1
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Adouane E, Mercier C, Mamelle J, Willocquet E, Intertaglia L, Burgunter-Delamare B, Leblanc C, Rousvoal S, Lami R, Prado S. Importance of quorum sensing crosstalk in the brown alga Saccharina latissima epimicrobiome. iScience 2024; 27:109176. [PMID: 38433891 PMCID: PMC10906538 DOI: 10.1016/j.isci.2024.109176] [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: 09/22/2023] [Revised: 12/07/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Brown macroalgae are colonized by diverse microorganisms influencing the physiology of their host. However, cell-cell interactions within the surface microbiome (epimicrobiome) are largely unexplored, despite the significance of specific chemical mediators in maintaining host-microbiome homeostasis. In this study, by combining liquid chromatography coupled to mass spectrometry (LC-MS) analysis and bioassays, we demonstrated that the widely diverse fungal epimicrobiota of the brown alga Saccharina latissima can affect quorum sensing (QS), a type of cell-cell interaction, as well as bacterial biofilm formation. We also showed the ability of the bacterial epimicrobiota to form and inhibit biofilm growth, as well as to activate or inhibit QS pathways. Overall, we demonstrate that QS and anti-QS compounds produced by the epimicrobiota are key metabolites in these brown algal epimicrobiota communities and highlight the importance of exploring this epimicrobiome for the discovery of new bioactive compounds, including potentially anti-QS molecules with antifouling properties.
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Affiliation(s)
- Emilie Adouane
- Muséum National d’Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-Organismes MCAM, UMR 7245, CNRS, Sorbonne Université, 75005 Paris, France
- Sorbonne Université, CNRS, UAR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Camille Mercier
- Sorbonne Université, CNRS, UAR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Jeanne Mamelle
- Sorbonne Université, CNRS, UAR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Emma Willocquet
- Sorbonne Université, CNRS, UAR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Laurent Intertaglia
- Sorbonne Université, CNRS, Bio2Mar, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Bertille Burgunter-Delamare
- Biologie Intégrative des Modèles Marins, LBI2M (Sorbonne Université/CNRS), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Catherine Leblanc
- Biologie Intégrative des Modèles Marins, LBI2M (Sorbonne Université/CNRS), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Sylvie Rousvoal
- Biologie Intégrative des Modèles Marins, LBI2M (Sorbonne Université/CNRS), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Raphaël Lami
- Sorbonne Université, CNRS, UAR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Soizic Prado
- Muséum National d’Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-Organismes MCAM, UMR 7245, CNRS, Sorbonne Université, 75005 Paris, France
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2
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Salehi-Najafabadi A, Tehrani Fateh S, Amoabediny G, Hamedi J. Insights into additional lactone-based signaling circuits in Streptomyces: existence of acyl-homoserine lactones and LuxI/LuxR homologs in six Streptomyces species. Front Microbiol 2024; 15:1342637. [PMID: 38389542 PMCID: PMC10883386 DOI: 10.3389/fmicb.2024.1342637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Acyl-homoserine lactones (AHLs), mediating pivotal physiological activities through quorum sensing (QS), have conventionally been considered limited to Gram-negative bacteria. However, few reports on the existence of AHLs in Gram-positive bacteria have questioned this conception. Streptomyces, as Gram-positive bacteria already utilizing a lactone-based QS molecule (i.e., gamma-butyrolactones), are yet to be explored for producing AHLs, considering their metabolic capacity and physiological distinction. In this regard, our study examined the potential production of AHLs within Streptomyces by deploying HPLC-MS/MS methods, which resulted in the discovery of multiple AHL productions by S. griseus, S. lavendulae FRI-5, S. clavuligerus, S. nodosus, S. lividans, and S. coelicolor A3(2). Each of these Streptomyces species possesses a combination of AHLs of different size ranges, possibly due to their distinct properties and regulatory roles. In light of additional lactone molecules, we further confirm that AHL- and GBL-synthases (i.e., LuxI and AfsA enzyme families, respectively) and their receptors (i.e., LuxR and ArpA) are evolutionarily distinct. To this end, we searched for the components of the AHL signaling circuit, i.e., AHL synthases and receptors, in the Streptomyces genus, and we have identified multiple potential LuxI and LuxR homologs in all 2,336 Streptomyces species included in this study. The 6 Streptomyces of interest in this study also had at least 4 LuxI homologs and 97 LuxR homologs. In conclusion, AHLs and associated gene regulatory systems could be more widespread within the prokaryotic realm than previously believed, potentially contributing to the control of secondary metabolites (e.g., antibiotics) and their complex life cycle, which leads to substantial industrial and clinical applications.
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Affiliation(s)
- Amir Salehi-Najafabadi
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
- Research Center for New Technologies in Life Science Engineering, University of Tehran, Tehran, Iran
| | - Sepand Tehrani Fateh
- Research Center for New Technologies in Life Science Engineering, University of Tehran, Tehran, Iran
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghasem Amoabediny
- Research Center for New Technologies in Life Science Engineering, University of Tehran, Tehran, Iran
- Faculty of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Javad Hamedi
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
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3
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Ma L, Li M, Gou S, Wang W, Liu K, Zhang Y. Native-compound-Coupled Affinity Matrix (NCAM) in target identification and validation of bioactive compounds: Application, mechanism and outlooks. Bioorg Chem 2023; 140:106828. [PMID: 37690368 DOI: 10.1016/j.bioorg.2023.106828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 09/12/2023]
Abstract
In drug discovery and development, the direct target identification of bioactive small molecules plays a significant role for understanding the mechanism of action, predicting the side effects, and rationally designing more potent compounds. However, due to the complicated regulatory processes in a cell together with thousands of biomacromolecules, target identification is always the major obstacle. New methods and technologies are continuously invented to tackle this problem. Nevertheless, the mainly used tools possess several disadvantages. High synthetic skills are typically required to laboriously synthesize a probe for protein enrichment. To detect the ligand-protein interaction by analyzing proteins' responses to proteolytic or thermal treatment, costly and precise instruments are always necessary. Therefore, convenient and practical techniques are urgently needed. Over the past decades, a strategy using native compounds without the requirement of chemical modification, also termed Native-compound-Coupled Affinity Matrix (NCAM), is developing continuously. Two practical tactics based on "label-free" compounds have been invented and used, that is Photo-cross-linked Small-molecule Affinity Matrix (PSAM) and Native-compound-Coupled CNBr-activated Beads (NCCB). Presently, we will elucidate the characteristics, coupling mechanism, advantages and disadvantages, and future prospect of NCAM in specific target identification and validation.
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Affiliation(s)
- Lu Ma
- Basic Medical Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Menglong Li
- Basic Medical Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Shanshan Gou
- Basic Medical Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Wei Wang
- Departments of Pharmacology & Toxicology and Chemistry & Biochemistry, and BIO5 Institute, University of Arizona, Tucson, AZ 85721, United States
| | - Kangdong Liu
- Basic Medical Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China; Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yueteng Zhang
- Basic Medical Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China.
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4
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Li Z, Li X, Xia H. Roles of LuxR-family regulators in the biosynthesis of secondary metabolites in Actinobacteria. World J Microbiol Biotechnol 2022; 38:250. [DOI: 10.1007/s11274-022-03414-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/11/2022] [Indexed: 10/31/2022]
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5
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Saito S, Funayama K, Kato W, Okuda M, Kawamoto M, Matsubara T, Sato T, Sato A, Otsuguro S, Sasaki M, Orba Y, Sawa H, Maenaka K, Shindo K, Imoto M, Arai MA. Dihydromaniwamycin E, a Heat-Shock Metabolite from Thermotolerant Streptomyces sp. JA74, Exhibiting Antiviral Activity against Influenza and SARS-CoV-2 Viruses. JOURNAL OF NATURAL PRODUCTS 2022; 85:2583-2591. [PMID: 36223390 PMCID: PMC9578650 DOI: 10.1021/acs.jnatprod.2c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Indexed: 06/16/2023]
Abstract
Dihydromaniwamycin E (1), a new maniwamycin derivative featuring an azoxy moiety, has been isolated from the culture extract of thermotolerant Streptomyces sp. JA74 along with the known analogue maniwamycin E (2). Compound 1 is produced only by cultivation of strain JA74 at 45 °C, and this type of compound has been previously designated a "heat shock metabolite (HSM)" by our research group. Compound 2 is detected as a production-enhanced metabolite at high temperature. Structures of 1 and 2 are elucidated by NMR and MS spectroscopic analyses. The absolute structure of 1 is determined after the total synthesis of four stereoisomers. Though the absolute structure of 2 has been proposed to be the same as the structure of maniwamycin D, the NMR and the optical rotation value of 2 are in agreement with those of maniwamycin E. Therefore, this study proposes a structural revision of maniwamycins D and E. Compounds 1 and 2 show inhibitory activity against the influenza (H1N1) virus infection of MDCK cells, demonstrating IC50 values of 25.7 and 63.2 μM, respectively. Notably, 1 and 2 display antiviral activity against SARS-CoV-2, the causative agent of COVID-19, when used to infect 293TA and VeroE6T cells, with 1 and 2 showing IC50 values (for infection of 293TA cells) of 19.7 and 9.7 μM, respectively. The two compounds do not exhibit cytotoxicity in these cell lines at those IC50 concentrations.
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Affiliation(s)
- Shun Saito
- Department of Biosciences and Informatics, Faculty of
Science and Technology, Keio University, Yokohama223-8522,
Japan
| | - Kayo Funayama
- Department of Biosciences and Informatics, Faculty of
Science and Technology, Keio University, Yokohama223-8522,
Japan
| | - Wataru Kato
- Department of Biosciences and Informatics, Faculty of
Science and Technology, Keio University, Yokohama223-8522,
Japan
| | - Mayu Okuda
- Department of Biosciences and Informatics, Faculty of
Science and Technology, Keio University, Yokohama223-8522,
Japan
| | - Meiko Kawamoto
- Department of Biosciences and Informatics, Faculty of
Science and Technology, Keio University, Yokohama223-8522,
Japan
| | - Teruhiko Matsubara
- Department of Biosciences and Informatics, Faculty of
Science and Technology, Keio University, Yokohama223-8522,
Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Faculty of
Science and Technology, Keio University, Yokohama223-8522,
Japan
| | - Akihiko Sato
- Drug Discovery and Disease Research Laboratory,
Shionogi & Co., Ltd., Osaka541-0045,
Japan
- Division of Molecular Pathobiology, International
Institute for Zoonosis Control, Hokkaido University,
Sapporo001-0020, Japan
| | - Satoko Otsuguro
- Laboratory of Biomolecular Science, Faculty of
Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812,
Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International
Institute for Zoonosis Control, Hokkaido University,
Sapporo001-0020, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International
Institute for Zoonosis Control, Hokkaido University,
Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for
Zoonosis Control, Hokkaido University, Sapporo001-0020,
Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International
Institute for Zoonosis Control, Hokkaido University,
Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for
Zoonosis Control, Hokkaido University, Sapporo001-0020,
Japan
- One Health Research Center, Hokkaido
University, Sapporo060-0818, Japan
- Global Virus Network,
Baltimore, Maryland21201, United States
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of
Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812,
Japan
| | - Kazutoshi Shindo
- Department of Food and Nutrition, Japan
Women’s University, Tokyo112-8681, Japan
| | - Masaya Imoto
- Department of Neurology, Juntendo
University School of Medicine, Tokyo113-8431,
Japan
| | - Midori A. Arai
- Department of Biosciences and Informatics, Faculty of
Science and Technology, Keio University, Yokohama223-8522,
Japan
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6
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Chávez-Moctezuma MP, Martínez-Cámara R, Hernández-Salmerón J, Moreno-Hagelsieb G, Santoyo G, Valencia-Cantero E. Comparative genomic and functional analysis of Arthrobacter sp. UMCV2 reveals the presence of luxR-related genes inducible by the biocompound N, N-dimethylhexadecilamine. Front Microbiol 2022; 13:1040932. [PMID: 36386619 PMCID: PMC9659744 DOI: 10.3389/fmicb.2022.1040932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/10/2022] [Indexed: 09/29/2023] Open
Abstract
Quorum sensing (QS) is a bacterial cell-cell communication system with genetically regulated mechanisms dependent on cell density. Canonical QS systems in gram-negative bacteria possess an autoinducer synthase (LuxI family) and a transcriptional regulator (LuxR family) that respond to an autoinducer molecule. In Gram-positive bacteria, the LuxR transcriptional regulators "solo" (not associated with a LuxI homolog) may play key roles in intracellular communication. Arthrobacter sp. UMCV2 is an actinobacterium that promotes plant growth by emitting the volatile organic compound N, N-dimethylhexadecylamine (DMHDA). This compound induces iron deficiency, defense responses in plants, and swarming motility in Arthrobacter sp. UMCV2. In this study, the draft genome of this bacterium was assembled and compared with the genomes of type strains of the Arthrobacter genus, finding that it does not belong to any previously described species. Genome explorations also revealed the presence of 16 luxR-related genes, but no luxI homologs were discovered. Eleven of these sequences possess the LuxR characteristic DNA-binding domain with a helix-turn-helix motif and were designated as auto-inducer-related regulators (AirR). Four sequences possessed LuxR analogous domains and were designated as auto-inducer analogous regulators (AiaR). When swarming motility was induced with DMHDA, eight airR genes and two aiaR genes were upregulated. These results indicate that the expression of multiple luxR-related genes is induced in actinobacteria, such as Arthrobacter sp. UMCV2, by the action of the bacterial biocompound DMHDA when QS behavior is produced.
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Affiliation(s)
| | - Ramiro Martínez-Cámara
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
- Tecnológico Nacional de México, Morelia, Michoacán, Mexico
| | | | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Eduardo Valencia-Cantero
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
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7
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Takahashi S. Studies on Streptomyces sp. SN-593: reveromycin biosynthesis, β-carboline biomediator activating LuxR family regulator, and construction of terpenoid biosynthetic platform. J Antibiot (Tokyo) 2022; 75:432-444. [PMID: 35778609 DOI: 10.1038/s41429-022-00539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/09/2022]
Abstract
Streptomyces represents an important reservoir for biologically active natural products. Understanding the biosynthetic mechanism and the mode of gene expression is important for enhanced metabolite production and evaluation of biological activities. This review provides an overview of biosynthetic studies investigating reveromycin and β-carboline biomediators that enhanced the production of reveromycin in Streptomyces sp. SN-593 through activation of the LuxR family regulator. Furthermore, based on the optimal expression of a pathway specific regulator controlling the mevalonate pathway gene cluster, Streptomyces sp. SN-593 was developed as a platform for terpenoid compounds mass production.
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Affiliation(s)
- Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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8
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A Abdelhakim I, Bin Mahmud F, Motoyama T, Futamura Y, Takahashi S, Osada H. Dihydrolucilactaene, a Potent Antimalarial Compound from Fusarium sp. RK97-94. JOURNAL OF NATURAL PRODUCTS 2022; 85:63-69. [PMID: 34949088 DOI: 10.1021/acs.jnatprod.1c00677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A recently discovered secondary metabolism regulator, NPD938, was used to alter the secondary metabolite profile in Fusarium sp. RK97-94. Three lucilactaene analogues were detected via UPLC-ESI-MS analysis in NPD938-treated culture. The three metabolites were successfully purified and identified as dihydroNG391 (1), dihydrolucilactaene (2), and 13α-hydroxylucilactaene (3) via extensive spectroscopic analyses. DihydroNG391 (1) exhibited weak in vitro antimalarial activity (IC50 = 62 μM). In contrast, dihydrolucilactaene (2) and 13α-hydroxylucilactaene (3) showed very potent antimalarial activity (IC50 = 0.0015 and 0.68 μM, respectively). These findings provide insight into the structure-activity relationship of lucilactaene and its analogues as antimalarial lead compounds.
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Affiliation(s)
- Islam A Abdelhakim
- Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
- Natural Product Biosynthesis Research Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Fauze Bin Mahmud
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Sabah 88400, Malaysia
| | - Takayuki Motoyama
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
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6,9-Dihydroxytetrangulol, a novel angucyclinone antibiotic accumulated in kiqO gene disruptant in the biosynthesis of kinanthraquinone. J Antibiot (Tokyo) 2021; 74:593-595. [PMID: 34234285 DOI: 10.1038/s41429-021-00442-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/01/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
Abstract
A novel angucyclinone, 6,9-dihydroxytetrangulol, was isolated from Streptomyces lividans TK23 transformed with a kinanthraquinone biosynthetic gene cluster in which the kiqO gene was disrupted. The chemical structure was elucidated by spectroscopic analyses. It showed significant antibacterial activities with an IC50 value of 1.9 μM against Staphylococcus aureus and moderate anticancer activities against HL-60 cells.
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10
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Wu QB, Chen XA, Lv ZY, Zhang XY, Liu Y, Li YQ. Activation and discovery of tsukubarubicin from Streptomyces tsukubaensis through overexpressing SARPs. Appl Microbiol Biotechnol 2021; 105:4731-4741. [PMID: 34021812 DOI: 10.1007/s00253-021-11344-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/23/2021] [Accepted: 05/09/2021] [Indexed: 12/11/2022]
Abstract
Genome sequencing has revealed that each Streptomyces contains a wide range of biosynthetic gene clusters (BGCs) and has the capability to produce more novel natural products than what is expected. However, most gene clusters for secondary metabolite biosynthesis are cryptic under normal growth conditions. In Streptomyces tsukubaensis, combining overexpression of the putative SARPs (Streptomyces antibiotic regulatory proteins) and bioactivity-guided screening, the silent gene cluster (tsu) was successfully activated and a novel bioactive anthracycline tsukubarubicin was further isolated and identified. Biological activity assays demonstrated that tsukubarubicin possessed much better antitumor bioactivities against various human cancer cell lines (especially the breast cancer cell lines) than clinically used doxorubicin. Moreover, the previously unreported gene cluster (tsu) for biosynthesis of tsukubarubicin was first characterized and detailed annotations of this gene cluster were also conducted. Our strategy presented in this work is broadly applicable in other Streptomyces and will assist in enriching the natural products for potential drug leads. KEY POINTS: • Generally scalable strategy to activate silent gene clusters by manipulating SARPs. • The novel anthracycline tsukubarubicin with potent antitumor bioactivities. • Identification and annotation of the previously uncharacterized tsu gene cluster.
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Affiliation(s)
- Qing-Bin Wu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Xin-Ai Chen
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zhong-Yuan Lv
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Xiao-Ying Zhang
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yu Liu
- Zhejiang University College of Life Sciences, Hangzhou, 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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11
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Panthee S, Paudel A, Hamamoto H, Ogasawara AA, Iwasa T, Blom J, Sekimizu K. Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium. Genomics 2021; 113:1534-1542. [PMID: 33771633 DOI: 10.1016/j.ygeno.2021.03.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/10/2021] [Accepted: 03/21/2021] [Indexed: 12/22/2022]
Abstract
Enterococcus faecalis is a common human gut commensal bacterium. While some E. faecalis strains are probiotic, others are known to cause opportunistic infections, and clear distinction between these strains is difficult using traditional taxonomic approaches. In this study, we completed the genome sequencing of EF-2001, a probiotic strain, using our in-house hybrid assembly approach. Comparative analysis showed that EF-2001 was devoid of cytolysins, major factors associated with pathogenesis, and was phylogenetically distant from pathogenic E. faecalis V583. Genomic analysis of strains with a publicly available complete genome sequence predicted that drug-resistance genes- dfrE, efrA, efrB, emeA, and lsaA were present in all strains, and EF-2001 lacked additional drug-resistance genes. Core- and pan-genome analyses revealed a higher degree of genomic fluidity. We found 49 genes specific to EF-2001, further characterization of which may provide insights into its diverse biological activities. Our comparative genomic analysis approach could help predict the pathogenic or probiotic potential of E. faecalis leading to an early distinction based on genome sequences.
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Affiliation(s)
- Suresh Panthee
- Teikyo University Institute of Medical Mycology, Hachioji, Otsuka 359, Tokyo 192-0395, Japan.
| | - Atmika Paudel
- Teikyo University Institute of Medical Mycology, Hachioji, Otsuka 359, Tokyo 192-0395, Japan; Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10, Kita-ku, Sapporo Hokkaido 001-0020, Japan.
| | - Hiroshi Hamamoto
- Teikyo University Institute of Medical Mycology, Hachioji, Otsuka 359, Tokyo 192-0395, Japan.
| | | | - Toshihiro Iwasa
- NIHON BERUMU CO., LTD., 2-14-3 Nagatacho, Chiyoda-ku, Tokyo 100-0014, Japan.
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany.
| | - Kazuhisa Sekimizu
- Teikyo University Institute of Medical Mycology, Hachioji, Otsuka 359, Tokyo 192-0395, Japan.
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Takao R, Sakai K, Koshino H, Osada H, Takahashi S. Identification of the kinanthraquinone biosynthetic gene cluster by expression of an atypical response regulator. Biosci Biotechnol Biochem 2021; 85:714-721. [DOI: 10.1093/bbb/zbaa082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/29/2020] [Indexed: 01/15/2023]
Abstract
ABSTRACT
Recent advances in genome sequencing have revealed a variety of secondary metabolite biosynthetic gene clusters in actinomycetes. Understanding the biosynthetic mechanism controlling secondary metabolite production is important for utilizing these gene clusters. In this study, we focused on the kinanthraquinone biosynthetic gene cluster, which has not been identified yet in Streptomyces sp. SN-593. Based on chemical structure, 5 type II polyketide synthase gene clusters were listed from the genome sequence of Streptomyces sp. SN-593. Among them, a candidate gene cluster was selected by comparing the gene organization with grincamycin, which is synthesized through an intermediate similar to kinanthraquinone. We initially utilized a BAC library for subcloning the kiq gene cluster, performed heterologous expression in Streptomyces lividans TK23, and identified the production of kinanthraquinone and kinanthraquinone B. We also found that heterologous expression of kiqA, which belongs to the DNA-binding response regulator OmpR family, dramatically enhanced the production of kinanthraquinones.
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Affiliation(s)
- Risa Takao
- Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama-shi, Saitama, Japan
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Wako, Saitama, Japan
| | - Katsuyuki Sakai
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroyuki Koshino
- Molecular Structure Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Centre for Sustainable Resource Science, Wako, Saitama, Japan
| | - Shunji Takahashi
- Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama-shi, Saitama, Japan
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Wako, Saitama, Japan
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Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO, Cho BK. Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes. Nat Prod Rep 2021; 38:1330-1361. [PMID: 33393961 DOI: 10.1039/d0np00071j] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2010 to 2020 Over the last few decades, Streptomyces have been extensively investigated for their ability to produce diverse bioactive secondary metabolites. Recent advances in Streptomyces research have been largely supported by improvements in high-throughput technology 'omics'. From genomics, numerous secondary metabolite biosynthetic gene clusters were predicted, increasing their genomic potential for novel bioactive compound discovery. Additional omics, including transcriptomics, translatomics, interactomics, proteomics and metabolomics, have been applied to obtain a system-level understanding spanning entire bioprocesses of Streptomyces, revealing highly interconnected and multi-layered regulatory networks for secondary metabolism. The comprehensive understanding derived from this systematic information accelerates the rational engineering of Streptomyces to enhance secondary metabolite production, integrated with the exploitation of the highly efficient 'Design-Build-Test-Learn' cycle in synthetic biology. In this review, we describe the current status of omics applications in Streptomyces research to better understand the organism and exploit its genetic potential for higher production of valuable secondary metabolites and novel secondary metabolite discovery.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yeo Joon Yoon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA. and Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
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