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Proteogenomics Study of Blastobotrys adeninivorans TMCC 70007—A Dominant Yeast in the Fermentation Process of Pu-erh Tea
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    Proteogenomics Study of Blastobotrys adeninivorans TMCC 70007—A Dominant Yeast in the Fermentation Process of Pu-erh Tea
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    • Fei Tian
      Fei Tian
      Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
      State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
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    • Jiahui Shi
      Jiahui Shi
      State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
      Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding 071002, China
      More by Jiahui Shi
    • Yanchang Li
      Yanchang Li
      State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
      More by Yanchang Li
    • Huiying Gao
      Huiying Gao
      State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
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    • Lei Chang
      Lei Chang
      State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
      More by Lei Chang
    • Yao Zhang
      Yao Zhang
      State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
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    • Linrui Gao
      Linrui Gao
      Yunnan Pu-erh Tea Fermentation Engineering Research Center, Yunnan TAETEA Microbial Technology Co., Ltd., Kunming 650217, China
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    • Ping Xu*
      Ping Xu
      State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
      Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding 071002, China
      *Email: [email protected]
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    • Shukun Tang*
      Shukun Tang
      Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
      Yunnan Pu-erh Tea Fermentation Engineering Research Center, Yunnan TAETEA Microbial Technology Co., Ltd., Kunming 650217, China
      *Email: [email protected]
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    Other Access OptionsSupporting Information (7)

    Journal of Proteome Research

    Cite this: J. Proteome Res. 2021, 20, 6, 3290–3304
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    https://doi.org/10.1021/acs.jproteome.1c00205
    Published May 19, 2021
    Copyright © 2021 American Chemical Society

    Abstract

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    Blastobotrys adeninivorans plays an essential role in pile-fermenting of Pu-erh tea. Its ability to assimilate various carbon and nitrogen sources makes it available for application in a wide range of industry sectors. The genome of B. adeninivorans TMCC 70007 isolated from pile-fermented Pu-erh tea was sequenced and assembled. Proteomics analysis indicated that 4900 proteins in TMCC 70007 were expressed under various culture conditions. Proteogenomics mapping revealed 48 previously unknown genes and corrected 118 gene models predicted by GeneMark-ES. Ortho-proteogenomics analysis identified 17 previously unidentified genes in B. adeninivorans LS3, the first strain with a sequenced genome among the genus Blastobotrys as well. More importantly, five species specific genes were identified from TMCC 70007, which could serve as a barcode for strain typing and were applicable for fermentation process protection of this industrial species. The datasets generated from tea aqueous extract culture not only increased the proteome coverage and accuracy but also contributed to the identification of proteins related to polyphenols and caffeine, which were considered to change greatly during the microbial fermentation of Pu-erh tea. This study provides a proteome perspective on TMCC 70007, which was considered to be an important strain in the production of Pu-erh tea. The systematic proteogenomics analysis not only made a better annotation on the genome of B. adeninivorans TMCC 70007 as previous proteogenomics study but also provided solution for fermentation process protection on valuable industrial species with species specific genes uniquely identified from proteogenomics study.

    Copyright © 2021 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.jproteome.1c00205.

    • Genes predicted, proteomics identifications, and functional annotations (Table S1) (XLSX)

    • List of previously unidentified genes (Table S2) (XLSX)

    • List of previously unidentified genes revealed by ortho-proteogenomics mapping in B. adeninivorans LS3 (Table S3) (XLSX)

    • List of Acetyl[ProteinN-term] modified peptides (Table S4) (XLSX)

    • List of revised genes (Table S5) (XLSX)

    • Identification of proteins involved in phenol metabolism (Table S6) (XLSX)

    • Comparison of the proteomics results of different datasets (Figure S1); confirmation of predicted genes (Figure S2); comparison of the proteogenomics results of different datasets (Figure S3); identification of a short CDS (Figure S4); protein N-terminal acetylation in B. adeninivorans TMCC 70007 (Figure S5); translation initiation site (TIS) correction (Figure S6); protein identification under YPD and TAE conditions (Figure S7); and barcode sequences supported by proteomics data can be used for strain typing (Figure S8) (PDF)

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    Cited By

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    This article is cited by 6 publications.

    1. Cunqiang Ma, Bingsong Ma, Binxing Zhou, Longjie Xu, Zhihang Hu, Xinghui Li, Xuan Chen. Pile-fermentation mechanism of ripened Pu-erh tea: Omics approach, chemical variation and microbial effect. Trends in Food Science & Technology 2024, 146 , 104379. https://doi.org/10.1016/j.tifs.2024.104379
    2. Yuanyuan Yi, Jiabao Li, Pan Zhou, Fenglin Jia, Yichao Chen, Dong Li. Production of single cell protein rich in potassium by Nectaromyces rattus using biogas slurry and molasses. Journal of Environmental Management 2024, 350 , 119627. https://doi.org/10.1016/j.jenvman.2023.119627
    3. Menglei Shuai, Yuanqing Fu, Hai-li Zhong, Wanglong Gou, Zengliang Jiang, Yuhui Liang, Zelei Miao, Jin-Jian Xu, Tien Huynh, Mark L Wahlqvist, Yu-ming Chen, Ju-Sheng Zheng. Mapping the human gut mycobiome in middle-aged and elderly adults: multiomics insights and implications for host metabolic health. Gut 2022, 71 (9) , 1812-1820. https://doi.org/10.1136/gutjnl-2021-326298
    4. Sunan Wang, Yi Qiu, Ren-You Gan, Fan Zhu. Chemical constituents and biological properties of Pu-erh tea. Food Research International 2022, 154 , 110899. https://doi.org/10.1016/j.foodres.2021.110899
    5. Jiahui Shi, Shuhong Meng, Li Wan, Zhenpeng Zhang, Songhao Jiang, Huiming Zhu, Erhei Dai, Lei Chang, Huiying Gao, Kanglin Wan, Liqun Zhang, Xiuqin Zhao, Haican Liu, Zhitang Lyu, Yao Zhang, Ping Xu. Deep N-terminomics of Mycobacterium tuberculosis H37Rv extensively correct annotated encoding genes. Genomics 2022, 114 (1) , 292-304. https://doi.org/10.1016/j.ygeno.2021.12.001
    6. Karin Ernits, Christian Kjeldsen, Karina Persson, Eliis Grigor, Tiina Alamäe, Triinu Visnapuu. Structural Insight into a Yeast Maltase—The BaAG2 from Blastobotrys adeninivorans with Transglycosylating Activity. Journal of Fungi 2021, 7 (10) , 816. https://doi.org/10.3390/jof7100816

    Journal of Proteome Research

    Cite this: J. Proteome Res. 2021, 20, 6, 3290–3304
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jproteome.1c00205
    Published May 19, 2021
    Copyright © 2021 American Chemical Society

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