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Veilumuthu P, Nagarajan T, Magar S, Sundaresan S, Moses LJ, Theodore T, Christopher JG. Genomic insights into an endophytic Streptomyces sp. VITGV156 for antimicrobial compounds. Front Microbiol 2024; 15:1407289. [PMID: 38887720 PMCID: PMC11180775 DOI: 10.3389/fmicb.2024.1407289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/29/2024] [Indexed: 06/20/2024] Open
Abstract
Endophytic Streptomyces sp. are recognized as a potential resource for valuable natural products but are less explored. This study focused on exploring endophytic Streptomyces species residing within tomato plants (Solanum lycopersicum) harboring genes for the production of a novel class of antibiotics. Our research involved the isolation and characterization of Streptomyces sp. VITGV156, a newly identified endophytic Streptomyces species that produces antimicrobial products. VITGV156 harbors a genome of 8.18 mb and codes 6,512 proteins, of which 4,993 are of known function (76.67%) and 1,519 are of unknown function (23.32%). By employing genomic analysis, we elucidate the genome landscape of this microbial strain and shed light on various BGCs responsible for producing polyketide antimicrobial compounds, with particular emphasis on the antibiotic kendomycin. We extended our study by evaluating the antibacterial properties of kendomycin. Overall, this study provides valuable insights into the genome of endophytic Streptomyces species, particularly Streptomyces sp. VITGV156, which are prolific producers of antimicrobial agents. These findings hold promise for further research and exploitation of pharmaceutical compounds, offering opportunities for the development of novel antimicrobial drugs.
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Affiliation(s)
- Pattapulavar Veilumuthu
- Department of Biomedical Sciences, School of BioSciences and Technology, Vellore Institute of Technology, Vellore, India
| | - T. Nagarajan
- Department of Biological Sciences, SRM University-AP, Amaravathi, India
| | - Sharayu Magar
- Department of Biological Sciences, SRM University-AP, Amaravathi, India
| | - Sasikumar Sundaresan
- Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Lenus Joy Moses
- Department of Biomedical Sciences, School of BioSciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Thomas Theodore
- School of Chemical Engineering, Vellore Institute of Technology, Vellore, India
| | - John Godwin Christopher
- Department of Biomedical Sciences, School of BioSciences and Technology, Vellore Institute of Technology, Vellore, India
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2
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Identification and Heterologous Expression of the Kendomycin B Biosynthetic Gene Cluster from Verrucosispora sp. SCSIO 07399. Mar Drugs 2021; 19:md19120673. [PMID: 34940672 PMCID: PMC8708025 DOI: 10.3390/md19120673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Verrucosispora sp. SCSIO 07399, a rare marine-derived actinomycete, produces a set of ansamycin-like polyketides kendomycin B–D (1–3) which possess potent antibacterial activities and moderate tumor cytotoxicity. Structurally, kendomycin B–D contain a unique aliphatic macrocyclic ansa scaffold in which the highly substituted pyran ring is connected to the quinone moiety. In this work, a type I/type III polyketide synthase (PKS) hybrid biosynthetic gene cluster coding for assembly of kendomycin B (kmy), and covering 33 open reading frames, was identified from Verrucosispora sp. SCSIO 07399. The kmy cluster was found to be essential for kendomycin B biosynthesis as verified by gene disruption and heterologous expression. Correspondingly, a biosynthetic pathway was proposed based on bioinformatics, cluster alignments, and previous research. Additionally, the role of type III PKS for generating the precursor unit 3,5-dihydroxybenzoic acid (3,5-DHBA) was demonstrated by chemical complementation, and type I PKS executed the polyketide chain elongation. The kmy cluster was found to contain a positive regulatory gene kmy4 whose regulatory effect was identified using real-time quantitative PCR (RT-qPCR). These advances shed important new insights into kendomycin B biosynthesis and help to set the foundation for further research aimed at understanding and exploiting the carbacylic ansa scaffold.
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Tranter D, Filipuzzi I, Lochmann T, Knapp B, Kellosalo J, Estoppey D, Pistorius D, Meissner A, Paavilainen VO, Hoepfner D. Kendomycin Cytotoxicity against Bacterial, Fungal, and Mammalian Cells Is Due to Cation Chelation. JOURNAL OF NATURAL PRODUCTS 2020; 83:965-971. [PMID: 32182062 PMCID: PMC7497661 DOI: 10.1021/acs.jnatprod.9b00826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Indexed: 06/10/2023]
Abstract
Kendomycin is a small-molecule natural product that has gained significant attention due to reported cytotoxicity against pathogenic bacteria and fungi as well as a number of cancer cell lines. Despite significant biomedical interest and attempts to reveal its mechanism of action, the cellular target of kendomycin remains disputed. Herein it is shown that kendomycin induces cellular responses indicative of cation stress comparable to the effects of established iron chelators. Furthermore, addition of excess iron and copper attenuated kendomycin cytotoxicity in bacteria, yeast, and mammalian cells. Finally, NMR analysis demonstrated a direct interaction with cations, corroborating a close link between the observed kendomycin polypharmacology across different species and modulation of iron and/or copper levels.
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Affiliation(s)
- Dale Tranter
- Institute
of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Ireos Filipuzzi
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Thomas Lochmann
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Britta Knapp
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Juho Kellosalo
- Institute
of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - David Estoppey
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Dominik Pistorius
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Axel Meissner
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
| | | | - Dominic Hoepfner
- Novartis
Institutes for BioMedical Research, 4056 Basel, Switzerland
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Zhang S, Xie Q, Sun C, Tian XP, Gui C, Qin X, Zhang H, Ju J. Cytotoxic Kendomycins Containing the Carbacylic Ansa Scaffold from the Marine-Derived Verrucosispora sp. SCSIO 07399. JOURNAL OF NATURAL PRODUCTS 2019; 82:3366-3371. [PMID: 31765156 DOI: 10.1021/acs.jnatprod.9b00654] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Three new kendomycin analogues, kendomycins B-D (1-3), were discovered from the marine-derived actinomycete Verrucosispora sp. SCSIO 07399. The structures of 1-3 were elucidated using diverse spectroscopic data analyses, X-ray crystallography, and semisynthetic derivatization. In vitro antimicrobial assays revealed that 1-3 all display good antibacterial activities against six Gram-positive bacteria with MIC values ranging from 0.5 to 8.0 μg/mL. Additionally, 1-3 were found to be moderately cytotoxic against MGC803, A549, HeLa, HepG2, MCF-7, and RKO human tumor cell lines; IC50 values ranged from 2.2 to 44 μM.
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Affiliation(s)
- Shanwen Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , People's Republic of China
- College of Oceanology , University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 110039 , People's Republic of China
| | - Qing Xie
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine , Guangdong Medical University , Dongguan 523808 , People's Republic of China
| | - Changli Sun
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , People's Republic of China
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , People's Republic of China
| | - Chun Gui
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , People's Republic of China
- College of Oceanology , University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 110039 , People's Republic of China
| | - Xiangjing Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , People's Republic of China
| | - Hua Zhang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine , Guangdong Medical University , Dongguan 523808 , People's Republic of China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , People's Republic of China
- College of Oceanology , University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 110039 , People's Republic of China
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5
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Gomathi A, Gothandam KM. Investigation of anti‐inflammatory and toxicity effects of mangrove‐derived
Streptomyces rochei
strain VITGAP173. J Cell Biochem 2019; 120:17080-17097. [DOI: 10.1002/jcb.28969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/23/2019] [Accepted: 03/26/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Ajitha Gomathi
- Department of Biotechnology, School of Bio Sciences and Technology Vellore Institute of Technology (VIT) Vellore Tamil Nadu India
| | - Kodiveri Muthukalianan Gothandam
- Department of Biotechnology, School of Bio Sciences and Technology Vellore Institute of Technology (VIT) Vellore Tamil Nadu India
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6
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Strategies for construction of the all-carbon macrocyclic skeleton of the ansamycin antibiotic—kendomycin. J Antibiot (Tokyo) 2016; 69:203-12. [DOI: 10.1038/ja.2016.5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/09/2016] [Accepted: 01/15/2016] [Indexed: 11/08/2022]
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A. Elnakady Y, Chatterjee I, Bischoff M, Rohde M, Josten M, Sahl HG, Herrmann M, Müller R. Investigations to the Antibacterial Mechanism of Action of Kendomycin. PLoS One 2016; 11:e0146165. [PMID: 26795276 PMCID: PMC4721675 DOI: 10.1371/journal.pone.0146165] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 12/14/2015] [Indexed: 11/25/2022] Open
Abstract
Purpose The emergence of bacteria that are resistant to many currently used drugs emphasizes the need to discover and develop new antibiotics that are effective against such multi-resistant strains. Kendomycin is a novel polyketide that has a unique quinone methide ansa structure and various biological properties. This compound exhibits strong antibacterial activity against Gram-negative and Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Despite the promise of kendomycinin in several therapeutic areas, its mode of action has yet to be identified. Methods In this study, we used a multidisciplinary approach to gain insight into the antibacterial mechanism of this compound. Results The antibacterial activity of kendomycin appears to be bacteriostatic rather than bactericidal. Kendomycin inhibited the growth of the MRSA strain COL at a low concentration (MIC of 5 μg/mL). Proteomic analysis and gene transcription profiling of kendomycin-treated cells indicated that this compound affected the regulation of numerous proteins and genes involved in central metabolic pathways, such as the tricarboxylic acid (TCA) cycle (SdhA) and gluconeogenesis (PckA and GapB), cell wall biosynthesis and cell division (FtsA, FtsZ, and MurAA), capsule production (Cap5A and Cap5C), bacterial programmed cell death (LrgA and CidA), the cellular stress response (ClpB, ClpC, ClpP, GroEL, DnaK, and GrpE), and oxidative stress (AhpC and KatA). Electron microscopy revealed that kendomycin strongly affected septum formation during cell division. Most kendomycin-treated cells displayed incomplete septa with abnormal morphology. Conclusions Kendomycin might directly or indirectly affect the cell division machinery, protein stability, and programmed cell death in S. aureus. Additional studies are still needed to obtain deeper insight into the mode of action of kendomycin.
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Affiliation(s)
- Yasser A. Elnakady
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
- Faculty of Science, Zoology Department, King Saud University, Riyadh, Saudi Arabia
| | - Indranil Chatterjee
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Manfred Rohde
- Department of Medical Microbiology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Michaele Josten
- Department of Medical Microbiology, Bonn University, Bonn, Germany
| | - Hans-Georg Sahl
- Department of Medical Microbiology, Bonn University, Bonn, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
- * E-mail:
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8
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Yassien MA, Abdallah HM, El-Halawany AM, Jiman-Fatani AAM. Anti-tuberculous activity of treponemycin produced by a streptomyces strain MS-6-6 isolated from Saudi Arabia. Molecules 2015; 20:2576-90. [PMID: 25648598 PMCID: PMC6272392 DOI: 10.3390/molecules20022576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 01/27/2015] [Indexed: 11/21/2022] Open
Abstract
A Streptomyces strain MS-6-6 with promising anti-tuberculous activity was isolated from soil samples in Saudi Arabia. The nucleotide sequence of its 16S rRNA gene (1426 bp) evidenced a 100% similarity to Streptomyces mutabilis. Through an anti-tuberculous activity-guided approach, a polyketide macrolide was isolated and identified as treponemycin (TP). The structure of the isolated compound was determined by comprehensive analyses of its 1D and 2D NMR as well as HRESI-MS. In addition to the promising anti-tuberculous activity (MIC = 13.3 µg/mL), TP showed broad spectrum of activity against the Gram positive, Gram negative strains, and Candida albicans. Improvement of TP productivity (150%) was achieved through modification in liquid starch nitrate medium by replacing KNO3 with corn steep liquor and yeast extract or tryptone, and removing CaCO3 and K2HPO4. The follow up of TP percentage as well as its metabolites profile for each media was assessed by LC/DAD/MS.
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Affiliation(s)
- Mahmoud A Yassien
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, P.O. Box 80260, Jeddah 21589, Saudi Arabia.
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain-Shams University, Cairo, Egypt.
| | - Hossam M Abdallah
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, P.O. Box 80260, Jeddah 21589, Saudi Arabia.
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt.
| | - Ali M El-Halawany
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, P.O. Box 80260, Jeddah 21589, Saudi Arabia.
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt.
| | - Asif A M Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, P.O. Box 80260, Jeddah 21589, Saudi Arabia.
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9
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Tanaka K, Matsuyama H, Watanabe M, Fujimori Y, Ishibashi K, Ozawa T, Sato T, Saikawa Y, Nakata M. Synthesis and Biological Evaluation of Kendomycin and Its Analogues. J Org Chem 2014; 79:9922-47. [DOI: 10.1021/jo5015273] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyosuke Tanaka
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Hiroshi Matsuyama
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Masahito Watanabe
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Yukiko Fujimori
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kodai Ishibashi
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Tomohiro Ozawa
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Tomoharu Sato
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Yoko Saikawa
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Masaya Nakata
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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10
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Beck P, Heinemeyer W, Späth AL, Elnakady Y, Müller R, Groll M. Interactions of the natural product kendomycin and the 20S proteasome. J Mol Biol 2014; 426:3108-3117. [PMID: 25038530 DOI: 10.1016/j.jmb.2014.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 06/13/2014] [Accepted: 06/26/2014] [Indexed: 01/05/2023]
Abstract
Natural products are a valuable source for novel lead structures in drug discovery, but for the majority of isolated bioactive compounds, the cellular targets are unknown. The structurally unique ansa-polyketide kendomycin (KM) was reported to exert its potent cytotoxic effects via impairment of the ubiquitin proteasome system, but the exact mode of action remained unclear. Here, we present a systematic biochemical characterization of KM-proteasome interactions in vitro and in vivo, including complex structures of wild type and mutant yeast 20S proteasome with KM. Our results provide evidence for a polypharmacological mode of action for KM's cytotoxic effect on cancer cells.
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Affiliation(s)
- Philipp Beck
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
| | - Wolfgang Heinemeyer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
| | - Anna-Lena Späth
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
| | - Yasser Elnakady
- Helmholtz Center for Infectious Research (HZI), Department Microbial Natural Products, Saarland University, Campus C2 3, Saarbrücken 66041, Germany
| | - Rolf Müller
- Helmholtz Center for Infectious Research (HZI), Department Microbial Natural Products, Saarland University, Campus C2 3, Saarbrücken 66041, Germany
| | - Michael Groll
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany.
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11
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Sengoku T, Xu S, Ogura K, Emori Y, Kitada K, Uemura D, Arimoto H. Total Synthesis of the Antibiotic Kendomycin: A Macrocyclization Using the Tsuji-Trost Etherification. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Sengoku T, Xu S, Ogura K, Emori Y, Kitada K, Uemura D, Arimoto H. Total Synthesis of the Antibiotic Kendomycin: A Macrocyclization Using the Tsuji-Trost Etherification. Angew Chem Int Ed Engl 2014; 53:4213-6. [DOI: 10.1002/anie.201400305] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Indexed: 11/10/2022]
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13
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Hoffmeister L, Persich P, Fürstner A. Formal Total Synthesis of Kendomycin by Way of Alkyne Metathesis/Gold Catalysis. Chemistry 2014; 20:4396-402. [DOI: 10.1002/chem.201304580] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 12/23/2022]
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14
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Schuler M, Keller A, Backes C, Philippar K, Lenhof HP, Bauer P. Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana. BMC PLANT BIOLOGY 2011; 11:87. [PMID: 21592396 PMCID: PMC3114716 DOI: 10.1186/1471-2229-11-87] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 05/18/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND High-throughput technologies have opened new avenues to study biological processes and pathways. The interpretation of the immense amount of data sets generated nowadays needs to be facilitated in order to enable biologists to identify complex gene networks and functional pathways. To cope with this task multiple computer-based programs have been developed. GeneTrail is a freely available online tool that screens comparative transcriptomic data for differentially regulated functional categories and biological pathways extracted from common data bases like KEGG, Gene Ontology (GO), TRANSPATH and TRANSFAC. Additionally, GeneTrail offers a feature that allows screening of individually defined biological categories that are relevant for the respective research topic. RESULTS We have set up GeneTrail for the use of Arabidopsis thaliana. To test the functionality of this tool for plant analysis, we generated transcriptome data of root and leaf responses to Fe deficiency and the Arabidopsis metal homeostasis mutant nas4x-1. We performed Gene Set Enrichment Analysis (GSEA) with eight meaningful pairwise comparisons of transcriptome data sets. We were able to uncover several functional pathways including metal homeostasis that were affected in our experimental situations. Representation of the differentially regulated functional categories in Venn diagrams uncovered regulatory networks at the level of whole functional pathways. Over-Representation Analysis (ORA) of differentially regulated genes identified in pairwise comparisons revealed specific functional plant physiological categories as major targets upon Fe deficiency and in nas4x-1. CONCLUSION Here, we obtained supporting evidence, that the nas4x-1 mutant was defective in metal homeostasis. It was confirmed that nas4x-1 showed Fe deficiency in roots and signs of Fe deficiency and Fe sufficiency in leaves. Besides metal homeostasis, biotic stress, root carbohydrate, leaf photosystem and specific cell biological categories were discovered as main targets for regulated changes in response to--Fe and nas4x-1. Among 258 differentially expressed genes in response to--Fe and nas4x-1 five functional categories were enriched covering metal homeostasis, redox regulation, cell division and histone acetylation. We proved that GeneTrail offers a flexible and user-adapted way to identify functional categories in large-scale plant transcriptome data sets. The distinguished feature that allowed analysis of individually assembled functional categories facilitated the study of the Arabidopsis thaliana transcriptome.
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Affiliation(s)
- Mara Schuler
- Dept. of Biosciences - Botany, Campus A2.4, Saarland University, D-66123 Saarbrücken, Germany
| | - Andreas Keller
- Dept. of Informatics - Center for Bioinformatics, Campus E1.1, Saarland University, D-66123 Saarbrücken, Germanys
| | - Christina Backes
- Dept. of Informatics - Center for Bioinformatics, Campus E1.1, Saarland University, D-66123 Saarbrücken, Germanys
| | - Katrin Philippar
- Dept. Biology I - Plant Biochemistry and Physiology, Biocenter of the Ludwig-Maximilians-University München, Großhadernerstr. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Hans-Peter Lenhof
- Dept. of Informatics - Center for Bioinformatics, Campus E1.1, Saarland University, D-66123 Saarbrücken, Germanys
| | - Petra Bauer
- Dept. of Biosciences - Botany, Campus A2.4, Saarland University, D-66123 Saarbrücken, Germany
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15
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Martin H, Magauer T, Mulzer J. In Pursuit of a Competitive Target: Total Synthesis of the Antibiotic Kendomycin. Angew Chem Int Ed Engl 2010; 49:5614-26. [DOI: 10.1002/anie.201000227] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Martin H, Magauer T, Mulzer J. Einem kompetitiven Zielmolekül auf den Fersen: Totalsynthese des Antibiotikums Kendomycin. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000227] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Magauer T, Martin HJ, Mulzer J. Ring-closing metathesis and photo-fries reaction for the construction of the ansamycin antibiotic kendomycin: development of a protecting group free oxidative endgame. Chemistry 2010; 16:507-19. [PMID: 19950336 DOI: 10.1002/chem.200902226] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Two convergent total syntheses of the ansa-polyketide (-)-kendomycin (1) are described. The syntheses benefit from the use of readily available and cheap starting materials. Highly complex diastereoselective Claisen-Ireland rearrangements were used to introduce the (E)-double bond and the C16-Me group. The ring closure of the strained ansa macrocycle was achieved by ring-closing metathesis and a highly efficient combination of macrolactonization and photo-Fries reaction. A protecting group free endgame via an unstable o-quinone is presented. Additionally some unsuccessful synthetic efforts towards the total synthesis of 1 are described.
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Affiliation(s)
- Thomas Magauer
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090 Vienna, Austria
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Cheng KW, Wong CC, Wang M, He QY, Chen F. Identification and characterization of molecular targets of natural products by mass spectrometry. MASS SPECTROMETRY REVIEWS 2010; 29:126-155. [PMID: 19319922 DOI: 10.1002/mas.20235] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Natural products, and their derivatives and mimics, have contributed to the development of important therapeutics to combat diseases such as infections and cancers over the past decades. The value of natural products to modern drug discovery is still considerable. However, its development is hampered by a lack of a mechanistic understanding of their molecular action, as opposed to the emerging molecule-targeted therapeutics that are tailored to a specific protein target(s). Recent advances in the mass spectrometry-based proteomic approaches have the potential to offer unprecedented insights into the molecular action of natural products. Chemical proteomics is established as an invaluable tool for the identification of protein targets of natural products. Small-molecule affinity selection combined with mass spectrometry is a successful strategy to "fish" cellular targets from the entire proteome. Mass spectrometry-based profiling of protein expression is also routinely employed to elucidate molecular pathways involved in the therapeutic and possible toxicological responses upon treatment with natural products. In addition, mass spectrometry is increasingly utilized to probe structural aspects of natural products-protein interactions. Limited proteolysis, photoaffinity labeling, and hydrogen/deuterium exchange in conjunction with mass spectrometry are sensitive and high-throughput strategies that provide low-resolution structural information of non-covalent natural product-protein complexes. In this review, we provide an overview on the applications of mass spectrometry-based techniques in the identification and characterization of natural product-protein interactions, and we describe how these applications might revolutionize natural product-based drug discovery.
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Affiliation(s)
- Ka-Wing Cheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Wenzel SC, Bode HB, Kochems I, Müller R. A Type I/Type III Polyketide Synthase Hybrid Biosynthetic Pathway for the Structurally UniqueansaCompound Kendomycin. Chembiochem 2008; 9:2711-21. [DOI: 10.1002/cbic.200800456] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Bahnck KB, Rychnovsky SD. Formal synthesis of (-)-kendomycin featuring a Prins-cyclization to construct the macrocycle. J Am Chem Soc 2008; 130:13177-81. [PMID: 18767844 PMCID: PMC2697922 DOI: 10.1021/ja805187p] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kendomycin skeleton was prepared by a highly convergent strategy in which the benzofuran fragment and the acyclic iodide fragment were prepared by standard methods and joined using a Suzuki coupling. The distinctive reaction in our approach was an intramolecular Prins cyclization that assembles the macrocyclic ring in good yield. Modeling studies demonstrate that the acyclic chain is predisposed for macrocycle formation. Ultimately, the product was correlated with one of Lee's advanced intermediates for a formal total synthesis of kendomycin.
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Affiliation(s)
- Kevin B. Bahnck
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California, 92697-2025
| | - Scott D. Rychnovsky
- Department of Chemistry, 1102 Natural Sciences II, University of California, Irvine, California, 92697-2025
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21
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Abstract
An enantioselective synthesis of (-)-kendomycin is described and is based on the application of the organosilane-based [4 + 2]-annulation strategy for the assembly of the C1a-C10 fragment. An underutilized samarium(II) iodide-assisted cyclization (intramolecular Barbier-type reaction) is employed to afford the protected macrocycle.
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Affiliation(s)
- Jason T Lowe
- Department of Chemistry, Metcalf Center for Science and Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
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22
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Küntzer J, Backes C, Blum T, Gerasch A, Kaufmann M, Kohlbacher O, Lenhof HP. BNDB - the Biochemical Network Database. BMC Bioinformatics 2007; 8:367. [PMID: 17910766 PMCID: PMC2092437 DOI: 10.1186/1471-2105-8-367] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 10/02/2007] [Indexed: 12/04/2022] Open
Abstract
Background Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. Description We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. Conclusion BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at .
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Affiliation(s)
- Jan Küntzer
- Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany
| | - Christina Backes
- Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany
| | - Torsten Blum
- Center for Bioinformatics/Wilhelm Schickard Institute for Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Andreas Gerasch
- Center for Bioinformatics/Wilhelm Schickard Institute for Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Michael Kaufmann
- Center for Bioinformatics/Wilhelm Schickard Institute for Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics/Wilhelm Schickard Institute for Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany
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