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Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz MDC, Sahin N, Smith DL, Kim KE, Peluso P, Deshpande S, Woyke T, Shapiro N, Kyrpides NC, Klenk HP, Göker M, Goodfellow M. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 2018; 8:525. [PMID: 29323202 PMCID: PMC5765111 DOI: 10.1038/s41598-017-17392-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022] Open
Abstract
There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK.
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Vartul Sangal
- Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
| | - Martha E Trujillo
- Departamento de Microbiologia y Genetica, Lab 214, Universidad de Salamanca, Salamanca, Spain
| | | | - Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, Kurupelit-Samsun, Turkey
| | - Darren Lee Smith
- Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Kristi E Kim
- Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA
| | - Paul Peluso
- Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK.
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
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Ettari R, Zappalà M, Grasso S, Musolino C, Innao V, Allegra A. Immunoproteasome-selective and non-selective inhibitors: A promising approach for the treatment of multiple myeloma. Pharmacol Ther 2017; 182:176-192. [PMID: 28911826 DOI: 10.1016/j.pharmthera.2017.09.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ubiquitin-proteasome system (UPS) is the major non-lysosomal proteolytic system for the degradation of abnormal or damaged proteins no longer required. The proteasome is involved in degradation of numerous proteins which regulate the cell cycle, indicating a role in controlling cell proliferation and maintaining cell survival. Defects in the UPS can lead to anarchic cell proliferation and to tumor development. For these reasons UPS inhibition has become a significant new strategy for drug development in cancer treatment. In addition to the constitutive proteasome, which is expressed in all cells and tissues, higher organisms such as vertebrates possess two immune-type proteasomes, the thymoproteasome and the immunoproteasome. The thymoproteasome is specifically expressed by thymic cortical epithelial cells and has a role in positive selection of CD8+ T cells, whereas the immunoproteasome is predominantly expressed in monocytes and lymphocytes and is responsible for the generation of antigenic peptides for cell-mediated immunity. Recent studies demonstrated that the immunoproteasome has a preservative role during oxidative stress and is up-regulated in a number of pathological disorders including cancer, inflammatory and autoimmune diseases. As a consequence, immunoproteasome-selective inhibitors are currently the focus of anticancer drug design. At present, the commercially available proteasome inhibitors bortezomib and carfilzomib which have been validated in multiple myeloma and other model systems, appear to target both the constitutive and immunoproteasomes, indiscriminately. This lack of specificity may, in part, explain some of the side effects of these agents, such as peripheral neuropathy and gastrointestinal effects, which may be due to targeting of the constitutive proteasome in these tissues. In contrast, by selectively inhibiting the immunoproteasome, it may be possible to maintain the antimyeloma and antilymphoma efficacy while reducing these toxicities, thereby increasing the therapeutic index. This review article will be focused on the discussion of the most promising immunoproteasome specific inhibitors which have been developed in recent years. Particular attention will be devoted to the description of their mechanism of action, their structure-activity relationship, and their potential application in therapy.
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Affiliation(s)
- Roberta Ettari
- Dipartimento di Scienze del Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, Viale Annunziata, 98168 Messina, Italy
| | - Maria Zappalà
- Dipartimento di Scienze del Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, Viale Annunziata, 98168 Messina, Italy
| | - Silvana Grasso
- Dipartimento di Scienze del Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, Viale Annunziata, 98168 Messina, Italy
| | - Caterina Musolino
- Division of Hematology, Department of Patologia Umana dell'Adulto e dell'Età Evolutiva, University of Messina, Via Consolare Valeria, 90100 Messina, Italy
| | - Vanessa Innao
- Division of Hematology, Department of Patologia Umana dell'Adulto e dell'Età Evolutiva, University of Messina, Via Consolare Valeria, 90100 Messina, Italy
| | - Alessandro Allegra
- Division of Hematology, Department of Patologia Umana dell'Adulto e dell'Età Evolutiva, University of Messina, Via Consolare Valeria, 90100 Messina, Italy.
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53
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Yeoh YK, Dennis PG, Paungfoo-Lonhienne C, Weber L, Brackin R, Ragan MA, Schmidt S, Hugenholtz P. Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nat Commun 2017; 8:215. [PMID: 28790312 PMCID: PMC5548757 DOI: 10.1038/s41467-017-00262-8] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 06/14/2017] [Indexed: 11/30/2022] Open
Abstract
Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. However, these studies have mostly focussed on model plants and crops. Here, we examine the root microbiomes of multiple plant phyla including lycopods, ferns, gymnosperms, and angiosperms across a soil chronosequence using 16S rRNA gene amplicon profiling. We confirm that soil type is the primary determinant of root-associated bacterial community composition, but also observe a significant correlation with plant phylogeny. A total of 47 bacterial genera are associated with roots relative to bulk soil microbial communities, including well-recognized plant-associated genera such as Bradyrhizobium, Rhizobium, and Burkholderia, and major uncharacterized lineages such as WPS-2, Ellin329, and FW68. We suggest that these taxa collectively constitute an evolutionarily conserved core root microbiome at this site. This lends support to the inference that a core root microbiome has evolved with terrestrial plants over their 400 million year history. Yeoh et al. study root microbiomes of different plant phyla across a tropical soil chronosequence. They confirm that soil type is the primary determinant of root-associated bacterial communities, but also observe a clear correlation with plant phylogeny and define a core root microbiome at this site.
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Affiliation(s)
- Yun Kit Yeoh
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Paul G Dennis
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Lui Weber
- Biodiversity Assessment and Management, 26-40 Delancey Street, Cleveland, QLD, 4163, Australia
| | - Richard Brackin
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Susanne Schmidt
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Wang L, Zhang M, Li Y, Cui Y, Zhang Y, Wang Z, Wang M, Huang Y. Application of response surface methodology to optimize the production of antimicrobial metabolites by Micromonospora Y15. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1356689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Liping Wang
- Department of Food Biotechnology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-Processing Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai Ocean University, Shanghai, China
| | - Meng Zhang
- Department of Food Biotechnology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yuntao Li
- Department of Food Biotechnology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yunyun Cui
- Department of Food Biotechnology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yu Zhang
- Department of Food Biotechnology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Zhengquan Wang
- Department of Food Biotechnology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Mingfu Wang
- Department of Food Biotechnology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yuliang Huang
- Department of Food Biotechnology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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55
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Millán-Aguiñaga N, Chavarria KL, Ugalde JA, Letzel AC, Rouse GW, Jensen PR. Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations. Sci Rep 2017; 7:3564. [PMID: 28620214 PMCID: PMC5472633 DOI: 10.1038/s41598-017-02845-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/18/2017] [Indexed: 11/12/2022] Open
Abstract
Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.
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Affiliation(s)
- Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.,Universidad Autónoma de Baja California. Facultad de Ciencias Marinas, Ensenada, Baja California, Mexico
| | - Krystle L Chavarria
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Juan A Ugalde
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.,Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bella, Santiago, Chile
| | - Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Greg W Rouse
- Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States. .,Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.
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56
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Liu SW, Tuo L, Li XJ, Li FN, Li J, Jiang MG, Chen L, Hu L, Sun CH. Mangrovihabitans endophyticus gen. nov., sp. nov., a new member of the family Micromonosporaceae isolated from Bruguiera sexangula. Int J Syst Evol Microbiol 2017; 67:1629-1636. [DOI: 10.1099/ijsem.0.001764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shao-Wei Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li Tuo
- Research Center for Medicine & Biology, Zunyi Medical University, Zunyi 563003, PR China
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Xiao-Jun Li
- College of Laboratory Medical Science, Hebei North University, Zhangjiakou 075000, PR China
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Fei-Na Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Jing Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Ming-Guo Jiang
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, Guangxi University for Nationalities, Nanning 530006, PR China
| | - Li Chen
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Li Hu
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Cheng-Hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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57
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Eliwa EM, Abdel-Razek AS, Frese M, Wibberg D, Halawa AH, El-Agrody AM, Bedair AH, Kalinowski J, Sewald N, Shaaban M. New bioactive compounds from the marine-derived actinomycete Nocardiopsis lucentensis sp. ASMR2. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/znb-2016-0250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In the search for new bioactive compounds from extremophilic actinomycetes, a new marine actinomycete strain, Nocardiopsis lucentensis sp. ASMR2 has been isolated and taxonomically identified from marine plants collected in the Red Sea at Hurghada coasts. A large-scale fermentation of the strain on modified rice solid medium was performed, followed by work-up and purification of the obtained extract using a series of chromatographic purifications, delivering the novel butenolide system 3′-hydroxy-N-(2-oxo-2,5-dihydrofuran-4-yl)propionamide (1a) along with the naturally new 4-methoxy-2H-isoquinolin-1-one (2). Furthermore, eight known bioactive compounds are also reported, namely, indole-3-carboxylic acid, indole-3-acetic acid, indole-3-acetic acid methyl ester, furan-2,5-dimethanol, tyrosol, glycerol linoleate, cyclo-(Tyr, Pro), and adenosine. The chemical structures of the new compounds (1a, 2) were confirmed by extensive one- and two-dimensional (1D and 2D) nuclear magnetic resonance (NMR) spectroscopy, electron ionization high resolution (EI-HR) mass spectrometry, and by comparison with literature data. The antimicrobial activity of the strain extract, as well as of compounds 1a and 2, were studied using a panel of pathogenic microorganisms. The in vitro cytotoxicity of the bacterial extract and compounds 1a and 2 were studied against the human cervix carcinoma cell line (KB-3-1) and its multidrug-resistant subclone (KB-V1).
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Affiliation(s)
- Essam M. Eliwa
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City-Cairo 11884, Egypt
| | - Ahmed S. Abdel-Razek
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Microbial Chemistry Department, Division of Genetic Engineering and Biotechnology Research, National Research Centre, El-Behoos St. 33, Dokki-Cairo 12622, Egypt
| | - Marcel Frese
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
| | - Daniel Wibberg
- Centrum für Biotechnologie (CeBiTec), Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Ahmed H. Halawa
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City-Cairo 11884, Egypt
| | - Ahmed M. El-Agrody
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City-Cairo 11884, Egypt
| | - Ahmed H. Bedair
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City-Cairo 11884, Egypt
| | - Jörn Kalinowski
- Centrum für Biotechnologie (CeBiTec), Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
| | - Mohamed Shaaban
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Chemistry of Natural Compounds Department, Division of Pharmaceutical Industries, National Research Centre, El-Behoos St. 33, Dokki, Cairo 12622, Egypt , Tel.: +202-270-1728/int-2609. Fax: +202-333-70931
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Crüsemann M, O’Neill EC, Larson CB, Melnik AV, Floros DJ, da Silva RR, Jensen PR, Dorrestein PC, Moore BS. Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols. JOURNAL OF NATURAL PRODUCTS 2017; 80:588-597. [PMID: 28335604 PMCID: PMC5367486 DOI: 10.1021/acs.jnatprod.6b00722] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In order to expedite the rapid and efficient discovery and isolation of novel specialized metabolites, while minimizing the waste of resources on rediscovery of known compounds, it is crucial to develop efficient approaches for strain prioritization, rapid dereplication, and the assessment of favored cultivation and extraction conditions. Herein we interrogated bacterial strains by systematically evaluating cultivation and extraction parameters with LC-MS/MS analysis and subsequent dereplication through the Global Natural Product Social Molecular Networking (GNPS) platform. The developed method is fast, requiring minimal time and sample material, and is compatible with high-throughput extract analysis, thereby streamlining strain prioritization and evaluation of culturing parameters. With this approach, we analyzed 146 marine Salinispora and Streptomyces strains that were grown and extracted using multiple different protocols. In total, 603 samples were analyzed, generating approximately 1.8 million mass spectra. We constructed a comprehensive molecular network and identified 15 molecular families of diverse natural products and their analogues. The size and breadth of this network shows statistically supported trends in molecular diversity when comparing growth and extraction conditions. The network provides an extensive survey of the biosynthetic capacity of the strain collection and a method to compare strains based on the variety and novelty of their metabolites. This approach allows us to quickly identify patterns in metabolite production that can be linked to taxonomy, culture conditions, and extraction methods, as well as informing the most valuable growth and extraction conditions.
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Affiliation(s)
- Max Crüsemann
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Ellis C. O’Neill
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Charles B. Larson
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Alexey V. Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dimitrios J Floros
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo R. da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
- Research Support Center in Natural and Synthetic Products, Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, 14040-903, Brazil
| | - Paul R. Jensen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bradley S. Moore
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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Müller JB, Ramos DT, Larose C, Fernandes M, Lazzarin HSC, Vogel TM, Corseuil HX. Combined iron and sulfate reduction biostimulation as a novel approach to enhance BTEX and PAH source-zone biodegradation in biodiesel blend-contaminated groundwater. JOURNAL OF HAZARDOUS MATERIALS 2017; 326:229-236. [PMID: 28033549 DOI: 10.1016/j.jhazmat.2016.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 05/22/2023]
Abstract
The use of biodiesel as a transportation fuel and its growing mandatory blending percentage in diesel increase the likelihood of contaminating groundwater with diesel/biodiesel blends. A 100L-field experiment with B20 (20% biodiesel and 80% diesel, v/v) was conducted to assess the potential for the combined biostimulation of iron and sulfate reducing bacteria to enhance BTEX and PAH biodegradation in a diesel/biodiesel blend-contaminated groundwater. A B20 field experiment under monitored natural attenuation (MNA) was used as a baseline control. Ammonium acetate and a low-cost and sustainable product recovered from acid mine drainage treatment were used to stimulate iron and sulfate-reducing conditions. As a result, benzene and naphthalene concentrations (maximum concentrations were 28.1μgL-1 and 10.0μgL-1, respectively) remained lower than the MNA experiment (maximum concentrations were 974.7μgL-1 and 121.3μgL-1, respectively) over the whole experiment. Geochemical changes were chronologically consistent with the temporal change of the predominance of Geobacter and GOUTA19 which might be the key players responsible for the rapid attenuation of benzene and naphthalene. To the best of our knowledge, this is the first field experiment to demonstrate the potential for the combined iron and sulfate biostimulation to enhance B20 source-zone biodegradation.
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Affiliation(s)
- Juliana B Müller
- Federal University of Santa Catarina, Department of Sanitary and Environmental Engineering, Florianópolis, Santa Catarina, Brazil.
| | - Débora T Ramos
- Federal University of Santa Catarina, Department of Sanitary and Environmental Engineering, Florianópolis, Santa Catarina, Brazil.
| | - Catherine Larose
- Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de Lyon, Ecully, France.
| | - Marilda Fernandes
- Federal University of Santa Catarina, Department of Sanitary and Environmental Engineering, Florianópolis, Santa Catarina, Brazil.
| | - Helen S C Lazzarin
- Federal University of Santa Catarina, Department of Sanitary and Environmental Engineering, Florianópolis, Santa Catarina, Brazil.
| | - Timothy M Vogel
- Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de Lyon, Ecully, France.
| | - Henry X Corseuil
- Federal University of Santa Catarina, Department of Sanitary and Environmental Engineering, Florianópolis, Santa Catarina, Brazil.
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Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities. Appl Environ Microbiol 2017; 83:AEM.02676-16. [PMID: 27986719 DOI: 10.1128/aem.02676-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/07/2016] [Indexed: 02/06/2023] Open
Abstract
Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.
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Prieto-Davó A, Dias T, Gomes SE, Rodrigues S, Parera-Valadez Y, Borralho PM, Pereira F, Rodrigues CMP, Santos-Sanches I, Gaudêncio SP. The Madeira Archipelago As a Significant Source of Marine-Derived Actinomycete Diversity with Anticancer and Antimicrobial Potential. Front Microbiol 2016; 7:1594. [PMID: 27774089 PMCID: PMC5053986 DOI: 10.3389/fmicb.2016.01594] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/23/2016] [Indexed: 12/21/2022] Open
Abstract
Marine-derived actinomycetes have demonstrated an ability to produce novel compounds with medically relevant biological activity. Studying the diversity and biogeographical patterns of marine actinomycetes offers an opportunity to identify genera that are under environmental pressures, which may drive adaptations that yield specific biosynthetic capabilities. The present study describes research efforts to explore regions of the Atlantic Ocean, specifically around the Madeira Archipelago, where knowledge of the indigenous actinomycete diversity is scarce. A total of 400 actinomycetes were isolated, sequenced, and screened for antimicrobial and anticancer activities. The three most abundant genera identified were Streptomyces, Actinomadura, and Micromonospora. Phylogenetic analyses of the marine OTUs isolated indicated that the Madeira Archipelago is a new source of actinomycetes adapted to life in the ocean. Phylogenetic differences between offshore (>100 m from shore) and nearshore (< 100 m from shore) populations illustrates the importance of sampling offshore in order to isolate new and diverse bacterial strains. Novel phylotypes from chemically rich marine actinomycete groups like MAR4 and the genus Salinispora were isolated. Anticancer and antimicrobial assays identified Streptomyces, Micromonospora, and Salinispora as the most biologically active genera. This study illustrates the importance of bioprospecting efforts at unexplored regions of the ocean to recover bacterial strains with the potential to produce novel and interesting chemistry.
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Affiliation(s)
- Alejandra Prieto-Davó
- Laboratorio de Productos Naturales Marinos, Facultad de Química, Universidad Nacional Autónoma de México, Unidad Sisal Sisal, Mexico
| | - Tiago Dias
- LAQV-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal; UCIBIO-REQUIMTE, Department of Life Sciences, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal
| | - Sofia E Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa Lisbon, Portugal
| | - Sara Rodrigues
- LAQV-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal; UCIBIO-REQUIMTE, Department of Life Sciences, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal
| | - Yessica Parera-Valadez
- Laboratorio de Productos Naturales Marinos, Facultad de Química, Universidad Nacional Autónoma de México, Unidad Sisal Sisal, Mexico
| | - Pedro M Borralho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de LisboaLisbon, Portugal; Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de LisboaLisbon, Portugal
| | - Florbela Pereira
- LAQV-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa Caparica, Portugal
| | - Cecilia M P Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de LisboaLisbon, Portugal; Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de LisboaLisbon, Portugal
| | - Ilda Santos-Sanches
- UCIBIO-REQUIMTE, Department of Life Sciences, Faculty of Science and Technology, Universidade NOVA de Lisboa Caparica, Portugal
| | - Susana P Gaudêncio
- LAQV-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal; UCIBIO-REQUIMTE, Department of Life Sciences, Faculty of Science and Technology, Universidade NOVA de LisboaCaparica, Portugal
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Suriya J, Bharathiraja S, Manivasagan P, Kim SK. Enzymes From Rare Actinobacterial Strains. ADVANCES IN FOOD AND NUTRITION RESEARCH 2016; 79:67-98. [PMID: 27770864 DOI: 10.1016/bs.afnr.2016.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Actinobacteria constitute rich sources of novel biocatalysts and novel natural products for medical and industrial utilization. Although actinobacteria are potential source of economically important enzymes, the isolation and culturing are somewhat tough because of its extreme habitats. But now-a-days, the rate of discovery of novel compounds producing actinomycetes from soil, freshwater, and marine ecosystem has increased much through the developed culturing and genetic engineering techniques. Actinobacteria are well-known source of their bioactive compounds and they are the promising source of broad range of industrially important enzymes. The bacteria have the capability to degrade a range of pesticides, hydrocarbons, aromatic, and aliphatic compounds (Sambasiva Rao, Tripathy, Mahalaxmi, & Prakasham, 2012). Most of the enzymes are mainly derived from microorganisms because of their easy of growth, minimal nutritional requirements, and low-cost for downstream processing. The focus of this review is about the new, commercially useful enzymes from rare actinobacterial strains. Industrial requirements are now fulfilled by the novel actinobacterial enzymes which assist the effective production. Oxidative enzymes, lignocellulolytic enzymes, extremozymes, and clinically useful enzymes are often utilized in many industrial processes because of their ability to catalyze numerous reactions. Novel, extremophilic, oxidative, lignocellulolytic, and industrially important enzymes from rare Actinobacterial population are discussed in this chapter.
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Affiliation(s)
- J Suriya
- School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - S Bharathiraja
- CAS in Marine Biology, Annamalai University, Porto Novo, Tamil Nadu, India
| | - P Manivasagan
- Marine Bioprocess Research Center, Pukyong National University, Busan, Republic of Korea.
| | - S-K Kim
- Marine Bioprocess Research Center, Pukyong National University, Busan, Republic of Korea; Specialized Graduate School Science & Technology Convergence, Pukyong National University, Busan, Republic of Korea.
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63
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Mingma R, Tanaka K, Ōmura S, Takahashi Y, Matsumoto A. Actinorhabdospora filicis gen. nov., sp. nov., a new member of the family Micromonosporaceae. Int J Syst Evol Microbiol 2016; 66:3071-3077. [DOI: 10.1099/ijsem.0.001145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ratchanee Mingma
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kazuki Tanaka
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yōko Takahashi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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64
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Undabarrena A, Beltrametti F, Claverías FP, González M, Moore ERB, Seeger M, Cámara B. Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile. Front Microbiol 2016; 7:1135. [PMID: 27486455 PMCID: PMC4949237 DOI: 10.3389/fmicb.2016.01135] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/07/2016] [Indexed: 11/13/2022] Open
Abstract
Bioprospecting natural products in marine bacteria from fjord environments are attractive due to their unique geographical features. Although, Actinobacteria are well known for producing a myriad of bioactive compounds, investigations regarding fjord-derived marine Actinobacteria are scarce. In this study, the diversity and biotechnological potential of Actinobacteria isolated from marine sediments within the Comau fjord, in Northern Chilean Patagonia, were assessed by culture-based approaches. The 16S rRNA gene sequences revealed that members phylogenetically related to the Micrococcaceae, Dermabacteraceae, Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, Dietziaceae, Nocardiaceae, and Streptomycetaceae families were present at the Comau fjord. A high diversity of cultivable Actinobacteria (10 genera) was retrieved by using only five different isolation media. Four isolates belonging to Arthrobacter, Brevibacterium, Corynebacterium and Kocuria genera showed 16S rRNA gene identity <98.7% suggesting that they are novel species. Physiological features such as salt tolerance, artificial sea water requirement, growth temperature, pigmentation and antimicrobial activity were evaluated. Arthrobacter, Brachybacterium, Curtobacterium, Rhodococcus, and Streptomyces isolates showed strong inhibition against both Gram-negative Pseudomonas aeruginosa, Escherichia coli and Salmonella enterica and Gram-positive Staphylococcus aureus, Listeria monocytogenes. Antimicrobial activities in Brachybacterium, Curtobacterium, and Rhodococcus have been scarcely reported, suggesting that non-mycelial strains are a suitable source of bioactive compounds. In addition, all strains bear at least one of the biosynthetic genes coding for NRPS (91%), PKS I (18%), and PKS II (73%). Our results indicate that the Comau fjord is a promising source of novel Actinobacteria with biotechnological potential for producing biologically active compounds.
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Affiliation(s)
- Agustina Undabarrena
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
| | | | - Fernanda P. Claverías
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
| | - Myriam González
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
| | - Edward R. B. Moore
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of GothenburgGothenburg, Sweden
- Department of Infectious Diseases, Sahlgrenska Academy, University of GothenburgGothenburg, Sweden
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
| | - Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
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65
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Ettoumi B, Chouchane H, Guesmi A, Mahjoubi M, Brusetti L, Neifar M, Borin S, Daffonchio D, Cherif A. Diversity, ecological distribution and biotechnological potential of Actinobacteria inhabiting seamounts and non-seamounts in the Tyrrhenian Sea. Microbiol Res 2016; 186-187:71-80. [DOI: 10.1016/j.micres.2016.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 03/31/2016] [Indexed: 11/26/2022]
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66
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Kirsebom LA, Dasgupta S, Fredrik Pettersson BM. Pleiomorphism in Mycobacterium. ADVANCES IN APPLIED MICROBIOLOGY 2016; 80:81-112. [PMID: 22794145 DOI: 10.1016/b978-0-12-394381-1.00004-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Morphological variants in mycobacterial cultures under different growth conditions, including aging of the culture, have been shown to include fibrous aggregates, biofilms, coccoids, and spores. Here we discuss the diversity in shape and size changes demonstrated by bacterial cells with special reference to pleiomorphism observed in Mycobacterium spp. in response to nutritional and other environmental stresses. Inherent asymmetry in cell division and compartmentalization of cell interior under different growth conditions might contribute toward the observed pleiomorphism in mycobacteria. The regulatory genes comprising the bacterial signaling pathway responsible for initiating morphogenesis are speculated upon from bioinformatic identifications of genes for known sensors, kinases, and phosphatases existing in mycobacterial genomes as well as on the basis of what is known in other bacteria.
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67
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Manivasagan P, Nam SY, Oh J. Marine microorganisms as potential biofactories for synthesis of metallic nanoparticles. Crit Rev Microbiol 2016; 42:1007-19. [DOI: 10.3109/1040841x.2015.1137860] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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68
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Také A, Nakashima T, Inahashi Y, Shiomi K, Takahashi Y, Ōmura S, Matsumoto A. Analyses of the cell-wall peptidoglycan structures in three genera Micromonospora, Catenuloplanes, and Couchioplanes belonging to the family Micromonosporaceae by derivatization with FDLA and PMP using LC/MS. J GEN APPL MICROBIOL 2016; 62:199-205. [DOI: 10.2323/jgam.2016.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Akira Také
- Graduate School of Infection Control Sciences, Kitasato University
| | | | - Yuki Inahashi
- Kitasato Institute for Life Sciences, Kitasato University
| | - Kazuro Shiomi
- Graduate School of Infection Control Sciences, Kitasato University
- Kitasato Institute for Life Sciences, Kitasato University
| | - Yōko Takahashi
- Kitasato Institute for Life Sciences, Kitasato University
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University
| | - Atsuko Matsumoto
- Graduate School of Infection Control Sciences, Kitasato University
- Kitasato Institute for Life Sciences, Kitasato University
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69
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Barbie P, Kazmaier U. Total synthesis of desoxycyclomarin C and the cyclomarazines A and B. Org Biomol Chem 2016; 14:6055-64. [DOI: 10.1039/c6ob00801a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Removing the β-hydroxy group from the prenylated tryptophan moiety of cyclomarins simplifies the synthesis of these interesting natural products significantly, without having a noteworthy effect on the anti-tuberculosis activity of the cyclomarins.
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Affiliation(s)
- Philipp Barbie
- Institute of Organic Chemistry
- Saarland University
- 66041 Saarbrücken
- Germany
| | - Uli Kazmaier
- Institute of Organic Chemistry
- Saarland University
- 66041 Saarbrücken
- Germany
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70
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Actinobacteria and Myxobacteria—Two of the Most Important Bacterial Resources for Novel Antibiotics. Curr Top Microbiol Immunol 2016; 398:273-302. [DOI: 10.1007/82_2016_503] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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71
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Karuppiah V, Sun W, Li Z. Natural Products of Actinobacteria Derived from Marine Organisms. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2016. [DOI: 10.1016/b978-0-444-63602-7.00013-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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72
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Duran R, Bielen A, Paradžik T, Gassie C, Pustijanac E, Cagnon C, Hamer B, Vujaklija D. Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15215-29. [PMID: 25712885 DOI: 10.1007/s11356-015-4240-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/13/2015] [Indexed: 05/27/2023]
Abstract
The exploration of marine Actinobacteria has as major challenge to answer basic questions of microbial ecology that, in turn, will provide useful information to exploit Actinobacteria metabolisms in biotechnological processes. The ecological functions performed by Actinobacteria in marine sediments are still unclear and belongs to the most burning basic questions. The comparison of Actinobacteria communities inhabiting marine sediments that are under the influence of different contamination types will provide valuable information in the adaptation capacities of Actinobacteria to colonize specific ecological niche. In the present study, the characterization of different Actinobacteria assemblages according to contamination type revealed the ecological importance of Actinobacteria for maintaining both general biogeochemical functions through a "core" Actinobacteria community and specific roles associated with the presence of contaminants. Indeed, the results allowed to distinguish Actinobacteria genera and species operational taxonomic units (OTUs) able to cope with the presence of either (i) As, (ii) metals Ni, Fe, V, Cr, and Mn, or (iii) polycyclic aromatic hydrocarbons (PAHs) and toxic metals (Hg, Cd, Cu, Pb, and Zn). Such observations highlighted the metabolic capacities of Actinobacteria and their potential that should be taken into consideration and advantage during the implementation of bioremediation processes in marine ecosystems.
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Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
- Université de Pau et des Pays de l'Adour, Bâtiment IBEAS, BP1155, 64013, Pau Cedex, France.
| | - Ana Bielen
- Division of Molecular Biology, Institute Ruđer Bošković, Bijenička 54, 10000, Zagreb, Croatia
| | - Tina Paradžik
- Division of Molecular Biology, Institute Ruđer Bošković, Bijenička 54, 10000, Zagreb, Croatia
| | - Claire Gassie
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Emina Pustijanac
- Juraj Dobrila University of Pula, Zagrebačka 30, 52100, Pula, Croatia
| | - Christine Cagnon
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Bojan Hamer
- Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210, Rovinj, Croatia
| | - Dušica Vujaklija
- Division of Molecular Biology, Institute Ruđer Bošković, Bijenička 54, 10000, Zagreb, Croatia
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73
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Genome-scale reconstruction of Salinispora tropica CNB-440 metabolism to study strain-specific adaptation. Antonie van Leeuwenhoek 2015; 108:1075-90. [DOI: 10.1007/s10482-015-0561-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/18/2015] [Indexed: 12/22/2022]
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74
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Azman AS, Othman I, Velu SS, Chan KG, Lee LH. Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity. Front Microbiol 2015; 6:856. [PMID: 26347734 PMCID: PMC4542535 DOI: 10.3389/fmicb.2015.00856] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 08/06/2015] [Indexed: 11/13/2022] Open
Abstract
Actinobacteria are one of the most important and efficient groups of natural metabolite producers. The genus Streptomyces have been recognized as prolific producers of useful natural compounds as they produced more than half of the naturally-occurring antibiotics isolated to-date and continue as the primary source of new bioactive compounds. Lately, Streptomyces groups isolated from different environments produced the same types of compound, possibly due to frequent genetic exchanges between species. As a result, there is a dramatic increase in demand to look for new compounds which have pharmacological properties from another group of Actinobacteria, known as rare actinobacteria; which is isolated from special environments such as mangrove. Recently, mangrove ecosystem is becoming a hot spot for studies of bioactivities and the discovery of natural products. Many novel compounds discovered from the novel rare actinobacteria have been proven as potential new drugs in medical and pharmaceutical industries such as antibiotics, antimicrobials, antibacterials, anticancer, and antifungals. This review article highlights the latest studies on the discovery of natural compounds from the novel mangrove rare actinobacteria and provides insight on the impact of these findings.
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Affiliation(s)
- Adzzie-Shazleen Azman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
| | - Iekhsan Othman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
| | - Saraswati S Velu
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
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75
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Álvarez-Micó X, Rocha DD, Guimarães LA, Ambrose A, Chapman E, Costa-Lotufo LV, La Clair JJ, Fenical W. The Hybrid Pyrroloisoindolone-Dehydropyrrolizine Alkaloid (-)-Chlorizidine A Targets Proteins within the Glycolytic Pathway. Chembiochem 2015; 16:2002-6. [PMID: 26267855 DOI: 10.1002/cbic.201500229] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 01/25/2023]
Abstract
The cytotoxic activity of (-)-chlorizidine A, a marine alkaloid containing a unique fusion between a pyrroloisoindolone and dehydropyrrolizine, was explored by using a combination of cellular and molecular methods. Our studies began by applying preliminary SAR evidence gathered from semisynthetic bioactivity evaluations to prepare an active immunoaffinity fluorescent (IAF) probe. This probe was then used to identify two cytosolic proteins, GAPDH and hENO1, as the targets of (-)-chlorizidine A.
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Affiliation(s)
- Xavier Álvarez-Micó
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0204, USA
| | - Danilo D Rocha
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, CE, 60.430-270, Brazil
| | - Larissa A Guimarães
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, CE, 60.430-270, Brazil
| | - Andrew Ambrose
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, P.O. Box 210207, Tucson, AZ, 85721, USA
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, P.O. Box 210207, Tucson, AZ, 85721, USA
| | - Leticia V Costa-Lotufo
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, CE, 60.430-270, Brazil.,Departamento de Farmacologia, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093-0358, USA.
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0204, USA.
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76
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Patin NV, Duncan KR, Dorrestein PC, Jensen PR. Competitive strategies differentiate closely related species of marine actinobacteria. ISME JOURNAL 2015; 10:478-90. [PMID: 26241505 DOI: 10.1038/ismej.2015.128] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/26/2015] [Accepted: 06/18/2015] [Indexed: 01/12/2023]
Abstract
Although competition, niche partitioning, and spatial isolation have been used to describe the ecology and evolution of macro-organisms, it is less clear to what extent these principles account for the extraordinary levels of bacterial diversity observed in nature. Ecological interactions among bacteria are particularly challenging to address due to methodological limitations and uncertainties over how to recognize fundamental units of diversity and link them to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies. Using a direct challenge assay to investigate inhibitory interactions with members of the bacterial community, we observed a temporal difference in the onset of inhibition. The majority of inhibitory activity exhibited by Salinispora arenicola occurred early in its growth cycle and was linked to antibiotic production. In contrast, most inhibition by Salinispora tropica occurred later in the growth cycle and was more commonly linked to nutrient depletion or other sources. Comparative genomics support these differences, with S. arenicola containing nearly twice the number of secondary metabolite biosynthetic gene clusters as S. tropica, indicating a greater potential for secondary metabolite production. In contrast, S. tropica is enriched in gene clusters associated with the acquisition of growth-limiting nutrients such as iron. Coupled with differences in growth rates, the results reveal that S. arenicola uses interference competition at the expense of growth, whereas S. tropica preferentially employs a strategy of exploitation competition. The results support the ecological divergence of two co-occurring and closely related species of marine bacteria by providing evidence they have evolved fundamentally different strategies to compete in marine sediments.
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Affiliation(s)
- Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Katherine R Duncan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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77
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Claverías FP, Undabarrena A, González M, Seeger M, Cámara B. Culturable diversity and antimicrobial activity of Actinobacteria from marine sediments in Valparaíso bay, Chile. Front Microbiol 2015; 6:737. [PMID: 26284034 PMCID: PMC4516979 DOI: 10.3389/fmicb.2015.00737] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022] Open
Abstract
Marine-derived Actinobacteria are a source of a broad variety of secondary metabolites with diverse biological activities, such as antibiotics and antitumorals; many of which have been developed for clinical use. Rare Actinobacteria represent an untapped source of new bioactive compounds that have been scarcely recognized. In this study, rare Actinobacteria from marine sediments were isolated from the Valparaíso bay, Chile, and their potential to produce antibacterial compounds was evaluated. Different culture conditions and selective media that select the growth of Actinobacteria were used leading to the isolation of 68 bacterial strains. Comparative analysis of the 16S rRNA gene sequences led to identifying isolates that belong to the phylum Actinobacteria with genetic affiliations to 17 genera: Aeromicrobium, Agrococcus, Arthrobacter, Brachybacterium, Corynebacterium, Dietzia, Flaviflexus, Gordonia, Isoptericola, Janibacter, Microbacterium, Mycobacterium, Ornithinimicrobium, Pseudonocardia, Rhodococcus, Streptomyces, and Tessaracoccus. Also, one isolate could not be consistently classified and formed a novel phylogenetic branch related to the Nocardiopsaceae family. The antimicrobial activity of these isolates was evaluated, demonstrating the capability of specific novel isolates to inhibit the growth of Gram-positive and Gram-negative bacteria. In conclusion, this study shows a rich biodiversity of culturable Actinobacteria, associated to marine sediments from Valparaíso bay, highlighting novel rare Actinobacteria, and their potential for the production of biologically active compounds.
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Affiliation(s)
| | | | | | | | - Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
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78
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Yousif G, Busarakam K, Kim BY, Goodfellow M. Streptomyces mangrovi sp. nov., isolated from mangrove forest sediment. Antonie van Leeuwenhoek 2015; 108:783-91. [DOI: 10.1007/s10482-015-0533-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/11/2015] [Indexed: 02/06/2023]
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79
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Komaki H, Tamura T, Ichikawa N, Oguchi A, Hamada M, Suzuki KI, Fujita N. Genome-based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in a novel strain taxonomically close to the genus Salinispora. J Antibiot (Tokyo) 2015; 68:767-70. [PMID: 26126742 DOI: 10.1038/ja.2015.69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/03/2015] [Accepted: 05/17/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation, Chiba, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation, Chiba, Japan
| | - Natsuko Ichikawa
- Biological Resource Center, National Institute of Technology and Evaluation, Tokyo, Japan
| | - Akio Oguchi
- Biological Resource Center, National Institute of Technology and Evaluation, Tokyo, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation, Chiba, Japan
| | - Ken-Ichiro Suzuki
- Biological Resource Center, National Institute of Technology and Evaluation, Chiba, Japan
| | - Nobuyuki Fujita
- Biological Resource Center, National Institute of Technology and Evaluation, Tokyo, Japan
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80
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Fang Y, Wang S, Liu S, Jiao Y. Discovery a novel organic solvent tolerant esterase from Salinispora arenicola CNP193 through genome mining. Int J Biol Macromol 2015; 80:334-40. [PMID: 26118483 DOI: 10.1016/j.ijbiomac.2015.06.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 12/15/2022]
Abstract
An esterase gene, encoding a 325-amino-acid protein (SAestA), was mined form obligate marine actinomycete strain Salinispora arenicola CNP193 genome sequence. Phylogenetic analysis of the deduced amino acid sequence showed that the enzyme belonged to the family IV of lipolytic enzymes. The gene was cloned, expressed in Escherichia coli as a His-tagged protein, purified and characterized. The molecular weight of His-tagged SAestA is ∼38 kDa. SAestA-His6 was active in a temperature (5-40 °C) and pH range (7.0-11.0), and maximal activity was determined at pH 9.0 and 30 °C. The activity was severely inhibited by Hg(2+), Cu(2+), and Zn(2+). In particular, this enzyme showed remarkable stability in presence of organic solvents (25%, v/v) with log P>2.0 even after incubation for 7 days. All these characteristics suggested that SAestA may be a potential candidate for application in industrial processes in aqueous/organic media.
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Affiliation(s)
- Yaowei Fang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang, 222005, China; Jiangsu Marine Resources Development Research Institute, Lianyungang, 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang, 222005, China; Jiangsu Marine Resources Development Research Institute, Lianyungang, 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Shu Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang, 222005, China; Jiangsu Marine Resources Development Research Institute, Lianyungang, 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Yuliang Jiao
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang, 222005, China; Jiangsu Marine Resources Development Research Institute, Lianyungang, 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
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81
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Jensen PR, Moore BS, Fenical W. The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery. Nat Prod Rep 2015; 32:738-51. [PMID: 25730728 PMCID: PMC4414829 DOI: 10.1039/c4np00167b] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review covers the initial discovery of the marine actinomycete genus Salinispora through its development as a model for natural product research. A focus is placed on the novel chemical structures reported with reference to their biological activities and the synthetic and biosynthetic studies they have inspired. The time line of discoveries progresses from more traditional bioassay-guided approaches through the application of genome mining and genetic engineering techniques that target the products of specific biosynthetic gene clusters. This overview exemplifies the extraordinary biosynthetic diversity that can emanate from a narrowly defined genus and supports future efforts to explore marine taxa in the search for novel natural products.
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Affiliation(s)
- Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.
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82
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Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. ACTA ACUST UNITED AC 2015; 22:460-471. [PMID: 25865308 DOI: 10.1016/j.chembiol.2015.03.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/26/2015] [Accepted: 03/10/2015] [Indexed: 12/12/2022]
Abstract
Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.
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Affiliation(s)
- Katherine R Duncan
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Max Crüsemann
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Anna Lechner
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Anindita Sarkar
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Jie Li
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Nadine Ziemert
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Paul R Jensen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA.
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83
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Valan AM, Asha KRT, Duraipandiyan V, Ignacimuthu S, Agastian P. Characterization and phylogenetic analysis of novel polyene type antimicrobial metabolite producing actinomycetes from marine sediments: Bay of Bengal, India. Asian Pac J Trop Biomed 2015; 2:803-10. [PMID: 23569851 DOI: 10.1016/s2221-1691(12)60233-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 04/27/2011] [Accepted: 06/28/2011] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE To isolate and indentify the promising antimicrobial metabolite producing Streptomyces strains from marine sediment samples from Andrapradesh coast of India. METHODS Antagonistic actinomycetes were isolated by starch casein agar medium and modified nutrient agar medium with 1% glucose used as a base for primary screening. Significant antimicrobial metabolite producing strains were selected and identified by using biochemical and 16S rDNA level. Minimum inhibitory concentrations of the organic extracts were done by using broth micro dilution method. RESULTS Among the 210 actinomycetes, 64.3% exhibited activity against Gram positive bacteria, 48.5 % showed activity towards Gram negative bacteria, 38.8% exhibited both Gram positive and negative bacteria and 80.85 % isolates revealed significant antifungal activity. However, five isolates AP-5, AP-18, AP-41 and AP-70 showed significant antimicrobial activity. The analysis of cell wall hydrolysates showed the presence of LL-diaminopimelic acid and glycine in all the isolates. Sequencing analysis indicated that the isolates shared 98.5%-99.8% sequence identity to the 16S rDNA gene sequences of the Streptomyces taxons. The antimicrobial substances were extracted using hexane and ethyl acetate from spent medium in which strains were cultivated at 30°Cfor five days. The antimicrobial activity was assessed using broth micro dilution technique. Each of the culture extracts from these five strains showed a typical polyene-like property. The lowest minimum inhibitory concentrations of ethyl acetate extracts against Escherichia coli and Curvularia lunata were 67.5 and 125.0 µg/mL, respectively. CONCLUSIONS It can be concluded that hexane and ethyl acetate soluble extracellular products of novel isolates are effective against pathogenic bacteria and fungi.
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Affiliation(s)
- Arasu M Valan
- Division of Microbiology, Entomology Research Institute, Loyola College, Chennai, India
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84
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Bonet B, Teufel R, Crüsemann M, Ziemert N, Moore BS. Direct capture and heterologous expression of Salinispora natural product genes for the biosynthesis of enterocin. JOURNAL OF NATURAL PRODUCTS 2015; 78:539-42. [PMID: 25382643 PMCID: PMC4380194 DOI: 10.1021/np500664q] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Heterologous expression of secondary metabolic pathways is a promising approach for the discovery and characterization of bioactive natural products. Herein we report the first heterologous expression of a natural product from the model marine actinomycete genus Salinispora. Using the recently developed method of yeast-mediated transformation-associated recombination for natural product gene clusters, we captured a type II polyketide synthase pathway from Salinispora pacifica with high homology to the enterocin pathway from Streptomyces maritimus and successfully produced enterocin in two different Streptomyces host strains. This result paves the way for the systematic interrogation of Salinispora's promising secondary metabolome.
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Affiliation(s)
- Bailey Bonet
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Robin Teufel
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Max Crüsemann
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Nadine Ziemert
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
- E-mail:
| | - Bradley S. Moore
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- E-mail:
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85
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Schulze CJ, Navarro G, Ebert D, DeRisi J, Linington RG. Salinipostins A–K, Long-Chain Bicyclic Phosphotriesters as a Potent and Selective Antimalarial Chemotype. J Org Chem 2015; 80:1312-20. [DOI: 10.1021/jo5024409] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Christopher J. Schulze
- 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
| | - Daniel Ebert
- Department
of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States
| | - Joseph DeRisi
- Department
of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States
| | - Roger G. Linington
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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86
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LC-MS-based metabolomics study of marine bacterial secondary metabolite and antibiotic production in Salinispora arenicola. Mar Drugs 2015; 13:249-66. [PMID: 25574739 PMCID: PMC4306935 DOI: 10.3390/md13010249] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/29/2014] [Indexed: 01/06/2023] Open
Abstract
An LC-MS-based metabolomics approach was used to characterise the variation in secondary metabolite production due to changes in the salt content of the growth media as well as across different growth periods (incubation times). We used metabolomics as a tool to investigate the production of rifamycins (antibiotics) and other secondary metabolites in the obligate marine actinobacterial species Salinispora arenicola, isolated from Great Barrier Reef (GBR) sponges, at two defined salt concentrations and over three different incubation periods. The results indicated that a 14 day incubation period is optimal for the maximum production of rifamycin B, whereas rifamycin S and W achieve their maximum concentration at 29 days. A "chemical profile" link between the days of incubation and the salt concentration of the growth medium was shown to exist and reliably represents a critical point for selection of growth medium and harvest time.
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87
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Hamedi J, Mohammadipanah F, Panahi HKS. Biotechnological Exploitation of Actinobacterial Members. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2015. [DOI: 10.1007/978-3-319-14595-2_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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88
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Richter TKS, Hughes CC, Moore BS. Sioxanthin, a novel glycosylated carotenoid, reveals an unusual subclustered biosynthetic pathway. Environ Microbiol 2014; 17:2158-71. [PMID: 25329237 DOI: 10.1111/1462-2920.12669] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/26/2014] [Accepted: 10/12/2014] [Indexed: 01/30/2023]
Abstract
Members of the marine actinomycete genus Salinispora constitutively produce a characteristic orange pigment during vegetative growth. Contrary to the understanding of widespread carotenoid biosynthesis pathways in bacteria, Salinispora carotenoid biosynthesis genes are not confined to a single cluster. Instead, bioinformatic and genetic investigations confirm that four regions of the Salinispora tropica CNB-440 genome, consisting of two gene clusters and two independent genes, contribute to the in vivo production of a single carotenoid. This compound, namely (2'S)-1'-(β-D-glucopyranosyloxy)-3',4'-didehydro-1',2'-dihydro-φ,ψ-caroten-2'-ol, is novel and has been given the trivial name 'sioxanthin'. Sioxanthin is a C40 -carotenoid, glycosylated on one end of the molecule and containing an aryl moiety on the opposite end. Glycosylation is unusual among actinomycete carotenoids, and sioxanthin joins a rare group of carotenoids with polar and non-polar head groups. Gene sequence homology predicts that the sioxanthin biosynthetic pathway is present in all of the Salinispora as well as other members of the family Micromonosporaceae. Additionally, this study's investigations of clustering of carotenoid biosynthetic genes in heterotrophic bacteria show that a non-clustered genome arrangement is more common than previously suggested, with nearly half of the investigated genomes showing a non-clustered architecture.
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Affiliation(s)
- Taylor K S Richter
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Chambers C Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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89
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Bioactive Potential of Actinomycetes from Less Explored Ecosystems against Mycobacterium tuberculosis and Other Nonmycobacterial Pathogens. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:812974. [PMID: 27437460 PMCID: PMC4897172 DOI: 10.1155/2014/812974] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 10/20/2014] [Indexed: 11/17/2022]
Abstract
Bioactive potential of actinomycetes isolated from certain less explored Indian ecosystems against Mycobacterium tuberculosis and other nonmycobacterial pathogens was investigated. Actinomycetes were isolated from the soil samples collected from desert, coffee plantation, rubber forest, and hill area and their cultural and micromorphological characteristics were studied. Crude extracts were prepared by agar surface fermentation and tested against M. tuberculosis isolates by luciferase reporter phage (LRP) assay at 100 µg/mL. Activity against nonmycobacterial pathogens was studied by agar plug method. Totally 54 purified cultures of actinomycetes including 43 Streptomyces and 11 non-Streptomyces were isolated. While screening for antitubercular activity, extracts of 39 actinomycetes showed activity against one or more M. tuberculosis isolates whereas 27 isolates exhibited antagonistic activity against nonmycobacterial pathogens. In particular crude extracts from sixteen actinomycete isolates inhibited all the three M. tuberculosis isolates tested. Findings of the present study concluded that less explored ecosystems investigated in this study are the potential resource for bioactive actinomycetes. Further purification and characterization of active molecule from the potential extracts will pave the way for determination of MIC, toxicity, and specificity studies.
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90
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Singh S, Prasad P, Subramani R, Aalbersberg W. Production and purification of a bioactive substance against multi-drug resistant human pathogens from the marine-sponge-derived Salinispora sp. Asian Pac J Trop Biomed 2014. [DOI: 10.12980/apjtb.4.2014c1154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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91
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Liu M, Zhang L, Ren B, Yang N, Yu X, Wang J, Ding L, Liu X, Liu Z, Goodfellow M, Zhang L. Prauserella shujinwangii sp. nov., from a desert environment. Int J Syst Evol Microbiol 2014; 64:3833-3837. [PMID: 25158847 DOI: 10.1099/ijs.0.065425-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, spore-forming, rod-shaped actinomycete, designated XJ46(T), was isolated from Xinjiang Uyghur Autonomous Region, China and subjected to a polyphasic taxonomic analysis. Morphological and chemotaxonomic characteristics of XJ46(T) were identified as being similar to those of members of the genus Prauserella. The phylogenetic tree based on 16S rRNA gene sequences showed that XJ46(T) shared the highest similarity (95.9%) with Prauserella marina MS498(T). Based on its phenotypic characteristics, chemotaxonomic analysis and 16S rRNA gene sequence analysis, strain XJ46(T) is proposed to represent a novel species of the genus Prauserella, named Prauserella shujinwangii sp. nov. The type strain is XJ46(T) ( =CGMCC 4.7125(T) =JCM 19736(T)).
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Affiliation(s)
- Mei Liu
- University of Chinese Academy of Sciences, Beijing, 100049, PR China.,Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Li Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, PR China.,Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Biao Ren
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Na Yang
- University of Chinese Academy of Sciences, Beijing, 100049, PR China.,Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Xiaoyun Yu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, PR China.,Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Jian Wang
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Linxian Ding
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, PR China.,College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, PR China
| | - Xueting Liu
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Zhiheng Liu
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Michael Goodfellow
- Division of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Lixin Zhang
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
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92
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Ng YK, Hodson MP, Hewavitharana AK, Bose U, Shaw PN, Fuerst JA. Effects of salinity on antibiotic production in sponge-derived Salinispora actinobacteria. J Appl Microbiol 2014; 117:109-25. [PMID: 24684523 DOI: 10.1111/jam.12507] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 03/02/2014] [Accepted: 03/14/2014] [Indexed: 11/28/2022]
Abstract
AIMS To investigate the effects of growth conditions related to marine habitat on antibiotic production in sponge-derived Salinispora actinobacteria. METHODS AND RESULTS Media with varying salt concentration were used to investigate the effects of salinity in relation to Salinispora growth and rifamycin production. The chemotypic profiles of the model strain Salinispora arenicola M413 was then assessed using metabolomic fingerprints from high-pressure liquid chromatography with diode array detection (HPLC-DAD) and multivariate data analysis, before extending this approach to two other strains of S. arenicola. Fingerprint data were generated from extracts of S. arenicola broth cultures grown in media of varying salt (NaCl) concentrations. These fingerprints were then compared using multivariate analysis methods such as principal components analysis (PCA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA). From the analysis, a low-sodium growth condition (1% NaCl) was found to delay the onset of growth of the model S. arenicola M413 strain when compared to growth in media with either 3% artificial sea salt or 3% NaCl. However, low-sodium growth conditions also increased cell mass yield and contributed to at least a significant twofold increase in rifamycin yield when compared to growth in 3% artificial sea salt and 3% NaCl. CONCLUSIONS The integration of HPLC-DAD and multivariate analysis proved to be an effective method of assessing chemotypic variations in Salinispora grown in different salt conditions, with clear differences between strain-related chemotypes apparent due to varying salt concentrations. SIGNIFICANCE AND IMPACT OF THE STUDY The observed variation in S. arenicola chemotypic profiles further suggests diversity in secondary metabolites in this actinomycete in response to changes in the salinity of its environment.
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Affiliation(s)
- Y K Ng
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia
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93
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Bose U, Hewavitharana AK, Vidgen ME, Ng YK, Shaw PN, Fuerst JA, Hodson MP. Discovering the recondite secondary metabolome spectrum of Salinispora species: a study of inter-species diversity. PLoS One 2014; 9:e91488. [PMID: 24621594 PMCID: PMC3951395 DOI: 10.1371/journal.pone.0091488] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/11/2014] [Indexed: 12/23/2022] Open
Abstract
Patterns of inter-species secondary metabolite production by bacteria can provide valuable information relating to species ecology and evolution. The complex nature of this chemical diversity has previously been probed via directed analyses of a small number of compounds, identified through targeted assays rather than more comprehensive biochemical profiling approaches such as metabolomics. Insights into ecological and evolutionary relationships within bacterial genera can be derived through comparative analysis of broader secondary metabolite patterns, and this can also eventually assist biodiscovery search strategies for new natural products. Here, we investigated the species-level chemical diversity of the two marine actinobacterial species Salinispora arenicola and Salinispora pacifica, isolated from sponges distributed across the Great Barrier Reef (GBR), via their secondary metabolite profiles using LC-MS-based metabolomics. The chemical profiles of these two species were obtained by UHPLC-QToF-MS based metabolic profiling. The resultant data were interrogated using multivariate data analysis methods to compare their (bio)chemical profiles. We found a high level of inter-species diversity in strains from these two bacterial species. We also found rifamycins and saliniketals were produced exclusively by S. arenicola species, as the main secondary metabolites differentiating the two species. Furthermore, the discovery of 57 candidate compounds greatly increases the small number of secondary metabolites previously known to be produced by these species. In addition, we report the production of rifamycin O and W, a key group of ansamycin compounds, in S. arenicola for the first time. Species of the marine actinobacteria harbour a much wider spectrum of secondary metabolites than suspected, and this knowledge may prove a rich field for biodiscovery as well as a database for understanding relationships between speciation, evolution and chemical ecology.
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Affiliation(s)
- Utpal Bose
- School of Pharmacy, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Miranda E. Vidgen
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Yi Kai Ng
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - P. Nicholas Shaw
- School of Pharmacy, The University of Queensland, Brisbane, Queensland, Australia
| | - John A. Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark P. Hodson
- Metabolomics Australia, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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94
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Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora. Proc Natl Acad Sci U S A 2014; 111:E1130-9. [PMID: 24616526 DOI: 10.1073/pnas.1324161111] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Access to genome sequence data has challenged traditional natural product discovery paradigms by revealing that the products of most bacterial biosynthetic pathways have yet to be discovered. Despite the insight afforded by this technology, little is known about the diversity and distributions of natural product biosynthetic pathways among bacteria and how they evolve to generate structural diversity. Here we analyze genome sequence data derived from 75 strains of the marine actinomycete genus Salinispora for pathways associated with polyketide and nonribosomal peptide biosynthesis, the products of which account for some of today's most important medicines. The results reveal high levels of diversity, with a total of 124 pathways identified and 229 predicted with continued sequencing. Recent horizontal gene transfer accounts for the majority of pathways, which occur in only one or two strains. Acquired pathways are incorporated into genomic islands and are commonly exchanged within and between species. Acquisition and transfer events largely involve complete pathways, which subsequently evolve by gene gain, loss, and duplication followed by divergence. The exchange of similar pathway types at the precise chromosomal locations in different strains suggests that the mechanisms of integration include pathway-level homologous recombination. Despite extensive horizontal gene transfer there is clear evidence of species-level vertical inheritance, supporting the concept that secondary metabolites represent functional traits that help define Salinispora species. The plasticity of the Salinispora secondary metabolome provides an effective mechanism to maximize population-level secondary metabolite diversity while limiting the number of pathways maintained within any individual genome.
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95
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Diversity and novelty of actinobacteria in Arctic marine sediments. Antonie van Leeuwenhoek 2014; 105:743-54. [PMID: 24519808 DOI: 10.1007/s10482-014-0130-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/29/2014] [Indexed: 01/17/2023]
Abstract
The actinobacterial diversity of Arctic marine sediments was investigated using culture-dependent and culture-independent approaches. A total of 152 strains were isolated from seven different media; 18 isolates were selected for phylogenetic analysis on the basis of their 16S rRNA gene sequences. Results showed that the 18 isolates belonged to a potential novel genus and 10 known genera including Actinotalea, Arthrobacter, Brachybacterium, Brevibacterium, Kocuria, Kytococcus, Microbacterium, Micrococcus, Mycobacterium, and Pseudonocardia. Subsequently, 172 rDNA clones were selected by restriction fragment length polymorphism analysis from 692 positive clones within four actinobacteria-specific 16S rDNA libraries of Arctic marine sediments, and then these 172 clones were sequenced. In total, 67 phylotypes were clustered in 11 known genera of actinobacteria including Agrococcus, Cellulomonas, Demequina, Iamia, Ilumatobacter, Janibacter, Kocuria, Microbacterium, Phycicoccus, Propionibacterium, and Pseudonocardia, along with other, unidentified actinobacterial clones. Based on the detection of a substantial number of uncultured phylotypes showing low BLAST identities (<95 %), this study confirms that Arctic marine environments harbour highly diverse actinobacterial communities, many of which appear to be novel, uncultured species.
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96
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Abdelmohsen UR, Bayer K, Hentschel U. Diversity, abundance and natural products of marine sponge-associated actinomycetes. Nat Prod Rep 2014; 31:381-99. [DOI: 10.1039/c3np70111e] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review discusses the diversity, abundance and natural products repertoire of actinomycetes associated with marine sponges. Comprehensive phylogenetic analysis was carried out and qPCR data on actinomycete abundances in sponge ecosystems are presented.
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Affiliation(s)
- Usama Ramadan Abdelmohsen
- Department of Botany II
- Julius-von-Sachs-Institute for Biological Sciences
- University of Würzburg
- 97082 Würzburg, Germany
- Department of Pharmacognosy
| | - Kristina Bayer
- Department of Botany II
- Julius-von-Sachs-Institute for Biological Sciences
- University of Würzburg
- 97082 Würzburg, Germany
| | - Ute Hentschel
- Department of Botany II
- Julius-von-Sachs-Institute for Biological Sciences
- University of Würzburg
- 97082 Würzburg, Germany
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97
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Salinispora arenicola from temperate marine sediments: new intra-species variations and atypical distribution of secondary metabolic genes. Antonie van Leeuwenhoek 2013; 105:207-19. [DOI: 10.1007/s10482-013-0067-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 10/24/2013] [Indexed: 11/30/2022]
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98
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Allegra A, Alonci A, Gerace D, Russo S, Innao V, Calabrò L, Musolino C. New orally active proteasome inhibitors in multiple myeloma. Leuk Res 2013; 38:1-9. [PMID: 24239172 DOI: 10.1016/j.leukres.2013.10.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 10/17/2013] [Accepted: 10/20/2013] [Indexed: 12/25/2022]
Abstract
Bortezomib is the first proteasome inhibitor approved for the therapy of multiple myeloma (MM). Although Bortezomib has renovated the treatment of MM, a considerable proportion of subjects fail to respond to Bortezomib treatment and almost all patients relapse from this drug either alone or when used in combination therapies. However, the good clinical outcome of Bortezomib treatment in MM patients gave impulsion for the development of second generation proteasome inhibitors with the ambition of improving efficacy of proteasome inhibition, enhancing antitumor activity, and decreasing toxicity, as well as providing flexible dosing schedules and patient convenience. This review provides an overview of the role of oral proteasome inhibitors including Marizomib, Oprozomib, Delanzomib, chemical proteasome inhibitors, and cinnabaramides, in the therapy of MM, focusing on developments over the past five years. These emerging drugs with different mechanisms of action have exhibited promising antitumor activity in patients with relapsed/refractory MM, and they are creating chances to target multiple pathways, overcome resistance, and improve clinical outcomes, mainly for those subjects who are refractory to approved agents. Future steps in the clinical development of oral inhibitors include the optimization of the schedule and the definition of their antitumor activity in MM.
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Affiliation(s)
| | - Andrea Alonci
- Division of Hematology University of Messina, Messina, Italy
| | - Demetrio Gerace
- Division of Hematology University of Messina, Messina, Italy
| | - Sabina Russo
- Division of Hematology University of Messina, Messina, Italy
| | - Vanessa Innao
- Division of Hematology University of Messina, Messina, Italy
| | - Laura Calabrò
- Division of Hematology University of Messina, Messina, Italy
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99
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Challenges and triumphs to genomics-based natural product discovery. J Ind Microbiol Biotechnol 2013; 41:203-9. [PMID: 24104399 DOI: 10.1007/s10295-013-1353-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 09/18/2013] [Indexed: 12/16/2022]
Abstract
Genome sequencing is rapidly changing the field of natural products research by providing opportunities to assess the biosynthetic potential of strains prior to chemical analysis or biological testing. Ready access to sequence data is driving the development of new bioinformatic tools and methods to identify the products of silent or cryptic pathways. While genome mining has fast become a useful approach to natural product discovery, it has also become clear that identifying pathways of interest is much easier than finding the associated products. This has led to bottlenecks in the discovery process that must be overcome for the potential of genomics-based natural product discovery to be fully realized. In this perspective, we address some of these challenges in the context of our work with the marine actinomycete genus Salinispora, which is proving to be a useful model with which to apply genome mining as an approach to natural product discovery.
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100
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Jiao W, Zhang F, Zhao X, Hu J, Suh JW. A novel alkaloid from marine-derived actinomycete Streptomyces xinghaiensis with broad-spectrum antibacterial and cytotoxic activities. PLoS One 2013; 8:e75994. [PMID: 24098415 PMCID: PMC3787992 DOI: 10.1371/journal.pone.0075994] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/19/2013] [Indexed: 01/16/2023] Open
Abstract
Due to the increasing emergence of drug-resistant bacteria and tumor cell lines, novel antibiotics with antibacterial and cytotoxic activities are urgently needed. Marine actinobacteria are rich sources of novel antibiotics, and here we report the discovery of a novel alkaloid, xinghaiamine A, from a marine-derived actinomycete Streptomyces xinghaiensis NRRL B24674T. Xinghaiamine A was purified from the fermentation broth, and its structure was elucidated based on extensive spectroscopic analysis, including 1D and 2D NMR spectrum as well as mass spectrometry. Xinghaiamine A was identified to be a novel alkaloid with highly symmetric structure on the basis of sulfoxide functional group, and sulfoxide containing compound has so far never been reported in microorganisms. Biological assays revealed that xinghaiamine A exhibited broad-spectrum antibacterial activities to both Gram-negative persistent hospital pathogens (e.g. Acinetobacter baumannii, Pseudomonas aeruginosa and Escherichia coli) and Gram-positive ones, which include Staphylococcus aureus and Bacillus subtilis. In addition, xinghaiamine A also exhibited potent cytotoxic activity to human cancer cell lines of MCF-7 and U-937 with the IC50 of 0.6 and 0.5 µM, respectively.
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Affiliation(s)
- Wence Jiao
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Fenghua Zhang
- First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xinqing Zhao
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
- * E-mail:
| | - Jiehan Hu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Joo-Won Suh
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Korea
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