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Hu D, Zhang T, He S, Pu T, Yin Y, Hu Y. Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals. Microbiol Spectr 2024; 12:e0086424. [PMID: 39162518 DOI: 10.1128/spectrum.00864-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/14/2024] [Indexed: 08/21/2024] Open
Abstract
Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe-host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell-cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.IMPORTANCEThe gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host's physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.
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Affiliation(s)
- Dini Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Shunfu He
- Xining Wildlife Zoo, Xining, Qinghai, China
| | | | | | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Kusuma AB, Fenylestari G, Ammar F, Nououi I, Goodfellow M. Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus electrodiphilus (Ramaprasad et al. 2018) as a later heterotypic synonym of Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980). Int J Syst Evol Microbiol 2024; 74. [PMID: 38214280 DOI: 10.1099/ijsem.0.006236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
A polyphasic study was designed to determine the taxonomic status of isolate CSLK01-03T, which was recovered from an Indonesian neutral hot spring and provisionally assigned to the genus Rhodococcus. The isolate was found to have chemotaxonomic, cultural and morphological properties typical of rhodococci. It has a rod-coccus lifecycle and grows from 10 to 39 °C, from pH 6.5 to 8.0 and in the presence of 0-10 % (w/v) sodium chloride. Whole-organism hydrolysates contain meso-diaminopimelic acid, arabinose and galactose, the predominant menaquinone is MK-8 (H2), the polar lipid pattern consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylmethylethanolamine and two unidentified components, it produces mycolic acids, and C16:0 is the major fatty acid. Whole-genome analyses show that the isolate and Rhodococcus electrodiphilus LMG 29881T (GenBank accession: JAULCK000000000) have genome sizes of 5.5 and 5.1 Mbp, respectively. These strains and Rhodococcus aetherivorans DSM 44752T and Rhodococcus ruber DSM 43338T form well-supported lineages in 16S rRNA and whole-genome trees that are close to sister lineages composed of the type strains of Rhodococcus rhodochrous and related Rhodococcus species. The isolate can be distinguished from its closest evolutionary neighbours using combinations of cultural and phenotypic features, and by low DNA-DNA hybridization values. Based on these data it is proposed that isolate CSLK01-03T (=CCMM B1310T=ICEBB-06T=NCIMB 15214T) be classified in the genus Rhodococcus as Rhodococcus indonesiensis sp. nov. The genomes of the isolate and its closest phylogenomic relatives are rich in biosynthetic gene clusters with the potential to synthesize new natural products, notably antibiotics. In addition, whole-genome-based taxonomy revealed that Rhodococcus electrodiphilus LMG 29881T and Rhodococcus ruber DSM 43338T belong to a single species. It is, therefore, proposed that R. electrodiphilus be recognized as a heterotypic synonym of R. ruber.
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Affiliation(s)
- Ali Budhi Kusuma
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Indonesian Centre for Extremophile Bioresources and Biotechnology (ICEBB), Faculty of Life Sciences and Technology, Sumbawa University of Technology, Sumbawa Besar, 84371, Indonesia
- PT. Archipelago Biotechnology Indonesia (Archi Biotech), Sumbawa Besar, 84316, Indonesia
| | - Gita Fenylestari
- PT. Archipelago Biotechnology Indonesia (Archi Biotech), Sumbawa Besar, 84316, Indonesia
- Department of Research, Innovation and Development, Sumbawa Technopark (STP), Sumbawa Besar, 84371, Indonesia
| | - Fadhil Ammar
- PT. Archipelago Biotechnology Indonesia (Archi Biotech), Sumbawa Besar, 84316, Indonesia
- Department of Research, Innovation and Development, Sumbawa Technopark (STP), Sumbawa Besar, 84371, Indonesia
| | - Imen Nououi
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Imhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Shen Y, Bai X, Zhou X, Wang J, Guo N, Deng Y. Whole-Genome Analysis of Starmerella bacillaris CC-PT4 against MRSA, a Non- Saccharomyces Yeast Isolated from Grape. J Fungi (Basel) 2022; 8:1255. [PMID: 36547588 PMCID: PMC9784136 DOI: 10.3390/jof8121255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Starmerella bacillaris is often isolated from environments associated with grape and winemaking. S. bacillaris has many beneficial properties, including the ability to improve the flavor of wine, the production of beneficial metabolites, and the ability to biocontrol. S. bacillaris CC-PT4 (CGMCC No. 23573) was isolated from grape and can inhibit methicillin-resistant Staphylococcus aureus and adaptability to harsh environments. In this paper, the whole genome of S. bacillaris CC-PT4 was sequenced and bioinformatics analyses were performed. The S. bacillaris CC-PT4 genome was finally assembled into five scaffolds with a genome size of 9.45 Mb and a GC content of 39.5%. It was predicted that the strain contained 4150 protein-coding genes, of which two genes encoded killer toxin and one gene encoded lysostaphin. It also contains genes encoding F1F0-ATPases, Na(+)/H(+) antiporter, cation/H(+) antiporter, ATP-dependent bile acid permease, major facilitator superfamily (MFS) antiporters, and stress response protein, which help S. bacillaris CC-PT4 adapt to bile, acid, and other stressful environments. Proteins related to flocculation and adhesion have also been identified in the S. bacillaris CC-PT4 genome. Predicted by antiSMASH, two secondary metabolite biosynthesis gene clusters were found, and the synthesized metabolites may have antimicrobial effects. Furthermore, S. bacillaris CC-PT4 carried genes associated with pathogenicity and drug resistance. Overall, the whole genome sequencing and analysis of S. bacillaris CC-PT4 in this study provide valuable information for understanding the biological characteristics and further development of this strain.
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Affiliation(s)
- Yong Shen
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Xue Bai
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Xiran Zhou
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Jiaxi Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Na Guo
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Yanhong Deng
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
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Saricaoglu S, Saygin H, Topkara AR, Gencbay T, Guven K, Cetin D, Sahin N, Isik K. Actinomadura soli sp. nov., isolated from the top soil layer on basaltic material in Turkey. Int J Syst Evol Microbiol 2021; 71. [PMID: 34705623 DOI: 10.1099/ijsem.0.005062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinobacterium, designated 14C53T, was isolated from a soil sample on basaltic material from Samsun, Turkey. The growth ranges for NaCl concentration and pH of strain 14C53T were quite limited and the growth temperature range of the strain was 20-37 °C, with an optimum at 28 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain 14C53T was most closely related to Actinomadura geliboluensis A8036T (98.5 % similarity value), but in the phylogenetic tree, it formed a clade with Actinomadura alkaliterrae D310AT. The genome tree revealed a close relationship between the strain and Actinomadura pelletieri DSM 43383T. However, the digital DNA-DNA hybridization and average nucleotide identity values between strain 14C53T with Actinomadura geliboluensis A8036T and Actinomadura pelletieri DSM 43383T were 28.6-30.2 % and 84.3-85.5 %, respectively, and comparative analyses based on the genome sequences demonstrated that it represents a novel species of the genus Actinomadura. The genome size of strain 14C53T was approximately 9.0 Mb and the genomic DNA G+C content of the strain was 71.3 mol%. The major cellular fatty acids of strain 14C53T were C16 : 0 and iso-C16 : 0. Strain 14C53T contained meso-diaminopimelic acid as the diamino acid in the cell-wall peptidoglycan. The predominant menaquinones were MK-9(H8) and MK-9(H6). Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, a novel species Actinomadura soli sp. nov. is proposed, with 14C53T (=DSM 104447T=KCTC 39878T) as the type strain.
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Affiliation(s)
- Salih Saricaoglu
- Department of Basic Sciences, Faculty of Dentistry, Cankiri Karatekin University, 18200 Cankiri, Turkey
| | - Hayrettin Saygin
- Department of Molecular Biology and Genetics, Faculty of Sciences and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
| | - Ahmet Ridvan Topkara
- Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
| | - Talha Gencbay
- Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
| | - Kiymet Guven
- Department of Biology, Faculty of Science, Eskisehir Technical University, 26555 Eskisehir, Turkey
| | - Demet Cetin
- Division of Science Education, Department of Mathematics and Science Education, Gazi Faculty of Education, Gazi University, 06500 Ankara, Turkey
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Sciences and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
| | - Kamil Isik
- Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
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Baikalomycins A-C, New Aquayamycin-Type Angucyclines Isolated from Lake Baikal Derived Streptomyces sp. IB201691-2A. Microorganisms 2020; 8:microorganisms8050680. [PMID: 32392775 PMCID: PMC7284819 DOI: 10.3390/microorganisms8050680] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 01/06/2023] Open
Abstract
Natural products produced by bacteria found in unusual and poorly studied ecosystems, such as Lake Baikal, represent a promising source of new valuable drug leads. Here we report the isolation of a new Streptomyces sp. strain IB201691-2A from the Lake Baikal endemic mollusk Benedictia baicalensis. In the course of an activity guided screening three new angucyclines, named baikalomycins A–C, were isolated and characterized, highlighting the potential of poorly investigated ecological niches. Besides that, the strain was found to accumulate large quantities of rabelomycin and 5-hydroxy-rabelomycin, known shunt products in angucyclines biosynthesis. Baikalomycins A–C demonstrated varying degrees of anticancer activity. Rabelomycin and 5-hydroxy-rabelomycin further demonstrated antiproliferative activities. The structure elucidation showed that baikalomycin A is a modified aquayamycin with β-d-amicetose and two additional hydroxyl groups at unusual positions (6a and 12a) of aglycone. Baikalomycins B and C have alternating second sugars attached, α-l-amicetose and α-l-aculose, respectively. The gene cluster for baikalomycins biosynthesis was identified by genome mining, cloned using a transformation-associated recombination technique and successfully expressed in S. albus J1074. It contains a typical set of genes responsible for an angucycline core assembly, all necessary genes for the deoxy sugars biosynthesis, and three genes coding for the glycosyltransferase enzymes. Heterologous expression and deletion experiments allowed to assign the function of glycosyltransferases involved in the decoration of baikalomycins aglycone.
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Harunari E, Imada C, Igarashi Y. Konamycins A and B and Rubromycins CA1 and CA2, Aromatic Polyketides from the Tunicate-Derived Streptomyces hyaluromycini MB-PO13 T. JOURNAL OF NATURAL PRODUCTS 2019; 82:1609-1615. [PMID: 31181919 DOI: 10.1021/acs.jnatprod.9b00107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Four new aromatic polyketides, konamycins A (1) and B (2) and rubromycins CA1 (3) and CA2 (4), were isolated from the culture extract of the tunicate-derived Streptomyces hyaluromycini MB-PO13T. Compounds 1 and 2 possess a benzo[ b]fluorene aglycon modified by C-glycosylation with l-amicetose. Compounds 3 and 4 are the new congeners of rubromycin in which a naphthoquinone and carboxylated isocoumarin are joined through a spiroketal carbon. The structures of these compounds were determined by extensive analysis of 1D and 2D NMR spectroscopic data. Compound 1 showed radical scavenging activity in DPPH and superoxide quenching assays, and 3 and 4 displayed antimicrobial activity against Gram-positive bacteria.
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Affiliation(s)
- Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , 5180 Kurokawa , Imizu , Toyama 939-0398 , Japan
| | - Chiaki Imada
- Graduate School of Marine Science and Technology , Tokyo University of Marine Science and Technology , 4-5-7 Konan, Minato-ku , Tokyo 108-8477 , Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , 5180 Kurokawa , Imizu , Toyama 939-0398 , Japan
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7
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Fidan O, Yan R, Zhu D, Zhan J. Improved production of antifungal angucycline Sch47554 by manipulating three regulatory genes inStreptomycessp. SCC‐2136. Biotechnol Appl Biochem 2019; 66:517-526. [DOI: 10.1002/bab.1748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 03/27/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Ozkan Fidan
- Department of Biological EngineeringUtah State University Logan UT USA
| | - Riming Yan
- Department of Biological EngineeringUtah State University Logan UT USA
- Key Laboratory of Protection and Utilization of Subtropic PlantResources of Jiangxi ProvinceCollege of Life ScienceJiangxi Normal University Jiangxi People's Republic of China
| | - Du Zhu
- Key Laboratory of Protection and Utilization of Subtropic PlantResources of Jiangxi ProvinceCollege of Life ScienceJiangxi Normal University Jiangxi People's Republic of China
| | - Jixun Zhan
- Department of Biological EngineeringUtah State University Logan UT USA
- TCM and Ethnomedicine Innovation & Development LaboratorySchool of PharmacyHunan University of Chinese Medicine Changsha Hunan People's Republic of China
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8
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Fidan O, Yan R, Gladstone G, Zhou T, Zhu D, Zhan J. New Insights into the Glycosylation Steps in the Biosynthesis of Sch47554 and Sch47555. Chembiochem 2018; 19:1424-1432. [DOI: 10.1002/cbic.201800105] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Ozkan Fidan
- Department of Biological Engineering Utah State University 4105 Old Main Hill Logan UT 84322 USA
| | - Riming Yan
- Department of Biological Engineering Utah State University 4105 Old Main Hill Logan UT 84322 USA
- Key Laboratory of Protection and Utilization of Subtropic Plant, Resources of Jiangxi Province College of Life Science Jiangxi Normal University Nanchang Jiangxi 330022 P.R. China
| | - Gabrielle Gladstone
- Department of Biological Engineering Utah State University 4105 Old Main Hill Logan UT 84322 USA
| | - Tong Zhou
- Department of Biological Engineering Utah State University 4105 Old Main Hill Logan UT 84322 USA
| | - Du Zhu
- Key Laboratory of Protection and Utilization of Subtropic Plant, Resources of Jiangxi Province College of Life Science Jiangxi Normal University Nanchang Jiangxi 330022 P.R. China
| | - Jixun Zhan
- Department of Biological Engineering Utah State University 4105 Old Main Hill Logan UT 84322 USA
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Elshahawi SI, Shaaban KA, Kharel MK, Thorson JS. A comprehensive review of glycosylated bacterial natural products. Chem Soc Rev 2015; 44:7591-697. [PMID: 25735878 PMCID: PMC4560691 DOI: 10.1039/c4cs00426d] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A systematic analysis of all naturally-occurring glycosylated bacterial secondary metabolites reported in the scientific literature up through early 2013 is presented. This comprehensive analysis of 15 940 bacterial natural products revealed 3426 glycosides containing 344 distinct appended carbohydrates and highlights a range of unique opportunities for future biosynthetic study and glycodiversification efforts.
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Affiliation(s)
- Sherif I Elshahawi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Khaled A Shaaban
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Madan K Kharel
- School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
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Abstract
A method for the asymmetric synthesis of the disaccharide portion of SCH-47554 has been developed in 6 steps. The route is shorter than the reported route to a related disaccharide. The route involves the use of the Noyori reduction to establish the asymmetry of the d- and l-sugar portion of the molecule. Diastereoselective Pd-glycosylation reaction and subsequent post-glycosylation transformation are used to establish the remaining stereocenter.
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Affiliation(s)
- Xiaomei Yu
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Miaosheng Li
- Protea Biosciences, 955 Hartman Run Road, Morgantown, WV 26507
| | - George A O'Doherty
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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Morton GE, Barrett AGM. Iterative benzyne-furan cycloaddition reactions: studies toward the total synthesis of ent-Sch 47554 and ent-Sch 47555. Org Lett 2007; 8:2859-61. [PMID: 16774275 DOI: 10.1021/ol061007+] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] 7-Fluoro-5,8-dimethoxy-1-naphthol, prepared from the lithiation and benzyne formation from 1,4-difluoro-2,5-dimethoxybenzene and Diels-Alder cycloaddition with furan, was sequentially C-glycosidated under Suzuki conditions and O-glycosidated using di-O-acetyl-L-rhamnal to provide the corresponding beta-naphthyl C,O-disaccharide. Further lithiation, benzyne formation, and cycloaddition with furan gave an oxa-bridged 1,4-dihydroanthracenyl C,O-disaccharide, a model compound relevant to the total synthesis of Sch 47555.
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Affiliation(s)
- Gillian E Morton
- Department of Chemistry, Imperial College London, South Kensington, England
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Basil AJ, Strap JL, Knotek-Smith HM, Crawford DL. Studies on the microbial populations of the rhizosphere of big sagebrush (Artemisia tridentata). J Ind Microbiol Biotechnol 2004; 31:278-88. [PMID: 15221668 DOI: 10.1007/s10295-004-0140-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2003] [Accepted: 04/12/2004] [Indexed: 10/26/2022]
Abstract
Prolonged use of broad-spectrum antibiotics has led to the emergence of drug-resistant pathogens, both in medicine and in agriculture. New threats such as biological warfare have increased the need for novel and efficacious antimicrobial agents. Natural habitats not previously examined as sources of novel antibiotic-producing microorganisms still exist. One such habitat is the rhizosphere of desert shrubs. Here, we show that one desert shrub habitat, the rhizosphere of desert big sagebrush ( Artemisia tridentata) is a source of actinomycetes capable of producing an extensive array of antifungal metabolites. Culturable microbial populations from both the sagebrush rhizosphere and nearby bulk soils from three different sites were enumerated and compared, using traditional plate-count techniques and antibiotic activity bioassays. There were no statistical differences between the relative numbers of culturable non-actinomycete eubacteria, actinomycetes and fungi in the rhizosphere versus bulk soils, but PCR amplification of the 16S rRNA gene sequences of the total soil DNA and denaturing gradient gel electrophoresis showed that the community structure was different between the rhizosphere and the bulk soils. A high percentage of actinomycetes produced antimicrobials; and the percentage of active producers was significantly higher among the rhizosphere isolates, as compared with the bulk soil isolates. Also, the rhizosphere strains were more active in the production of antifungal compounds than antibacterial compounds. 16S rRNA gene sequence analysis showed that sagebrush rhizospheres contained a variety of Streptomyces species possessing broad spectrum antifungal activity. Scanning electron microscopy studies of sagebrush root colonization by one of the novel sagebrush rhizosphere isolates, Streptomyces sp. strain RG, showed that it aggressively colonized young sagebrush roots, whereas another plant rhizosphere-colonizing strain, S. lydicus WYEC108, not originally isolated from sagebrush, was a poor colonizer of the roots of this plant, as were two other Streptomyces isolates from forest soil. These results support the hypothesis that the rhizosphere of desert big sagebrush is a promising source of habitat-adapted actinomycetes, producing antifungal antibiotics.
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Affiliation(s)
- Antony J Basil
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, ID 83844-3052, USA
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Angucyclines: Total syntheses, new structures, and biosynthetic studies of an emerging new class of antibiotics. Top Curr Chem (Cham) 1997. [DOI: 10.1007/bfb0119236] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Chu M, Patel MG, Pai JK, Das PR, Puar MS. Sch 53823 and Sch 53825, novel fungal metabolites with phospholipase D inhibitory activity. Bioorg Med Chem Lett 1996. [DOI: 10.1016/0960-894x(96)00074-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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