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  1. Book: Non-ribosomal peptide biosynthesis and engineering

    Burkart, Michael / Ishikawa, Fumihiro

    methods and protocols

    (Methods in molecular biology ; 2670 ; Springer protocols)

    2023  

    Author's details edited by Michael Burkart, Fumihiro Ishikawa
    Series title Methods in molecular biology ; 2670
    Springer protocols
    Collection
    Keywords Peptides/Synthesis
    Subject code 572.65
    Language English
    Size xi, 321 Seiten, Illustrationen, 26 cm
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT030023989
    ISBN 978-1-0716-3213-0 ; 9781071632147 ; 1-0716-3213-2 ; 1071632140
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    Zs A 7042 -2670- not available for loan Lesesaal EG

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  2. Article: Development of a chemical scaffold for inhibiting nonribosomal peptide synthetases in live bacterial cells.

    Ishikawa, Fumihiro / Konno, Sho / Kakeya, Hideaki / Tanabe, Genzoh

    Beilstein journal of organic chemistry

    2024  Volume 20, Page(s) 445–451

    Abstract: The adenylation (A) domain is essential for non-ribosomal peptide synthetases (NRPSs), which synthesize various peptide-based natural products, including virulence factors, such as siderophores and genotoxins. Hence, the inhibition of A-domains could ... ...

    Abstract The adenylation (A) domain is essential for non-ribosomal peptide synthetases (NRPSs), which synthesize various peptide-based natural products, including virulence factors, such as siderophores and genotoxins. Hence, the inhibition of A-domains could attenuate the virulence of pathogens. 5'-
    Language English
    Publishing date 2024-02-26
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2192461-2
    ISSN 1860-5397
    ISSN 1860-5397
    DOI 10.3762/bjoc.20.39
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Chemoproteomic Profiling of Adenylation Domain Functions in Gramicidin S-Producing Non-ribosomal Peptide Synthetases.

    Ishikawa, Fumihiro / Tanabe, Genzoh

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2670, Page(s) 69–100

    Abstract: Many amino acid-containing natural products are biosynthesized by large, multifunctional enzymes known as non-ribosomal peptide synthetases (NRPSs). Adenylation (A) domains in NRPSs are responsible for the incorporation of amino acid building blocks and ... ...

    Abstract Many amino acid-containing natural products are biosynthesized by large, multifunctional enzymes known as non-ribosomal peptide synthetases (NRPSs). Adenylation (A) domains in NRPSs are responsible for the incorporation of amino acid building blocks and can be considered as engineering domains; therefore, advanced techniques are required to not only rapidly verify expression and folding, but also accelerate the functional prediction of the A-domains in lysates from native and heterologous systems. We recently developed activity-based protein profiling (ABPP) of NRPSs that offers a simple and robust analytical platform for A-domains and provides insights into their enzyme-substrate specificity. In this chapter, we describe the design and synthesis of these ABPP probes and provide a summary of our work on the development of a series of protocols for labeling, visualizing, and analyzing endogenous NRPSs in complex biological systems.
    MeSH term(s) Gramicidin ; Peptide Synthases/chemistry ; Substrate Specificity ; Amino Acids
    Chemical Substances non-ribosomal peptide synthase (EC 6.3.2.-) ; Gramicidin (1405-97-6) ; Peptide Synthases (EC 6.3.2.-) ; Amino Acids
    Language English
    Publishing date 2023-05-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3214-7_4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Chemical Labeling of Protein 4'-Phosphopantetheinylation in Surfactin-Producing Nonribosomal Peptide Synthetases.

    Ishikawa, Fumihiro / Tanabe, Genzoh

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2670, Page(s) 285–299

    Abstract: 4'-Phosphopantetheinylation is an essential posttranslational modification of the primary and secondary metabolic pathways in prokaryotes and eukaryotes. Several peptide-based natural products are biosynthesized by large, multifunctional enzymes known as ...

    Abstract 4'-Phosphopantetheinylation is an essential posttranslational modification of the primary and secondary metabolic pathways in prokaryotes and eukaryotes. Several peptide-based natural products are biosynthesized by large, multifunctional enzymes known as nonribosomal peptide synthetases (NRPSs), responsible for producing virulence factors and many pharmaceuticals. The thiolation (T) domain serves as a covalent tether for substrates and intermediates in nonribosomal peptide biosynthesis and must be posttranslationally modified with a 4'-phosphopantetheinyl group. To detect 4'-phosphopantetheinylation of NRPS in bacterial proteomes, we developed a 5'-(vinylsulfonylaminodeoxy)adenosine scaffold with a clickable functionality, enabling effective chemical labeling of 4'-phosphopantethylated NRPSs. In this chapter, we describe the design and synthesis of an activity-based protein profiling probe and summarize our work toward developing a series of protocols for the labeling and visualization of 4'-phosphopantetheinylation of endogenous NRPSs in complex proteomes.
    MeSH term(s) Proteome ; Adenosine/chemistry ; Bacteria/metabolism ; Peptide Synthases/chemistry
    Chemical Substances non-ribosomal peptide synthase (EC 6.3.2.-) ; Proteome ; Adenosine (K72T3FS567) ; Peptide Synthases (EC 6.3.2.-)
    Language English
    Publishing date 2023-04-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3214-7_15
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: [Protein degradation in bacteria: focus on the ClpP protease].

    Ishikawa, Fumihiro / Homma, Michio / Tanabe, Genzoh / Uchihashi, Takayuki

    Nihon saikingaku zasshi. Japanese journal of bacteriology

    2024  Volume 79, Issue 1, Page(s) 1–13

    Abstract: Proteins in the cells are born (synthesized), work, and die (decomposed). In the life of a protein, its birth is obviously important, but how it dies is equally important in living organisms. Proteases secreted into the outside of cells are used to ... ...

    Abstract Proteins in the cells are born (synthesized), work, and die (decomposed). In the life of a protein, its birth is obviously important, but how it dies is equally important in living organisms. Proteases secreted into the outside of cells are used to decompose the external proteins and the degradation products are taken as the nutrients. On the other hand, there are also proteases that decompose unnecessary or harmful proteins which are generated in the cells. In eukaryotes, a large enzyme complex called the proteasome is primarily responsible for degradation of such proteins. Bacteria, which are prokaryotes, have a similar system as the proteasome. We would like to explain the bacterial degradation system of proteins or the death of proteins, which is performed by ATP-dependent protease Clp, with a particular focus on the ClpXP complex, and with an aspect as a target for antibiotics against bacteria.
    MeSH term(s) Proteolysis ; Proteasome Endopeptidase Complex/metabolism ; ATP-Dependent Proteases/metabolism ; Bacteria/metabolism ; Biological Transport ; Bacterial Proteins/metabolism
    Chemical Substances Proteasome Endopeptidase Complex (EC 3.4.25.1) ; ATP-Dependent Proteases (EC 3.4.21.-) ; Bacterial Proteins
    Language Japanese
    Publishing date 2024-02-20
    Publishing country Japan
    Document type English Abstract ; Journal Article
    ZDB-ID 604101-2
    ISSN 1882-4110 ; 0021-4930
    ISSN (online) 1882-4110
    ISSN 0021-4930
    DOI 10.3412/jsb.79.1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Recent progress in the reprogramming of nonribosomal peptide synthetases.

    Ishikawa, Fumihiro / Nakamura, Shinya / Nakanishi, Isao / Tanabe, Genzoh

    Journal of peptide science : an official publication of the European Peptide Society

    2023  Volume 30, Issue 3, Page(s) e3545

    Abstract: Nonribosomal peptide synthetases (NRPSs) biosynthesize nonribosomal peptide (NRP) natural products, which belong to the most promising resources for drug discovery and development because of their wide range of therapeutic applications. The results of ... ...

    Abstract Nonribosomal peptide synthetases (NRPSs) biosynthesize nonribosomal peptide (NRP) natural products, which belong to the most promising resources for drug discovery and development because of their wide range of therapeutic applications. The results of genetic, biochemical, and bioinformatics analyses have enhanced our understanding of the mechanisms of the NRPS machinery. A major goal in NRP biosynthesis is to reprogram the NRPS machinery to enable the biosynthetic production of designed peptides. Reprogramming strategies for the NRPS machinery have progressed considerably in recent years, thereby increasing the yields and generating modified peptides. Here, the recent progress in NRPS reprogramming and its application in peptide synthesis are described.
    MeSH term(s) Peptide Synthases/genetics ; Peptide Synthases/analysis ; Peptide Synthases/metabolism ; Peptide Biosynthesis, Nucleic Acid-Independent ; Peptides ; Biological Products
    Chemical Substances non-ribosomal peptide synthase (EC 6.3.2.-) ; Peptide Synthases (EC 6.3.2.-) ; Peptides ; Biological Products
    Language English
    Publishing date 2023-09-18
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1234416-3
    ISSN 1099-1387 ; 1075-2617
    ISSN (online) 1099-1387
    ISSN 1075-2617
    DOI 10.1002/psc.3545
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  7. Article ; Online: Activity-based protein profiling of a surfactin-producing nonribosomal peptide synthetase in

    Ishikawa, Fumihiro / Ohnishi, Rina / Uchida, Chiharu / Tanabe, Genzoh

    STAR protocols

    2022  Volume 3, Issue 3, Page(s) 101462

    Abstract: We present ... ...

    Abstract We present an
    MeSH term(s) Bacillus subtilis/metabolism ; Escherichia coli/genetics ; Peptide Synthases/chemistry
    Chemical Substances Peptide Synthases (EC 6.3.2.-) ; non-ribosomal peptide synthase (EC 6.3.2.-)
    Language English
    Publishing date 2022-06-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2022.101462
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  8. Article ; Online: Role of the thiosugar ring in the inhibitory activity of salacinol, a potent natural α-glucosidase inhibitor.

    Takashima, Katsuki / Nakamura, Shinya / Nagayama, Maiko / Marumoto, Shinsuke / Ishikawa, Fumihiro / Xie, Weijia / Nakanishi, Isao / Muraoka, Osamu / Morikawa, Toshio / Tanabe, Genzoh

    RSC advances

    2024  Volume 14, Issue 7, Page(s) 4471–4481

    Abstract: Herein, ring-cleaved (24) and truncated (25) analogues of an azasugar, 1-deoxynojirimycin (23), exhibited inhibitory activity ( ...

    Abstract Herein, ring-cleaved (24) and truncated (25) analogues of an azasugar, 1-deoxynojirimycin (23), exhibited inhibitory activity (
    Language English
    Publishing date 2024-02-02
    Publishing country England
    Document type Journal Article
    ISSN 2046-2069
    ISSN (online) 2046-2069
    DOI 10.1039/d3ra08485j
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  9. Article ; Online: Exploring a chemical scaffold for rapid and selective photoaffinity labelling of non-ribosomal peptide synthetases in living bacterial cells.

    Ishikawa, Fumihiro / Konno, Sho / Uchiyama, Yuko / Kakeya, Hideaki / Tanabe, Genzoh

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2023  Volume 378, Issue 1871, Page(s) 20220026

    Abstract: Non-ribosomal peptide synthetases (NRPSs) biosynthesize many pharmaceuticals and virulence factors. The biosynthesis of these natural peptide products from biosynthetic gene clusters depends on complex regulations in bacteria. However, our current ... ...

    Abstract Non-ribosomal peptide synthetases (NRPSs) biosynthesize many pharmaceuticals and virulence factors. The biosynthesis of these natural peptide products from biosynthetic gene clusters depends on complex regulations in bacteria. However, our current knowledge of NRPSs is based on enzymological studies using full NRPS systems and/or a single NRPS domain in heterologous hosts. Chemical and/or biochemical strategies to capture the endogenous activities of NRPSs facilitate studies on NRPS cell biology in bacterial cells. Here, we describe a chemical scaffold for the rapid and selective photoaffinity labelling of NRPSs in purified systems, crude biological samples and living bacterial cells. We synthesized photoaffinity labelling probes coupled with 5'-
    MeSH term(s) Diazomethane/metabolism ; Bacteria/genetics ; Peptide Synthases/chemistry ; Peptide Synthases/genetics ; Peptide Synthases/metabolism ; Multigene Family
    Chemical Substances non-ribosomal peptide synthase (EC 6.3.2.-) ; Diazomethane (60A625P70P) ; Peptide Synthases (EC 6.3.2.-)
    Language English
    Publishing date 2023-01-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2022.0026
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    Einzelsignatur: Show issues

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  10. Article ; Online: An indispensable role of TAZ in anoikis resistance promoted by OTUB1 deubiquitinating enzyme in basal-like triple-negative breast cancer cells.

    Nakagawa, Hidetsugu / Higurashi, Masato / Ishikawa, Fumihiro / Mori, Kazunori / Shibanuma, Motoko

    Biochemical and biophysical research communications

    2023  Volume 649, Page(s) 1–9

    Abstract: Aggressive cancers, such as triple-negative breast cancer (TNBC), are mostly fatal because of their potential to metastasize to distant organs. Cancer cells acquire various abilities to metastasize, including resistance to anoikis, an apoptotic cell ... ...

    Abstract Aggressive cancers, such as triple-negative breast cancer (TNBC), are mostly fatal because of their potential to metastasize to distant organs. Cancer cells acquire various abilities to metastasize, including resistance to anoikis, an apoptotic cell death induced by loss of anchorage to the extracellular matrix. Transcriptional coactivator with PDZ binding motif (TAZ) and Yes-associated protein (YAP), the downstream effectors of the Hippo pathway, regulate cell- and tissue-level architectures by responding to mechanical microenvironments of cells, including the cell-extracellular matrix interaction. The Hippo pathway is frequently disrupted in cancer cells, and TAZ and YAP are irrelevantly activated, potentially resulting in anchorage-independent survival/proliferation of cancer cells and metastatic progression. The study aims to investigate the roles of TAZ and YAP in anoikis resistance in basal-like (BL) TNBC cells, which comprise a major subtype (>70%) of TNBC. We found that TAZ and YAP had nonredundant roles in anchorage-independent cancer cell survival or anoikis resistance. Particularly, TAZ was indispensable for anoikis resistance in BL-TNBC cells but not for survival of non-transformed mammary epithelial cells (MECs). In contrast, YAP, a paralog of TAZ, was indispensable for survival of both non-transformed MECs and cancer cells. Therefore, TAZ might be a preferable therapeutic target against dissemination of aggressive cancer cells without killing normal cells. Interestingly, TAZ was abnormally stabilized in BL-TNBC cells under non-adherent conditions, which promoted anoikis resistance. Furthermore, OTUB1, a deubiquitinating enzyme, was responsible for the stabilization of TAZ in detached BL-TNBC cells. Importantly, simultaneous high expression of TAZ and OTUB1 was associated with poor prognosis in BC. Thus, OTUB1 has emerged as a potentially druggable target. Successful inhibition of OTUB1 enzymatic activity is expected to downregulate TAZ and eventually prevents metastasis of aggressive cancers, such as BL-TNBC.
    MeSH term(s) Humans ; Adaptor Proteins, Signal Transducing/metabolism ; Anoikis/physiology ; Triple Negative Breast Neoplasms/pathology ; YAP-Signaling Proteins ; Deubiquitinating Enzymes/metabolism ; Tumor Microenvironment
    Chemical Substances Adaptor Proteins, Signal Transducing ; YAP-Signaling Proteins ; Deubiquitinating Enzymes (EC 3.4.19.12)
    Language English
    Publishing date 2023-01-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 205723-2
    ISSN 1090-2104 ; 0006-291X ; 0006-291X
    ISSN (online) 1090-2104 ; 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2023.01.080
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