jinan 250012, China
    ‡
    CAS Key Laboratory of Tropical Marine Bio
    -
    resources and Ecology, South China Sea Institute of
    Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
    *
    Email:
    jju@sdu.edu.cn
    2
    Table of Contents
    Supplementary Materials and Methods
    ................................
    ................................
    .....
    6
    1. General experimental procedures
    ................................
    ................................
    ..........................
    6
    2. Microorganism material
    ................................
    ................................
    ................................
    ........
    6
    3. DNA/RNA isolation, sequencing and manipulation
    ................................
    .............................
    6
    4. Bioinformatic analysis
    ................................
    ................................
    ................................
    ..........
    7
    5. HPLC analysis
    ................................
    ................................
    ................................
    .......................
    7
    6. Heterogenous expression strain construction
    ................................
    ................................
    ........
    7
    7. Transformation, culture and secondary metabolism analysis of heterogenous strains
    ..........
    7
    8. Cloning, overexpression and preparation of microsomal fraction of ExoC
    ..........................
    7
    9.
    In vitro
    biochemical reaction
    ................................
    ................................
    ................................
    .
    8
    10. Fermentation and isolation
    ................................
    ................................
    ................................
    ..
    8
    11. Creation of molecular network
    ................................
    ................................
    ............................
    9
    12. Docking simulation
    ................................
    ................................
    ................................
    .............
    9
    13. Characterization of compounds
    ................................
    ................................
    ...........................
    9
    14. Structural elucidation of new depside glycosides
    ................................
    .............................
    10
    Supplementary Tables
    ................................
    ................................
    ...............................
    12
    Table S1.
    The annotation of
    exo
    gene cluster in
    E
    .
    xenobiotica
    SDU 039
    .
    ............................
    12
    Table S2.
    Strains used and constructed in this study.
    ................................
    .............................
    12
    Table S3.
    Plasmids used in this study.
    ................................
    ................................
    ....................
    14
    Table S4.
    Primers used in this study.
    ................................
    ................................
    ......................
    15
    Table S5.
    Media and stock used in this study.
    ................................
    ................................
    ........
    17
    Table S6.
    Summary of
    1
    H and
    13
    C NMR data of compounds
    3
    –
    6
    in CD
    3
    OD.
    .......................
    19
    Table S7.
    Summary of
    1
    H and
    13
    C NMR data of compounds
    7
    –
    10
    in CD
    3
    OD.
    .....................
    21
    Table S8.
    Fungal PKSs used to create the phylogenetic tree and multiple sequence alignment
    .
    .
    ................................
    ................................
    ................................
    ................................
    ................
    23
    Table S9.
    The annotation of
    dep
    and
    spmt
    gene clusters.
    ................................
    .......................
    23
    Table S10.
    The protein sequence of ExoC (549AA), ExoC (520AA) and ExoC (513AA).
    ...
    24
    Supplementary Figures
    ................................
    ................................
    .............................
    25
    Figure S1.
    Clusters containing five homologous hits using the sequence of NR
    -
    PKS DrcA as
    a query analyzed by local BLAST.
    ................................
    ................................
    ..........................
    25
    Figure S2.
    Structures of depsides and depsidones from
    Aspergillus
    sp. SCSIO SX7S7 and
    Spiromastix
    sp. SCSIO F190
    .
    ................................
    ................................
    ................................
    ..
    26
    Figure S3.
    The biosynthetic pathway of depsides from SX7S7 and F190.
    ............................
    27
    Figure S4.
    (A) Clusters containing depsides
    -
    forming PKSs and homologues from SDU 039,
    F190 and SX7S7 analyzed by CAGECAT. (B) Clusters responsibe for the biosynthesis of
    1
    from
    Exophiala xenobiotica
    SDU 039 and phaeomoniecin D from
    Phaeomoniella
    chlamydospora
    CBS239.74 analyzed by
    CAGECAT.
    ................................
    ............................
    27
    Figure S5.
    Molecular network of depside glycoside analogues in extracts of
    E.
    xenobiotica

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    Organic Letters

    Cite this: Org. Lett. 2024, 26, 39, 8317–8322
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.orglett.4c03024
    Published September 20, 2024
    Copyright © 2024 American Chemical Society
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