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Cheun-Arom T, Chuanasa T. An Efficient DNA Extraction for a Blue Xestospongia sp. Sponge and Its Associated Microorganisms Containing Cytotoxic Substances. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:917-927. [PMID: 34714444 DOI: 10.1007/s10126-021-10075-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Extraction of high quantity and quality DNAs from marine sponges, which contain diverse and abundant microbial communities, is important to molecular biology techniques for the analysis of nucleic acids. Several marine sponges and their associated microorganisms have been known to produce cytotoxic natural products on several cancer cell lines via DNA damage mechanisms. These marine cytotoxic substances might be one of the factors that cause the low quantity and quality of DNAs during the DNA extraction from its living origin. Therefore, the extraction of DNA of a Thai blue marine sponge Xestospongia sp. with sufficient purity and quantity for molecular study can be challenging. In this study, we developed an efficient extraction method to prepare DNAs from a Thai blue marine sponge Xestospongia sp. which accumulated a highly potent cytotoxic alkaloid with DNA-damaging activity, named Renieramycin M (RM), as a major constituent in high quantity. We demonstrated that removal of RM from the sponge samples by a simple methanolic extraction before DNA extraction dramatically increased the yield and purity of DNAs compared to the RM-unremoved sponge samples. High molecular weight (HMW) genomic DNA was obtained from sponge samples with 8 times of RM elimination by using modified NaOAc salting-out extraction method. The quantity and quality of the prepared DNAs were comparatively determined via spectrophotometry, electrophoresis, and 16S rRNA gene amplification. Our result suggests that the removal of DNA-damaging constituents from the samples is a crucial step and must be seriously taken as the necessary consideration for the practical protocol of DNA extraction.
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Affiliation(s)
- Thaniwan Cheun-Arom
- Department of Biology, Faculty of Science, Ramkhamhaeng University, Bangkok, 10240, Thailand
| | - Taksina Chuanasa
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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Affiliation(s)
- Kai‐Xiong Ye
- Department of Development Technology of Marine ResourcesCollege of Life SciencesZhejiang Sci-Tech University Hangzhou 310018 People's Republic of China
| | - Ting‐Ting Fan
- Department of Development Technology of Marine ResourcesCollege of Life SciencesZhejiang Sci-Tech University Hangzhou 310018 People's Republic of China
| | - Lawrence Jordan Keen
- Department of Development Technology of Marine ResourcesCollege of Life SciencesZhejiang Sci-Tech University Hangzhou 310018 People's Republic of China
| | - Bing‐Nan Han
- Department of Development Technology of Marine ResourcesCollege of Life SciencesZhejiang Sci-Tech University Hangzhou 310018 People's Republic of China
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Okada M, Sugita T, Wong CP, Wakimoto T, Abe I. Identification of Pyridinium with Three Indole Moieties as an Antimicrobial Agent. JOURNAL OF NATURAL PRODUCTS 2017; 80:1205-1209. [PMID: 28290701 DOI: 10.1021/acs.jnatprod.6b01152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel pyridinium with three indole moieties, tricepyridinium, was obtained from the culture of an Escherichia coli clone incorporating metagenomic libraries from the marine sponge Discodermia calyx. For the important structural elements of tricepyridinium to be investigated for antibacterial activity, tricepyridinium and its analogues were chemically synthesized. Tricepyridinium had antimicrobial activity, but not against E. coli, and cytotoxicity against P388 cells. Additional bioassays with its synthetic analogues revealed that the intriguing combination of the indole moieties, most likely derived from three tryptamines, as well as the pyridinium moiety were chiefly responsible for its potent biological activities.
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Affiliation(s)
- Masahiro Okada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomotoshi Sugita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chin Piow Wong
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-0033, Japan
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Indole Derivatives Produced by the Metagenome Genes of the Escherichia coli-Harboring Marine Sponge Discodermia calyx. Molecules 2017; 22:molecules22050681. [PMID: 28441364 PMCID: PMC6154727 DOI: 10.3390/molecules22050681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 11/23/2022] Open
Abstract
Three indole derivatives, a novel benzoxazine-indole hybrid (1) and two known indole trimers (2, 3), were isolated from the metagenomic library of the marine sponge Discodermia calyx based on functional screening. Their structures were elucidated by extensive spectroscopic analysis and comparison of their NMR data to that of known compounds. The antibacterial assay indicated that only compound 2 displayed significant antibacterial activity against Bacillus cereus, with approximately 20 mm diameter growth inhibition at 10 µg/paper. HPLC analyses revealed that compound 2 is a newly induced metabolite, and the concentration of 3 was obviously enhanced in contrast to negative control, while 1 was not detected, allowing us to predict that the formation of 2 might be induced by exogenous genes derived from the sponge metagenome, whereas compound 1 could be formed through a non-enzymatic process during the isolation procedure.
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Nakashima Y, Egami Y, Kimura M, Wakimoto T, Abe I. Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by 'Entotheonella'. PLoS One 2016; 11:e0164468. [PMID: 27732651 PMCID: PMC5061366 DOI: 10.1371/journal.pone.0164468] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/26/2016] [Indexed: 11/19/2022] Open
Abstract
Sponge metagenomes are a useful platform to mine cryptic biosynthetic gene clusters responsible for production of natural products involved in the sponge-microbe association. Since numerous sponge-derived bioactive metabolites are biosynthesized by the symbiotic bacteria, this strategy may concurrently reveal sponge-symbiont produced compounds. Accordingly, a metagenomic analysis of the Japanese marine sponge Discodermia calyx has resulted in the identification of a hybrid type I polyketide synthase-nonribosomal peptide synthetase gene (kas). Bioinformatic analysis of the gene product suggested its involvement in the biosynthesis of kasumigamide, a tetrapeptide originally isolated from freshwater free-living cyanobacterium Microcystis aeruginosa NIES-87. Subsequent investigation of the sponge metabolic profile revealed the presence of kasumigamide in the sponge extract. The kasumigamide producing bacterium was identified as an ‘Entotheonella’ sp. Moreover, an in silico analysis of kas gene homologs uncovered the presence of kas family genes in two additional bacteria from different phyla. The production of kasumigamide by distantly related multiple bacterial strains implicates horizontal gene transfer and raises the potential for a wider distribution across other bacterial groups.
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Affiliation(s)
- Yu Nakashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yoko Egami
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Miki Kimura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
- * E-mail: (TW); (IA)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail: (TW); (IA)
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Arivaradarajan P, Warburton PJ, Paramasamy G, Nair SP, Allan E, Mullany P. Identification of an antibacterial protein by functional screening of a human oral metagenomic library. FEMS Microbiol Lett 2015; 362:fnv142. [PMID: 26347298 DOI: 10.1093/femsle/fnv142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2015] [Indexed: 11/13/2022] Open
Abstract
Screening of a bacterial artificial chromosome (BAC) library containing metagenomic DNA from human plaque and saliva allowed the isolation of four clones producing antimicrobial activity. Three of these were pigmented and encoded homologues of glutamyl-tRNA reductase (GluTR), an enzyme involved in the C5 pathway leading to tetrapyrole synthesis, and one clone had antibacterial activity with no pigmentation. The latter contained a BAC with an insert of 15.6 kb. Initial attempts to localize the gene(s) responsible for antimicrobial activity by subcloning into pUC-based vectors failed. A new plasmid for toxic gene expression (pTGEX) was designed enabling localization of the antibacterial activity to a 4.7-kb HindIII fragment. Transposon mutagenesis localized the gene to an open reading frame of 483 bp designated antibacterial protein1 (abp1). Abp1 was 94% identical to a hypothetical protein of Neisseria subflava (accession number WP_004519448.1). An Escherichia coli clone expressing Abp1 exhibited antibacterial activity against Bacillus subtilis BS78H, Staphylococcus epidermidis NCTC 11964 and B4268, and S. aureus NCTC 12493,ATCC 35696 and NCTC 11561. However, no antibacterial activity was observed against Pseudomonas aeruginosa ATCC 9027, N. subflava ATCC A1078, E. coli K12 JM109 and BL21(DE3) Fusobacterium nucleatum ATCC 25586 and NCTC 11326, Prevotella intermedia ATCC 25611, Veillonella parvula ATCC 10790 or Lactobacillus casei NCTC 6375.
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Affiliation(s)
- Preeti Arivaradarajan
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, India
| | | | - Gunasekaran Paramasamy
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, India
| | - Sean P Nair
- Department of Microbial Diseases, UCL Eastman Dental Institute, London WC1X 8LD, UK
| | - Elaine Allan
- Department of Microbial Diseases, UCL Eastman Dental Institute, London WC1X 8LD, UK
| | - Peter Mullany
- Department of Microbial Diseases, UCL Eastman Dental Institute, London WC1X 8LD, UK
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Takeshige Y, Egami Y, Wakimoto T, Abe I. Production of indole antibiotics induced by exogenous gene derived from sponge metagenomes. MOLECULAR BIOSYSTEMS 2015; 11:1290-4. [PMID: 25828760 DOI: 10.1039/c5mb00131e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sponge metagenomes are accessible genetic sources containing genes and gene clusters responsible for the biosynthesis of sponge-derived bioactive natural products. In this study, we obtained the clone pDC112, producing turbomycin A and 2,2-di(3-indolyl)-3-indolone, based on the functional screening of the metagenome library derived from the marine sponge Discodermia calyx. The subcloning experiment identified ORF 25, which is homologous to inosine 5'-monophosphate dehydrogenase and required for the production of 2,2-di(3-indolyl)-3-indolone in Escherichia coli.
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Affiliation(s)
- Yuya Takeshige
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Sanka Loganathachetti D, Muthuraman S. Biomedical potential of natural products derived through metagenomic approaches. RSC Adv 2015. [DOI: 10.1039/c5ra20116k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Microbes are ubiquitous, irrespective of the environment they thrive in. Only 1% of these are culturable in laboratory. Metagenomics is useful in exploring biomedically important small molecules using culture independent approaches.
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Wakimoto T, Egami Y, Nakashima Y, Wakimoto Y, Mori T, Awakawa T, Ito T, Kenmoku H, Asakawa Y, Piel J, Abe I. Calyculin biogenesis from a pyrophosphate protoxin produced by a sponge symbiont. Nat Chem Biol 2014; 10:648-55. [DOI: 10.1038/nchembio.1573] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 05/19/2014] [Indexed: 12/29/2022]
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Yang XL, Wakimoto T, Takeshige Y, He R, Egami Y, Awakawa T, Abe I. Indole–porphyrin hybrids produced by metagenomics. Bioorg Med Chem Lett 2013; 23:3810-3. [DOI: 10.1016/j.bmcl.2013.04.076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 04/29/2013] [Indexed: 12/01/2022]
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He R, Wakimoto T, Egami Y, Kenmoku H, Ito T, Asakawa Y, Abe I. Heterologously expressed β-hydroxyl fatty acids from a metagenomic library of a marine sponge. Bioorg Med Chem Lett 2012; 22:7322-5. [DOI: 10.1016/j.bmcl.2012.10.082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 10/16/2012] [Accepted: 10/17/2012] [Indexed: 10/27/2022]
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