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Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B. Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes. THE ISME JOURNAL 2023; 17:1660-1670. [PMID: 37452097 PMCID: PMC10504331 DOI: 10.1038/s41396-023-01466-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.
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Affiliation(s)
| | | | - Ashley G Bell
- School of Biosciences, University of Exeter, Exeter, UK
| | | | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK.
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2
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Ghotbi M, Kelting O, Blümel M, Tasdemir D. Gut and Gill-Associated Microbiota of the Flatfish European Plaice ( Pleuronectes platessa): Diversity, Metabolome and Bioactivity against Human and Aquaculture Pathogens. Mar Drugs 2022; 20:md20090573. [PMID: 36135762 PMCID: PMC9500656 DOI: 10.3390/md20090573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Similar to other marine holobionts, fish are colonized by complex microbial communities that promote their health and growth. Fish-associated microbiota is emerging as a promising source of bioactive metabolites. Pleuronectes platessa (European plaice, plaice), a flatfish with commercial importance, is common in the Baltic Sea. Here we used a culture-dependent survey followed by molecular identification to identify microbiota associated with the gills and the gastrointestinal tract (GIT) of P. platessa, then profiled their antimicrobial activity and metabolome. Altogether, 66 strains (59 bacteria and 7 fungi) were isolated, with Proteobacteria being the most abundant phylum. Gill-associated microbiota accounted for higher number of isolates and was dominated by the Proteobacteria (family Moraxellaceae) and Actinobacteria (family Nocardiaceae), whereas Gram-negative bacterial families Vibrionaceae and Shewanellaceae represented the largest group associated with the GIT. The EtOAc extracts of the solid and liquid media cultures of 21 bacteria and 2 fungi representing the diversity of cultivable plaice-associated microbiota was profiled for their antimicrobial activity against three fish pathogens, human bacterial pathogen panel (ESKAPE) and two human fungal pathogens. More than half of all tested microorganisms, particularly those originating from the GIT epithelium, exhibited antagonistic effect against fish pathogens (Lactococcus garvieae, Vibrio ichthyoenteri) and/or human pathogens (Enterococcus faecium, methicillin-resistant Staphylococcus aureus). Proteobacteria represented the most active isolates. Notably, the solid media extracts displayed higher activity against fish pathogens, while liquid culture extracts were more active against human pathogens. Untargeted metabolomics approach using feature-based molecular networking showed the high chemical diversity of the liquid extracts that contained undescribed clusters. This study highlights plaice-associated microbiota as a potential source of antimicrobials for the control of human and the aquaculture-associated infections. This is the first study reporting diversity, bioactivity and chemical profile of culture-dependent microbiota of plaice.
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Affiliation(s)
- Marjan Ghotbi
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Ole Kelting
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
- Correspondence: ; Tel.: +49-431-600-4430
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Wang T, Zhou J, Zou J, Shi Y, Zhou W, Shao P, Yu T, Cui W, Li X, Wu X, Ye J, Yan X, Naman CB, Lazaro JEH, He S. Discovery of Cymopolyphenols A-F From a Marine Mesophotic Zone Aaptos Sponge-Associated Fungus Cymostachys sp. NBUF082. Front Microbiol 2021; 12:638610. [PMID: 33692772 PMCID: PMC7937805 DOI: 10.3389/fmicb.2021.638610] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Mesophotic coral ecosystems (MCEs) have complex but understudied biodiversity, especially for natural products discovery. Untargeted metabolomics research on 80 extracts prepared from marine sponge-associated fungi, half from shallow reefs (<30 m) and half from MCEs (30–150 m), facilitated prioritization for further study a Cymostachys fungus from a 103 m deep Aaptos sponge. LC-MS target-directed isolation yielded a series of new compounds, cymopolyphenols A−F (1–6), and two known phenylspirodrimanes, F1839-I (7) and stachybotrylactone (8). This is the first report of natural products from the recently described genus, Cymostachys. Compounds 1–6 and 8 contain a dihydroisobenzofuran moiety, and 4–6 are low-order polymers of 1 with novel scaffolds. The structures of the compounds were established by spectroscopic and spectrometric data interpretation, with further support from X-ray crystallography studies of 3 and 4. Compound 3 undergoes facile racemization in solution and was found to crystalize as a racemic mixture. Compound 5 was also obtained in racemic form, and after chiral chromatography, both separated enantiomers racemized in solution by a presumed keto-enol tautomerization. Compounds 1 and 3–6 were found to be weakly antimicrobial (MIC 16–64 μg/ml) in vitro against several Gram-positive and Gram-negative human or aquatic pathogens, compound 5 was shown to chelate iron in vitro at 10 μM, and 8 activated plant disease resistance in vivo in a transgenic model organism.
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Affiliation(s)
- Tingting Wang
- Li Dak Sum Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Jing Zhou
- Li Dak Sum Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Jiabin Zou
- Li Dak Sum Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Yutong Shi
- Li Dak Sum Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Wenli Zhou
- College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Peng Shao
- College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Tianze Yu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Wei Cui
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Xiaohui Li
- Li Dak Sum Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Xingxin Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Jing Ye
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaojun Yan
- Li Dak Sum Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - C Benjamin Naman
- Li Dak Sum Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - J Enrico H Lazaro
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon, Philippines
| | - Shan He
- Li Dak Sum Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
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Wu J, Zhu Y, Zhang M, Li H, Sun P. Micaryolanes A and B, Two New Caryolane-Type Sesquiterpenoids from Marine Streptomyces sp. AH25. Chem Biodivers 2020; 17:e2000769. [PMID: 33140544 DOI: 10.1002/cbdv.202000769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/02/2020] [Indexed: 11/07/2022]
Abstract
Caryolanes, known as β-caryophyllene alcohols, are widely occurring sesquiterpenes in plants. From the cultures of marine Streptomyces sp. AH25, two new caryolane sesquiterpenes, micaryolanes A and B (1 and 2), together with caryolan-1,9β-diol (3) were isolated. Their structures were elucidated by extensive analyses of HR-MS and NMR spectroscopic data. The absolute configurations were assigned via the CD data of the in situ formed [Rh2 (OCOCF3 )4 ] complex and supported by comparison of experimental and calculated specific rotation values. Compounds 1-3 exhibited no activities against Hep3B or MG-63 cell lines or against Gram-positive and Gram-negative bacteria. The results not only enriched the caryolane family, but also proved bacteria as a productive source of terpene metabolites.
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Affiliation(s)
- Jiequn Wu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, P. R. China
| | - Yuqin Zhu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, P. R. China
| | - Mengxue Zhang
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai, 200433, P. R. China
| | - Hongji Li
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai, 200433, P. R. China
| | - Peng Sun
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai, 200433, P. R. China
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Highlights of marine natural products having parallel scaffolds found from marine-derived bacteria, sponges, and tunicates. J Antibiot (Tokyo) 2020; 73:504-525. [PMID: 32507851 PMCID: PMC7276339 DOI: 10.1038/s41429-020-0330-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022]
Abstract
Marine-derived bacteria are a prolific source of a wide range of structurally diverse natural products. This review, dedicated to Professor William Fenical, begins by showcasing many seminal discoveries made at the University of California San Diego from marine-derived actinomycetes. Discussed early on is the 20-year journey of discovery and advancement of the seminal actinomycetes natural product salinosporamide A into Phase III anticancer clinical trials. There are many fascinating parallels discussed that were gleaned from the comparative literature of marine sponge, tunicate, and bacteria-derived natural products. Identifying bacterial biosynthetic machinery housed in sponge and tunicate holobionts through both culture-independent and culture-dependent approaches is another important and expanding subject that is analyzed. Work reviewed herein also evaluates the hypotheses that many marine invertebrate-derived natural products are biosynthesised by associated or symbiotic bacteria. The insights and outcomes from metagenomic sequencing and synthetic biology to expand molecule discovery continue to provide exciting outcomes and they are predicted to be the source of the next generation of novel marine natural product chemical scaffolds.
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6
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Li H, Yu H, Wu W, Sun P. Chemical constituents of sponge Pseudoceratina sp. and their chemotaxonomic significance. BIOCHEM SYST ECOL 2020. [DOI: 10.1016/j.bse.2020.104002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Rodríguez JPG, Bernardi DI, Gubiani JR, Magalhães de Oliveira J, Morais-Urano RP, Bertonha AF, Bandeira KF, Bulla JIQ, Sette LD, Ferreira AG, Batista JM, Silva TDS, Santos RAD, Martins CHG, Lira SP, Cunha MGD, Trivella DBB, Grazzia N, Gomes NES, Gadelha F, Miguel DC, Cauz ACG, Brocchi M, Berlinck RGS. Water-Soluble Glutamic Acid Derivatives Produced in Culture by Penicillium solitum IS1-A from King George Island, Maritime Antarctica. JOURNAL OF NATURAL PRODUCTS 2020; 83:55-65. [PMID: 31895573 DOI: 10.1021/acs.jnatprod.9b00635] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A new method of screening was developed to generate 770 organic and water-soluble fractions from extracts of nine species of marine sponges, from the growth media of 18 species of marine-derived fungi, and from the growth media of 13 species of endophytic fungi. The screening results indicated that water-soluble fractions displayed significant bioactivity in cytotoxic, antibiotic, anti-Leishmania, anti-Trypanosoma cruzi, and inhibition of proteasome assays. Purification of water-soluble fractions from the growth medium of Penicillium solitum IS1-A provided the new glutamic acid derivatives solitumine A (1), solitumine B (2), and solitumidines A-D (3-6). The structures of compounds 1-6 have been established by analysis of spectroscopic data, chemical derivatizations, and vibrational circular dichroism calculations. Although no biological activity could be observed for compounds 1-6, the new structures reported for 1-6 indicate that the investigation of water-soluble natural products represents a relevant strategy in finding new secondary metabolites.
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Affiliation(s)
- Julie P G Rodríguez
- Instituto de Química de São Carlos , Universidade de São Paulo , CP 780, CEP 13560-970 , São Carlos , SP , Brazil
| | - Darlon I Bernardi
- Instituto de Química de São Carlos , Universidade de São Paulo , CP 780, CEP 13560-970 , São Carlos , SP , Brazil
| | - Juliana R Gubiani
- Instituto de Química de São Carlos , Universidade de São Paulo , CP 780, CEP 13560-970 , São Carlos , SP , Brazil
| | | | - Raquel P Morais-Urano
- Instituto de Química de São Carlos , Universidade de São Paulo , CP 780, CEP 13560-970 , São Carlos , SP , Brazil
| | - Ariane F Bertonha
- Instituto de Química de São Carlos , Universidade de São Paulo , CP 780, CEP 13560-970 , São Carlos , SP , Brazil
| | - Karin F Bandeira
- Instituto de Química de São Carlos , Universidade de São Paulo , CP 780, CEP 13560-970 , São Carlos , SP , Brazil
| | - Jairo I Q Bulla
- Instituto de Química de São Carlos , Universidade de São Paulo , CP 780, CEP 13560-970 , São Carlos , SP , Brazil
| | - Lara D Sette
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências , Universidade Estadual Paulista "Júlio de Mesquita Filho" , Campus Rio Claro, Avenida 24-A , 1515 , Rio Claro , SP , Brazil
| | - Antonio G Ferreira
- Departamento de Química , Universidade Federal de São Carlos , 13565-905 , São Carlos , SP , Brazil
| | - João M Batista
- Instituto de Ciência e Tecnologia , Universidade Federal de São Paulo , 12231-280 , São José dos Campos , SP , Brazil
| | - Thayná de Souza Silva
- Núcleo de Pesquisa em Ciência e Tecnologia , Universidade de Franca , Avenida Dr. Armando Salles Oliveira, 201. Pq. Universitário , 14404-600 , Franca , SP , Brazil
| | - Raquel Alves Dos Santos
- Núcleo de Pesquisa em Ciência e Tecnologia , Universidade de Franca , Avenida Dr. Armando Salles Oliveira, 201. Pq. Universitário , 14404-600 , Franca , SP , Brazil
| | - Carlos H G Martins
- Núcleo de Pesquisa em Ciência e Tecnologia , Universidade de Franca , Avenida Dr. Armando Salles Oliveira, 201. Pq. Universitário , 14404-600 , Franca , SP , Brazil
| | - Simone P Lira
- Departamento de Ciências Exatas, Escola Superior de Agricultura Luiz de Queiroz , Universidade de São Paulo , Avenida Pádua Dias, 11, CP 9, Agronomia, CEP 13418-900 , Piracicaba , SP , Brazil
| | - Marcos G da Cunha
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Material, Giuseppe Maximo Scolfaro , 10000, Pólo II de Alta Tecnologia de Campinas , 13083-970 Campinas , SP , Brazil
| | - Daniela B B Trivella
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Material, Giuseppe Maximo Scolfaro , 10000, Pólo II de Alta Tecnologia de Campinas , 13083-970 Campinas , SP , Brazil
| | - Nathalia Grazzia
- Instituto de Biologia , Universidade Estadual de Campinas , CEP 13083-862 , Campinas , SP , Brazil
| | - Natália E S Gomes
- Instituto de Biologia , Universidade Estadual de Campinas , CEP 13083-862 , Campinas , SP , Brazil
| | - Fernanda Gadelha
- Instituto de Biologia , Universidade Estadual de Campinas , CEP 13083-862 , Campinas , SP , Brazil
| | - Danilo C Miguel
- Instituto de Biologia , Universidade Estadual de Campinas , CEP 13083-862 , Campinas , SP , Brazil
| | - Ana Carolina G Cauz
- Instituto de Biologia , Universidade Estadual de Campinas , CEP 13083-862 , Campinas , SP , Brazil
| | - Marcelo Brocchi
- Instituto de Biologia , Universidade Estadual de Campinas , CEP 13083-862 , Campinas , SP , Brazil
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos , Universidade de São Paulo , CP 780, CEP 13560-970 , São Carlos , SP , Brazil
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Kundu T, Bhattacharjee B, Hazra S, Ghosh AK, Bandyopadhyay D, Pramanik A. Synthesis and Biological Assessment of Pyrrolobenzoxazine Scaffold as a Potent Antioxidant. J Med Chem 2019; 62:6315-6329. [PMID: 31246452 DOI: 10.1021/acs.jmedchem.9b00717] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reduction of mitochondrial oxidative stress-mediated diseases is an important pharmaceutical objective in recent biomedical research. In this context, a series of novel pyrrolobenzoxazines (PyBs) framework with enormous diversity (compounds 5a-w) was synthesized by employing a low-temperature greener pathway, and antioxidant property of the synthesized compounds was successfully demonstrated on preclinical model goat heart mitochondria, in vitro. Copper-ascorbate (Cu-As) was utilized as an oxidative stress generator. Out of screened PyBs, the compound possessing -OH and -OMe groups on benzene nucleus along with pyrrolobenzoxazine core moiety (compound 5w) displayed magnificent antioxidant property with a minimum effective dose of 66 μM during the biochemical assessment. The ameliorative effect of synthesized pyrrolobenzoxazine moiety on levels of biomarkers of oxidative stress, antioxidant enzyme, activities of Krebs cycle and respiratory chain enzymes, mitochondrial morphology, and Ca2+ permeability of mitochondrial membrane was investigated in the presence of Cu-As. Furthermore, the binding mode of Cu-As by compound 5w was explored successfully using isothermal titration calorimetry (ITC) analysis.
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Affiliation(s)
- Tania Kundu
- Department of Chemistry , University of Calcutta , 92, A. P. C. Road , Kolkata - 700 009 , India
| | - Bharati Bhattacharjee
- Department of Physiology, Oxidative Stress, and Free Radical Biology Laboratory , University of Calcutta , 92, A. P. C. Road , Kolkata - 700 009 , India
| | - Subhenjit Hazra
- Department of Chemistry , University of Calcutta , 92, A. P. C. Road , Kolkata - 700 009 , India
| | - Arnab K Ghosh
- Department of Physiology, Oxidative Stress, and Free Radical Biology Laboratory , University of Calcutta , 92, A. P. C. Road , Kolkata - 700 009 , India
| | - Debasish Bandyopadhyay
- Department of Physiology, Oxidative Stress, and Free Radical Biology Laboratory , University of Calcutta , 92, A. P. C. Road , Kolkata - 700 009 , India
| | - Animesh Pramanik
- Department of Chemistry , University of Calcutta , 92, A. P. C. Road , Kolkata - 700 009 , India
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Macrophage Migration Inhibitory Factor Acts as the Potential Target of a Newly Synthesized Compound, 1-(9'-methyl-3'-carbazole)-3, 4-dihydro-β-carboline. Sci Rep 2019; 9:2147. [PMID: 30765775 PMCID: PMC6375994 DOI: 10.1038/s41598-019-38590-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 01/03/2019] [Indexed: 12/26/2022] Open
Abstract
For a newly synthesized compound, identifying its target protein is a slow but pivotal step toward understand its pharmacologic mechanism. In this study, we systemically synthesized novel manzamine derivatives and chose 1-(9′-methyl-3′-carbazole)-3, 4-dihydro-β-carboline (MCDC) as an example to identify its target protein and function. MCDC had potent toxicity against several cancer cells. To identify its target protein, we first used a docking screen to predict macrophage migration inhibitory factor (MIF) as the potential target. Biochemical experiments, including mutation analysis and hydrogen-deuterium exchange assays, validated the binding of MCDC to MIF. Furthermore, MCDC was shown by microarrays to interfere with the cell cycle of breast cancer MCF7 cells. The activated signaling pathways included AKT phosphorylation and S phase-related proteins. Our results showed MIF as a potential direct target of a newly synthesized manzamine derivative, MCDC, and its pharmacologic mechanisms.
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Buijs Y, Bech PK, Vazquez-Albacete D, Bentzon-Tilia M, Sonnenschein EC, Gram L, Zhang SD. Marine Proteobacteria as a source of natural products: advances in molecular tools and strategies. Nat Prod Rep 2019; 36:1333-1350. [DOI: 10.1039/c9np00020h] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This review covers the recent advances in molecular tools and strategies for studies and use of natural products from marine Proteobacteria.
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Affiliation(s)
- Yannick Buijs
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Pernille Kjersgaard Bech
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Dario Vazquez-Albacete
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Eva C. Sonnenschein
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
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11
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Linear Aminolipids with Moderate Antimicrobial Activity from the Antarctic Gram-Negative Bacterium Aequorivita sp. Mar Drugs 2018; 16:md16060187. [PMID: 29843452 PMCID: PMC6025266 DOI: 10.3390/md16060187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 12/25/2022] Open
Abstract
The combination of LC-MS/MS based metabolomics approach and anti-MRSA activity-guided fractionation scheme was applied on the Gram-negative bacterium Aequorivita sp. isolated from shallow Antarctic sea sediment using a miniaturized culture chip technique. This methodology afforded the isolation of three new (1⁻3) and four known (4⁻7) N-terminal glycine- or serine-bearing iso-fatty acid amides esterified with another iso-fatty acid through their C-3 hydroxy groups. The chemical structures of the new compounds were elucidated using a set of spectroscopic (NMR, [α]D and FT-IR) and spectrometric (HRMS, HRMS/MS) methods. The aminolipids possessing an N-terminal glycine unit (1, 2, 4, 5) showed moderate in vitro antimicrobial activity against MRSA (IC50 values 22⁻145 μg/mL). This is the first in-depth chemistry and biological activity study performed on the microbial genus Aequorivita.
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12
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Genetic diversity detection and gene discovery of novel glycoside hydrolase family 48 from soil environmental genomic DNA. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1327-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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13
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Teta R, Marteinsson VT, Longeon A, Klonowski AM, Groben R, Bourguet-Kondracki ML, Costantino V, Mangoni A. Thermoactinoamide A, an Antibiotic Lipophilic Cyclopeptide from the Icelandic Thermophilic Bacterium Thermoactinomyces vulgaris. JOURNAL OF NATURAL PRODUCTS 2017; 80:2530-2535. [PMID: 28841315 DOI: 10.1021/acs.jnatprod.7b00560] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The thermophilic bacterium Thermoactinomyces vulgaris strain ISCAR 2354, isolated from a coastal hydrothermal vent in Iceland, was shown to contain thermoactinoamide A (1), a new cyclic hexapeptide composed of mixed d and l amino acids, along with five minor analogues (2-6). The structure of 1 was determined by one- and two-dimensional NMR spectroscopy, high-resolution tandem mass spectrometry, and advanced Marfey's analysis of 1 and of the products of its partial hydrolysis. Thermoactinoamide A inhibited the growth of Staphylococcus aureus ATCC 6538 with an MIC value of 35 μM. On the basis of literature data and this work, cyclic hexapeptides with mixed d/l configurations, one aromatic amino acid residue, and a prevalence of lipophilic residues can be seen as a starting point to define a new, easily accessible scaffold in the search for new antibiotic agents.
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Affiliation(s)
- Roberta Teta
- The NeaNat Group, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II , Via D. Montesano 49, 80131 Napoli, Italy
| | - Viggó Thór Marteinsson
- Matis ohf. , Vinlandsleid 12, 113 Reykjavik, Iceland
- Faculty of Food Science and Nutrition, University of Iceland , Saemundargata 2, 101 Reykjavik, Iceland
| | - Arlette Longeon
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes, UMR 7245 CNRS, Muséum National d'Histoire Naturelle , 57 Rue Cuvier (C.P. 54), 75005 Paris, France
| | | | - René Groben
- Matis ohf. , Vinlandsleid 12, 113 Reykjavik, Iceland
| | - Marie-Lise Bourguet-Kondracki
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes, UMR 7245 CNRS, Muséum National d'Histoire Naturelle , 57 Rue Cuvier (C.P. 54), 75005 Paris, France
| | - Valeria Costantino
- The NeaNat Group, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II , Via D. Montesano 49, 80131 Napoli, Italy
| | - Alfonso Mangoni
- The NeaNat Group, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II , Via D. Montesano 49, 80131 Napoli, Italy
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14
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Lorig-Roach N, Still PC, Coppage D, Compton JE, Crews MS, Navarro G, Tenney K, Crews P. Evaluating Nitrogen-Containing Biosynthetic Products Produced by Saltwater Culturing of Several California Littoral Zone Gram-Negative Bacteria. JOURNAL OF NATURAL PRODUCTS 2017; 80:2304-2310. [PMID: 28777571 PMCID: PMC5687060 DOI: 10.1021/acs.jnatprod.7b00302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The biosynthetic potential of marine-sediment-derived Gram-negative bacteria is poorly understood. Sampling of California near-shore marine environments afforded isolation of numerous Gram-negative bacteria in the Proteobacteria and Bacteriodetes phyla, which were grown in the laboratory to provide extracts whose metabolites were identified by comparative analyses of LC-mass spectrometry and MSn data. Overall, we developed an assemblage of seven bacterial strains grown in five different media types designed to coax out unique secondary metabolite production as a function of varying culture conditions. The changes in metabolite production patterns were tracked using the GNPS MS2 fragmentation pattern analysis tool. A variety of nitrogen-rich metabolites were visualized from the different strains grown in different media, and strikingly, all of the strains examined produced the same new, proton-atom-deficient compound, 1-methyl-4-methylthio-β-carboline (1), C13H12N2S. Scale-up liquid culture of Achromobacter spanius (order: Burkholderiales; class: Betaproteobacteria) provided material for the final structure elucidation. The methods successfully combined in this work should stimulate future studies of molecules from marine-derived Gram-negative bacteria.
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Affiliation(s)
- Nicholas Lorig-Roach
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Patrick C. Still
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - David Coppage
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Jennifer E. Compton
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Mitchell S. Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Gabriel Navarro
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Karen Tenney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Phillip Crews
- Corresponding Author Tel (P. Crews): (831) 459-2603. Fax: (831) 459-2935.
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15
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Timmermans ML, Paudel YP, Ross AC. Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies. Mar Drugs 2017; 15:E235. [PMID: 28762997 PMCID: PMC5577590 DOI: 10.3390/md15080235] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023] Open
Abstract
The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.
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Affiliation(s)
| | - Yagya P Paudel
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
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16
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Dávila-Céspedes A, Hufendiek P, Crüsemann M, Schäberle TF, König GM. Marine-derived myxobacteria of the suborder Nannocystineae: An underexplored source of structurally intriguing and biologically active metabolites. Beilstein J Org Chem 2016; 12:969-984. [PMID: 27340488 PMCID: PMC4902002 DOI: 10.3762/bjoc.12.96] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/25/2016] [Indexed: 12/28/2022] Open
Abstract
Myxobacteria are famous for their ability to produce most intriguing secondary metabolites. Till recently, only terrestrial myxobacteria were in the focus of research. In this review, however, we discuss marine-derived myxobacteria, which are particularly interesting due to their relatively recent discovery and due to the fact that their very existence was called into question. The to-date-explored members of these halophilic or halotolerant myxobacteria are all grouped into the suborder Nannocystineae. Few of them were chemically investigated revealing around 11 structural types belonging to the polyketide, non-ribosomal peptide, hybrids thereof or terpenoid class of secondary metabolites. A most unusual structural type is represented by salimabromide from Enhygromyxa salina. In silico analyses were carried out on the available genome sequences of four bacterial members of the Nannocystineae, revealing the biosynthetic potential of these bacteria.
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Affiliation(s)
| | - Peter Hufendiek
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Till F Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
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17
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Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes. Mar Drugs 2016; 14:md14040080. [PMID: 27092515 PMCID: PMC4849084 DOI: 10.3390/md14040080] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/01/2016] [Accepted: 04/08/2016] [Indexed: 11/17/2022] Open
Abstract
Considering that 70% of our planet's surface is covered by oceans, it is likely that undiscovered biodiversity is still enormous. A large portion of marine biodiversity consists of microbiomes. They are very attractive targets of bioprospecting because they are able to produce a vast repertoire of secondary metabolites in order to adapt in diverse environments. In many cases secondary metabolites of pharmaceutical and biotechnological interest such as nonribosomal peptides (NRPs) and polyketides (PKs) are synthesized by multimodular enzymes named nonribosomal peptide synthetases (NRPSes) and type-I polyketide synthases (PKSes-I), respectively. Novel findings regarding the mechanisms underlying NRPS and PKS evolution demonstrate how microorganisms could leverage their metabolic potential. Moreover, these findings could facilitate synthetic biology approaches leading to novel bioactive compounds. Ongoing advances in bioinformatics and next-generation sequencing (NGS) technologies are driving the discovery of NRPs and PKs derived from marine microbiomes mainly through two strategies: genome-mining and metagenomics. Microbial genomes are now sequenced at an unprecedented rate and this vast quantity of biological information can be analyzed through genome mining in order to identify gene clusters encoding NRPSes and PKSes of interest. On the other hand, metagenomics is a fast-growing research field which directly studies microbial genomes and their products present in marine environments using culture-independent approaches. The aim of this review is to examine recent developments regarding discovery strategies of bioactive compounds synthesized by NRPS and type-I PKS derived from marine microbiomes and to highlight the vast diversity of NRPSes and PKSes present in marine environments by giving examples of recently discovered bioactive compounds.
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18
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Deering RW, Chen J, Sun J, Ma H, Dubert J, Barja JL, Seeram NP, Wang H, Rowley DC. N-Acyl Dehydrotyrosines, Tyrosinase Inhibitors from the Marine Bacterium Thalassotalea sp. PP2-459. JOURNAL OF NATURAL PRODUCTS 2016; 79:447-50. [PMID: 26824128 PMCID: PMC5821419 DOI: 10.1021/acs.jnatprod.5b00972] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Thalassotalic acids A-C and thalassotalamides A and B are new N-acyl dehydrotyrosine derivatives produced by Thalassotalea sp. PP2-459, a Gram-negative bacterium isolated from a marine bivalve aquaculture facility. The structures were elucidated via a combination of spectroscopic analyses emphasizing two-dimensional NMR and high-resolution mass spectrometric data. Thalassotalic acid A (1) displays in vitro inhibition of the enzyme tyrosinase with an IC50 value (130 μM) that compares favorably to the commercially used control compounds kojic acid (46 μM) and arbutin (100 μM). These are the first natural products reported from a bacterium belonging to the genus Thalassotalea.
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Affiliation(s)
- Robert W. Deering
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Jianwei Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiadong Sun
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Hang Ma
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Javier Dubert
- Department of Microbiology and Parasitology, CIBUS- Faculty of Biology and Aquaculture Institute, University of Santiago de Compostela, Santiago de Compostela 17582, Spain
| | - Juan L. Barja
- Department of Microbiology and Parasitology, CIBUS- Faculty of Biology and Aquaculture Institute, University of Santiago de Compostela, Santiago de Compostela 17582, Spain
| | - Navindra P. Seeram
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Hong Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - David C. Rowley
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
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19
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Abstract
This review covers the literature published in 2014 for marine natural products (MNPs), with 1116 citations (753 for the period January to December 2014) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1378 in 456 papers for 2014), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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20
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Isolation and Biosynthetic Analysis of Haliamide, a New PKS-NRPS Hybrid Metabolite from the Marine Myxobacterium Haliangium ochraceum. Molecules 2016; 21:59. [PMID: 26751435 PMCID: PMC6274090 DOI: 10.3390/molecules21010059] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/29/2015] [Accepted: 12/31/2015] [Indexed: 02/02/2023] Open
Abstract
Myxobacteria of marine origin are rare and hard-to-culture microorganisms, but they genetically harbor high potential to produce novel antibiotics. An extensive investigation on the secondary metabolome of the unique marine myxobacterium Haliangium ochraceum SMP-2 led to the isolation of a new polyketide-nonribosomal peptide hybrid product, haliamide (1). Its structure was elucidated by spectroscopic analyses including NMR and HR-MS. Haliamide (1) showed cytotoxicity against HeLa-S3 cells with IC50 of 12 μM. Feeding experiments were performed to identify the biosynthetic building blocks of 1, revealing one benzoate, one alanine, two propionates, one acetate and one acetate-derived terminal methylene. The biosynthetic gene cluster of haliamide (hla, 21.7 kbp) was characterized through the genome mining of the producer, allowing us to establish a model for the haliamide biosynthesis. The sulfotransferase (ST)-thioesterase (TE) domains encoded in hlaB appears to be responsible for the terminal alkene formation via decarboxylation.
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21
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Whalen KE, Poulson-Ellestad KL, Deering RW, Rowley DC, Mincer TJ. Enhancement of antibiotic activity against multidrug-resistant bacteria by the efflux pump inhibitor 3,4-dibromopyrrole-2,5-dione isolated from a Pseudoalteromonas sp. JOURNAL OF NATURAL PRODUCTS 2015; 78:402-412. [PMID: 25646964 DOI: 10.1021/np500775e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Members of the resistance nodulation cell division (RND) of efflux pumps play essential roles in multidrug resistance (MDR) in Gram-negative bacteria. Here, we describe the search for new small molecules from marine microbial extracts to block efflux and thus restore antibiotic susceptibility in MDR bacterial strains. We report the isolation of 3,4-dibromopyrrole-2,5-dione (1), an inhibitor of RND transporters, from Enterobacteriaceae and Pseudomonas aeruginosa, from the marine bacterium Pseudoalteromonas piscicida. 3,4-Dibromopyrrole-2,5-dione decreased the minimum inhibitory concentrations (MICs) of two fluoroquinolones, an aminoglycoside, a macrolide, a beta-lactam, tetracycline, and chloramphenicol between 2- and 16-fold in strains overexpressing three archetype RND transporters (AcrAB-TolC, MexAB-OprM, and MexXY-OprM). 3,4-Dibromopyrrole-2,5-dione also increased the intracellular accumulation of Hoechst 33342 in wild-type but not in transporter-deficient strains and prevented H33342 efflux (IC50 = 0.79 μg/mL or 3 μM), a hallmark of efflux pump inhibitor (EPI) functionality. A metabolomic survey of 36 Pseudoalteromonas isolates mapped the presence of primarily brominated metabolites only within the P. piscicida phylogenetic clade, where a majority of antibiotic activity was also observed, suggesting a link between halogenation and enhanced secondary metabolite biosynthetic potential. In sum, 3,4-dibromopyrrole-2,5-dione is a potent EPI and deserves further attention as an adjuvant to enhance the effectiveness of existing antibiotics.
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Affiliation(s)
| | | | - Robert W Deering
- ‡College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - David C Rowley
- ‡College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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22
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Theodore CM, Lorig-Roach N, Still PC, Johnson TA, Drašković M, Schwochert JA, Naphen CN, Crews MS, Barker SA, Valeriote FA, Lokey RS, Crews P. Biosynthetic products from a nearshore-derived gram-negative bacterium enable reassessment of the kailuin depsipeptides. JOURNAL OF NATURAL PRODUCTS 2015; 78:441-52. [PMID: 25699470 PMCID: PMC4699550 DOI: 10.1021/np500840n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Sampling of California nearshore sediments resulted in the isolation of a Gram-negative bacterium, Photobacterium halotolerans, capable of producing unusual biosynthetic products. Liquid culture in artificial seawater-based media provided cyclic depsipeptides including four known compounds, kailuins B-E (2-5), and two new analogues, kailuins G and H (7 and 8). The structures of the new and known compounds were confirmed through extensive spectroscopic and Marfey's analyses. During the course of these studies, a correction was made to the previously reported double-bond geometry of kailuin D (4). Additionally, through the application of a combination of derivatization with Mosher's reagent and extensive (13)C NMR shift analysis, the previously unassigned chiral center at position C-3 of the β-acyloxy group of all compounds was determined. To evaluate bioactivity and structure-activity relationships, the kailuin core (13) and kailuin lactam (14) were prepared by chiral synthesis using an Fmoc solid-phase peptide strategy followed by solution-phase cyclization. All isolated compounds and synthetic cores were assayed for solid tumor cell cytotoxicity and showed only minimal activity, contrary to other published reports. Additional phenotypic screenings were done on 4 and 5, with little evidence of activity.
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Affiliation(s)
- Christine M. Theodore
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Nicholas Lorig-Roach
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Patrick C. Still
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Tyler A. Johnson
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Marija Drašković
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Joshua A. Schwochert
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Cassandra N. Naphen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Mitchell S. Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Simone A. Barker
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Frederick A. Valeriote
- Josephine Ford Cancer Center, Henry Ford Health System, Detroit, Michigan 48202, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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23
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Machado H, Sonnenschein EC, Melchiorsen J, Gram L. Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria. BMC Genomics 2015; 16:158. [PMID: 25879706 PMCID: PMC4359443 DOI: 10.1186/s12864-015-1365-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/20/2015] [Indexed: 11/10/2022] Open
Abstract
Background Antibiotic resistance in bacteria spreads quickly, overtaking the pace at which new compounds are discovered and this emphasizes the immediate need to discover new compounds for control of infectious diseases. Terrestrial bacteria have for decades been investigated as a source of bioactive compounds leading to successful applications in pharmaceutical and biotech industries. Marine bacteria have so far not been exploited to the same extent; however, they are believed to harbor a multitude of novel bioactive chemistry. To explore this potential, genomes of 21 marine Alpha- and Gammaproteobacteria collected during the Galathea 3 expedition were sequenced and mined for natural product encoding gene clusters. Results Independently of genome size, bacteria of all tested genera carried a large number of clusters encoding different potential bioactivities, especially within the Vibrionaceae and Pseudoalteromonadaceae families. A very high potential was identified in pigmented pseudoalteromonads with up to 20 clusters in a single strain, mostly NRPSs and NRPS-PKS hybrids. Furthermore, regulatory elements in bioactivity-related pathways including chitin metabolism, quorum sensing and iron scavenging systems were investigated both in silico and in vitro. Genes with siderophore function were identified in 50% of the strains, however, all but one harboured the ferric-uptake-regulator gene. Genes encoding the syntethase of acylated homoserine lactones were found in Roseobacter-clade bacteria, but not in the Vibrionaceae strains and only in one Pseudoalteromonas strains. The understanding and manipulation of these elements can help in the discovery and production of new compounds never identified under regular laboratory cultivation conditions. High chitinolytic potential was demonstrated and verified for Vibrio and Pseudoalteromonas species that commonly live in close association with eukaryotic organisms in the environment. Chitin regulation by the ChiS histidine-kinase seems to be a general trait of the Vibrionaceae family, however it is absent in the Pseudomonadaceae. Hence, the degree to which chitin influences secondary metabolism in marine bacteria is not known. Conclusions Utilizing the rapidly developing sequencing technologies and software tools in combination with phenotypic in vitro assays, we demonstrated the high bioactive potential of marine bacteria in an efficient, straightforward manner – an approach that will facilitate natural product discovery in the future.
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Affiliation(s)
- Henrique Machado
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allè 6, DK-2970, Hørsholm, Denmark. .,Department of Systems Biology, Technical University of Denmark, Matematiktorvet bldg 301, DK-2800, Kgs Lyngby, Denmark.
| | - Eva C Sonnenschein
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet bldg 301, DK-2800, Kgs Lyngby, Denmark.
| | - Jette Melchiorsen
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet bldg 301, DK-2800, Kgs Lyngby, Denmark.
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet bldg 301, DK-2800, Kgs Lyngby, Denmark.
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24
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Affiliation(s)
- Lone Gram
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet bldg. 301, DK-2800, Kgs. Lyngby, Denmark
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