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B T SK, Hebbar UH, Annapurna Singh S. Isolation, purification, and physio-chemical characterization of melanin pigment from nigerseed hulls ( Guizotia abysinica). Prep Biochem Biotechnol 2024:1-9. [PMID: 38995969 DOI: 10.1080/10826068.2024.2376579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Plant melanin, a natural pigment, has gained significant attention recently due to its potential therapeutic and industrial applications. In this study, melanin pigments were extracted from Nigerseed hulls (NH) via alkali and acid extraction methods, followed by acid hydrolysis, organic solvent treatment, and repeated precipitation. The solubility of NH melanin was assessed, revealing solubility in alkali and dimethyl sulfoxide (DMSO) but insolubility in other common organic solvents. High-performance liquid chromatography (HPLC) was employed to measure the purity of NH melanin in comparison to standard melanin, while elemental analysis indicated a similarity between melanin extracted from nigerseed hulls and the standard counterpart. LC-MS data revealed a molecular weight of NH melanin. Furthermore, the stability of melanin was evaluated under varying conditions including temperature, oxidants, reducing agents, light exposure, and metal ion presence. Results demonstrated significant effects of Mg2+, Cu2+, and Fe2+ metal ions on melanin stability, with a minor effect observed for Ca2+, while sodium hyposulfite was found to destabilize the pigments. Our findings suggest that nigerseed hulls hold promise as a novel source for efficient melanin production, with potential applications in the food sector, food packaging, and biomedical fields.
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Affiliation(s)
- Sunil Kumar B T
- Department of Traditional Foods and Applied Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Umesh H Hebbar
- Department of Food Engineering, CSIR-Central Food Technological Research Institute, Mysuru, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sridevi Annapurna Singh
- Department of Traditional Foods and Applied Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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2
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Goel N, Singh R, Sood S, Khare SK. Investigation of Streptomyces sp. Strain EMB24 Secondary Metabolite Profile Has Unraveled Its Extraordinary Antibacterial Potency Against Drug-Resistant Bacteria. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1168-1175. [PMID: 36220897 PMCID: PMC9553293 DOI: 10.1007/s10126-022-10168-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
With the overuse and misuse of antibiotics amid COVID-19 pandemic, the antimicrobial resistance, which is already a global challenge, has accelerated its pace significantly. Finding novel and potential antibiotics seems one of the probable solutions. In this work, a novel Streptomyces sp. strain EMB24 was isolated and found to be an excellent source of antimicrobials as confirmed by agar-plug assay. It showed antibacterial activity against infection-causing bacteria, namely Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. In addition, Streptomyces sp. strain EMB24 inhibited the growth methicillin-resistant Staphylococcus aureus (MRSA), tetracycline-resistant Neisseria gonorrhoeae, and ampicillin-resistant Neisseria gonorrhoeae. Furthermore, to get deep insights about the genome and biosynthetic gene clusters producing antibiotics, whole genome sequencing was done. The strain EMB24 is closely related to the Streptomyces longispororuber as revealed by phylogenetic analysis which is a potential source of antibiotics and pigments as undecylprodigiosin and metacycloprodigiosin belonging to the class prodigiosin. Naphthyridinomycin, alkylresorcinols, desferrioxamine B and E, venezuelin, aborycin, MS-271, and siamycin are potent therapeutics that shared 100% similarity with the reference strain as revealed by the online antiSMASH tool.
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Affiliation(s)
- Nikky Goel
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Rajendra Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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Quach NT, Vu THN, Bui TL, Le TTX, Nguyen TTA, Ngo CC, Phi QT. Genomic and physiological traits provide insights into ecological niche adaptations of mangrove endophytic Streptomyces parvulus VCCM 22513. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01684-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Abstract
Purpose
Endophytic Streptomyces parvulus VCCM 22513 isolated from Bruguiera gymnorrhiza in Quang Ninh mangrove forest, northern Vietnam showed abiotic stress tolerance consisting of antioxidant, salt-tolerant, and aromatic-compound degrading activities. The goal of this study was to shed light on genomic bases rendering mangrove endophytic S. parvulus more resilient to environmental stressors.
Methods
Phenotypic analysis including antioxidant activities, hydrogen peroxide and sodium chloride resistance, and aromatic compound utilization were evaluated. The genome of strain VCCM 22513 was sequenced using Illumina Miseq sequencing platform and assembled using SPAdes.
Results
Out of 15 endophytic actinomycetes associated with B. gymnorrhiza in Quang Ninh mangrove, northern Vietnam, VCCM 22513 extract showed remarkable antioxidant activities through (1,1-diphenyl-2-picrylhydrazyl) DPPH and superoxide radical scavenging assays of 72.1 ± 0.04% and 38.3 ± 0.16% at 1.6 mg/ml, respectively. The genome consists of a 7,688,855 bp linear chromosome, 6782 protein-coding sequences, and 68 tRNAs. Genomic analysis identified strain VCCM 22513 as Streptomyces parvulus and confirmed a highly conserved core genome and stability of S. parvulus under natural selection. Genome mining revealed the presence of genetic determinants involved in mycothiol and ergothioneine biosynthesis (26 genes), oxidative stress resistance (43 genes), osmoadaptation (87 genes), heat and cold stress (34 genes), aromatic compound degradation (55 genes). Further genome-wide comparison between S. parvulus VCCM 22513 and 11 Streptomyces genomes showed that VCCM 22513 possesses significantly higher copies of genes involved in mycothiol and ergothioneine biosynthesis. In support of this finding, the strain exhibited much resistance to 0.6–1.0 M H2O2 and 6% (w/v) NaCl as compared to Streptomyces cavourensis YBQ59 isolated from Cinnamomum cassia Prels. In addition, the complete pathways for degradation of aromatic compounds including protocatechuate, gentisate, 4-hydroxyphenylpyruvate, cinnamate, 3-phenylpropionate, and styrene were only identified in the genome of VCCM 22513.
Conclusions
The present study revealed for the first time adaptive responses of mangrove endophytic S. parvulus VCCM 22513 to survive in hostile environment. The information shown here provided better understanding of underlying mechanisms related to adaptation and partially plant-microbe interaction of Streptomyces associated with mangrove plants.
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Quach NT, Nguyen Vu TH, Bui TL, Pham AT, An Nguyen TT, Xuan Le TT, Thuy Ta TT, Dudhagara P, Phi QT. Genome-Guided Investigation Provides New Insights into Secondary Metabolites of Streptomyces parvulus SX6 from Aegiceras corniculatum. Pol J Microbiol 2022; 71:381-394. [DOI: 10.33073/pjm-2022-034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/13/2022] [Indexed: 11/07/2022] Open
Abstract
Abstract
Whole-genome sequencing and genome mining are recently considered an efficient approach to shine more light on the underlying secondary metabolites of Streptomyces. The present study unearths the biosynthetic potential of endophytic SX6 as a promising source of biologically active substances and plant-derived compounds for the first time. Out of 38 isolates associated with Aegiceras corniculatum (L.) Blanco, Streptomyces parvulus SX6 was highly active against Pseudomonas aeruginosa ATCC® 9027™ and methicillin-resistant Staphylococcus epidermidis (MRSE) ATCC® 35984™. Additionally, S. parvulus SX6 culture extract showed strong cytotoxicity against Hep3B, MCF-7, and A549 cell lines at a concentration of 30 μg/ml, but not in non-cancerous HEK-293 cells. The genome contained 7.69 Mb in size with an average G + C content of 72.8% and consisted of 6,779 protein-coding genes. AntiSMASH analysis resulted in the identification of 29 biosynthetic gene clusters (BGCs) for secondary metabolites. Among them, 4 BGCs showed low similarity (28–67% of genes show similarity) to actinomycin, streptovaricin, and polyoxypeptin gene clusters, possibly attributed to antibacterial and anticancer activities observed. In addition, the complete biosynthetic pathways of plant-derived compounds, including daidzein and genistein were identified using genome mining and HPLC-DAD-MS analysis. These findings portray an exciting avenue for future characterization of promising secondary metabolites from mangrove endophytic S. parvulus.
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Affiliation(s)
- Ngoc Tung Quach
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Hanh Nguyen Vu
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Lien Bui
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Anh Tuan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Thu An Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Thanh Xuan Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | | | - Pravin Dudhagara
- Department of Biosciences (UGC-SAP-II and DST-FIST-I), Veer Narmad South Gujarat University , Surat , India
| | - Quyet-Tien Phi
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
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Naligama KN, Weerasinghe KE, Halmillawewa AP. Characterization of Bioactive Actinomycetes Isolated from Kadolkele Mangrove Sediments, Sri Lanka. Pol J Microbiol 2022; 71:191-204. [PMID: 35676828 PMCID: PMC9252147 DOI: 10.33073/pjm-2022-017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/09/2022] [Indexed: 12/04/2022] Open
Abstract
Exploring untapped microbial potentials in previously uncharted environments has become crucial in discovering novel secondary metabolites and enzymes for biotechnological applications. Among prokaryotes, actinomycetes are well recognized for producing a vast range of secondary metabolites and extracellular enzymes. In the present study, we have used surface sediments from ‘Kadolkele’ mangrove ecosystem located in the Negombo lagoon area, Sri Lanka, to isolate actinomycetes with bioactive potentials. A total of six actinomycetes were isolated on modified-starch casein agar and characterized. The isolates were evaluated for their antibacterial activity against four selected bacterial strains and to produce extracellular enzymes: cellulase, amylase, protease, and lipase. Three out of the six isolates exhibited antibacterial activity against Staphylococcus aureus, Escherichia coli, and Bacillus cereus, but not against Listeria monocytogenes. Five strains could produce extracellular cellulase, while all six isolates exhibited amylase activity. Only three of the six isolates were positive for protease and lipase assays separately. Ac-1, Ac-2, and Ac-9, identified as Streptomyces spp. with the 16S rRNA gene sequencing, were used for pigment extraction using four different solvents. Acetone-extracted crude pigments of Ac-1 and Ac-2 were further used in well-diffusion assays, and growth inhibition of test bacteria was observed only with the crude pigment extract of Ac-2. Further, six different commercially available fabrics were dyed with crude pigments of Ac-1. The dyed fabrics retained the yellow color after acid, alkaline, and cold-water treatments suggesting the potential of the Ac-1 pigment to be used in biotechnological applications.
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Affiliation(s)
- Kishani N Naligama
- Department of Microbiology, Faculty of Science, University of Kelaniya, Kelaniya Sri Lanka
| | - Kavindi E Weerasinghe
- Department of Microbiology, Faculty of Science, University of Kelaniya, Kelaniya Sri Lanka
| | - Anupama P Halmillawewa
- Department of Microbiology, Faculty of Science, University of Kelaniya, Kelaniya Sri Lanka
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Frikha-Dammak D, Ayadi H, Hakim-Rekik I, Belbahri L, Maalej S. Genome analysis of the salt-resistant Paludifilum halophilum DSM 102817 T reveals genes involved in flux-tuning of ectoines and unexplored bioactive secondary metabolites. World J Microbiol Biotechnol 2021; 37:178. [PMID: 34549358 DOI: 10.1007/s11274-021-03147-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Paludifilum halophilum DSM 102817T is the first member of the genus Paludifilum in the Thermoactinomycetaceae family. The thermohalophilic bacterium was isolated from the solar saltern of Sfax, Tunisia and was shown to be able to produce ectoines with a relatively high-yield and to cope with salt stress conditions. In this study, the whole genome of P. halophilum was sequenced and analysed. Analysis revealed 3,789,765 base pairs with an average GC% content of 51.5%. A total of 3775 genes were predicted of which 3616 were protein-coding genes and 73 were RNA genes. The genes encoding key enzymes for ectoines (ectoine and hydroxyectoine) synthesis (ectABCD) were identified from the bacterial genome next to a gene cluster (ehuABCD) encoding a binding-protein-dependent ABC transport system responsible for ectoines mobility through the cell membrane. With the aid of KEGG analysis, we found that the central catabolic network of P. halophilum comprises the pathways of glycolysis, tricarboxylic acid cycle, and pentose phosphate. In addition, anaplerotic pathways replenishing oxaloacetate and glutamate synthesis from central metabolism needed for high ectoines biosynthetic fluxes were identified through several key enzymes. Furthermore, a total of 18 antiSMASH-predicted putative biosynthetic gene clusters for secondary metabolites with high novelty and diversity were identified in P. halophilum genome, including biosynthesis of colabomycine-A, fusaricidin-E, zwittermycin A, streptomycin, mycosubtilin and meilingmycin. Based on these data, P. halophilum emerged as a promising source for ectoines and antimicrobials with the potential to be scaled up for industrial production, which could benefit the pharmaceutical and cosmetic industries.
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Affiliation(s)
- Donyez Frikha-Dammak
- Laboratoire de Biodiversité Marine et Environnement (LR18ES30), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax, Tunisia
| | - Houda Ayadi
- Laboratoire de Biodiversité Marine et Environnement (LR18ES30), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax, Tunisia
| | - Imen Hakim-Rekik
- Unité de Génomique Fonctionnelle et Physiologie des Plantes, Université de Sfax, Institut Supérieur de Biotechnologie de Sfax, BP 1175, 3000, Sfax, Tunisia
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000, Neuchâtel, Switzerland
| | - Sami Maalej
- Laboratoire de Biodiversité Marine et Environnement (LR18ES30), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax, Tunisia.
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Chen J, Li HF, Zhao G, Lin JM, He X. Matrix-assisted laser desorption ionization mass spectrometry based quantitative analysis of cordycepin from Cordyceps militaris. J Pharm Anal 2021; 11:499-504. [PMID: 34513126 PMCID: PMC8424359 DOI: 10.1016/j.jpha.2021.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/29/2021] [Accepted: 05/27/2021] [Indexed: 11/20/2022] Open
Abstract
Cordycepin, which has great immunomodulatory activities such as anticancer, antifungal, antivirus, antileukemia and lipid-lowering ones, is the secondary metabolite of Cordyceps militaris (C. militaris). Liquid submerged fermentation is the common cultivation process to produce cordycepin. To optimize the fermentation process and improve production, monitoring the cordycepin secretion in the fermentation is essential. The measurement based on chromatography-mass spectrometry methods is generally involved in the complex sample pretreatments and time-consuming separation, so more rapid and convenient methods are required. Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) is more attractive for faster and direct detection. Therefore, MALDI-MS detection combined with isotope-labeled internal standard was applied to the measurement of cordycepin content in the fermentation broth and mycelium. This method made accurate quantification of cordycepin in the range of 5–400 μg/mL with a relative standard deviation of 5.6%. The recovery rates of fermentation samples after the 1, 13, and 25 days were 90.15%, 94.27%, and 95.06%, respectively. The contents of cordycepin in the mycelium and fermentation broth were 136 mg/g and 148.39 mg/mL on the 20th culture day, respectively. The cordycepin secretion curve of the liquid fermentation of C. militaris was real-time traced over 25 days. A rapid quantification method of cordycepin based on MALDI-MS is proposed. The quantification relies on the stable isotope standard method. Rapid determination of the cordycepin content in the liquid fermentation broth of Cordyceps militaris without pre-treatment. Monitoring the fermentation state of C. militaris fermentation broth is benefit to improve the yield of cordycepin.
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Affiliation(s)
- Jian Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.,Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Hai-Fang Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Guozhu Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Xiangwei He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China
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Rakhmawatie MD, Wibawa T, Lisdiyanti P, Pratiwi WR, Damayanti E, Mustofa. Potential secondary metabolite from Indonesian Actinobacteria (InaCC A758) against Mycobacterium tuberculosis. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:1058-1068. [PMID: 34804423 PMCID: PMC8591762 DOI: 10.22038/ijbms.2021.56468.12601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/04/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVES This study explored Indonesian Actinobacteria which were isolated from Curcuma zedoaria endophytic microbes and mangrove ecosystem for new antimycobacterial compounds. MATERIALS AND METHODS Antimycobacterial activity test was carried out against Mycobacterium tuberculosis H37Rv. Chemical profiling of secondary metabolite using Gas Chromatography-Mass Spectroscopy (GC-MS) and High Resolution-Mass Spectroscopy (HR-MS) was done to the ethyl acetate extract of active strain InaCC A758. Molecular taxonomy analysis based on 16S rRNA gene and biosynthetic gene clusters analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) from InaCC A758 have been carried out. Bioassay guided isolation of ethyl acetate extract was done, then structural elucidation of active compound was performed using UV-Vis, FT-IR, and NMR spectroscopy methods. RESULTS The chemical profiling using HR-MS revealed that InaCC A758 has the potential to produce new antimycobacterial compounds. The 16S rRNA gene sequencing showed that InaCC A758 has the closest homology to Streptomyces parvus strain NBRC 14599 (99.64%). In addition, InaCC A758 has NRPS gene and related to S. parvulus (92% of similarity), and also PKS gene related to PKS-type borrelidin of S. rochei and S. parvulus (74% of similarity). Two compounds with potential antimycobacterial were predicted as 1) Compound 1, similar to dimethenamid (C12H18ClNO2S; MW 275.0723), with MIC value of 100 µg/ml, and 2) Compound 2, actinomycin D (C62H86N12O16; MW 1254.6285), with MIC value of 0.78 µg/ml. CONCLUSION Actinomycin D has been reported to have antimycobacterial activity, however the compound has been predicted to resemble dimethenamid had not been reported to have similar activity.
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Affiliation(s)
- Maya Dian Rakhmawatie
- Doctoral Program in Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia , Department of Biomedical Sciences, Faculty of Medicine, Universitas Muhammadiyah Semarang, Semarang 50273, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesian Institute of Sciences, Kabupaten Bogor, West Java 16911, Indonesia
| | - Woro Rukmi Pratiwi
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Ema Damayanti
- Research Division of Natural Product Technology, Indonesian Institute of Sciences, Yogyakarta 55861, Indonesia
| | - Mustofa
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia,Corresponding author: Mustofa Mustofa. Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia. Tel +62 813 2874 9273;
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Kim DR, Kwak YS. A Genome-Wide Analysis of Antibiotic Producing Genes in Streptomyces globisporus SP6C4. THE PLANT PATHOLOGY JOURNAL 2021; 37:389-395. [PMID: 34365750 PMCID: PMC8357572 DOI: 10.5423/ppj.nt.03.2021.0047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 06/13/2023]
Abstract
Soil is the major source of plant-associated microbes. Several fungal and bacterial species live within plant tissues. Actinomycetes are well known for producing a variety of antibiotics, and they contribute to improving plant health. In our previous report, Streptomyces globisporus SP6C4 colonized plant tissues and was able to move to other tissues from the initially colonized ones. This strain has excellent antifungal and antibacterial activities and provides a suppressive effect upon various plant diseases. Here, we report the genome-wide analysis of antibiotic producing genes in S. globisporus SP6C4. A total of 15 secondary metabolite biosynthetic gene clusters were predicted using antiSMASH. We used the CRISPR/Cas9 mutagenesis system, and each biosynthetic gene was predicted via protein basic local alignment search tool (BLAST) and rapid annotation using subsystems technology (RAST) server. Three gene clusters were shown to exhibit antifungal or antibacterial activity, viz. cluster 16 (lasso peptide), cluster 17 (thiopeptide-lantipeptide), and cluster 20 (lantipeptide). The results of the current study showed that SP6C4 has a variety of antimicrobial activities, and this strain is beneficial in agriculture.
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Affiliation(s)
- Da-Ran Kim
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
- Division of Applied Life Science (BK21Plus) and IALS, Gyeongsang National University, Jinju 52828, Korea
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Hu D, Lee SMY, Li K, Mok KM. Secondary Metabolite Production Potential of Mangrove-Derived Streptomyces olivaceus. Mar Drugs 2021; 19:332. [PMID: 34201365 PMCID: PMC8228178 DOI: 10.3390/md19060332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 01/21/2023] Open
Abstract
Mangroves are intertidal extreme environments with rich microbial communities. Actinobacteria are well known for producing antibiotics. The search for biosynthetic potential of Actinobacteria from mangrove environments could provide more possibilities for useful secondary metabolites. In this study, whole genome sequencing and MS/MS analysis were used to explore the secondary metabolite production potential of one actinobacterial strain of Streptomyces olivaceus sp., isolated from a mangrove in Macau, China. The results showed that a total of 105 gene clusters were found in the genome of S. olivaceus sp., and 53 known secondary metabolites, including bioactive compounds, peptides, and other products, were predicted by genome mining. There were 28 secondary metabolites classified as antibiotics, which were not previously known from S. olivaceus. ISP medium 2 was then used to ferment the S. olivaceus sp. to determine which predicted secondary metabolite could be truly produced. The chemical analysis revealed that ectoine, melanin, and the antibiotic of validamycin A could be observed in the fermentation broth. This was the first observation that these three compounds can be produced by a strain of S. olivaceus. Therefore, it can be concluded that Actinobacteria isolated from the mangrove environment have unknown potential to produce bioactive secondary metabolites.
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Affiliation(s)
- Dini Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China;
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macao, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China;
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China;
| | - Kai Meng Mok
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macao, China
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11
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Baltz RH. Genome mining for drug discovery: cyclic lipopeptides related to daptomycin. J Ind Microbiol Biotechnol 2021; 48:6178872. [PMID: 33739403 PMCID: PMC9113097 DOI: 10.1093/jimb/kuab020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/17/2020] [Indexed: 11/25/2022]
Abstract
The cyclic lipopeptide antibiotics structurally related to daptomycin were first reported in the 1950s. Several have common lipopeptide initiation, elongation, and termination mechanisms. Initiation requires the use of a fatty acyl-AMP ligase (FAAL), a free-standing acyl carrier protein (ACP), and a specialized condensation (CIII) domain on the first NRPS elongation module to couple the long chain fatty acid to the first amino acid. Termination is carried out by a dimodular NRPS that contains a terminal thioesterase (Te) domain (CAT-CATTe). Lipopeptide BGCs also encode ABC transporters, apparently for export and resistance. The use of this mechanism of initiation, elongation, and termination, coupled with molecular target-agnostic resistance, has provided a unique basis for robust natural and experimental combinatorial biosynthesis to generate a large variety of structurally related compounds, some with altered or different antibacterial mechanisms of action. The FAAL, ACP, and dimodular NRPS genes were used as molecular beacons to identify phylogenetically related BGCs by BLASTp analysis of finished and draft genome sequences. These and other molecular beacons have identified: (i) known, but previously unsequenced lipopeptide BGCs in draft genomes; (ii) a new daptomycin family BGC in a draft genome of Streptomyces sedi; and (iii) novel lipopeptide BGCs in the finished genome of Streptomyces ambofaciens and the draft genome of Streptomyces zhaozhouensis.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting, 7757 Uliva Way, Sarasota, FL 34238, USA
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Hu D, Sun C, Jin T, Fan G, Mok KM, Li K, Lee SMY. Exploring the Potential of Antibiotic Production From Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis. Front Microbiol 2020; 11:1540. [PMID: 32922368 PMCID: PMC7375171 DOI: 10.3389/fmicb.2020.01540] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/12/2020] [Indexed: 11/26/2022] Open
Abstract
Actinobacteria are well recognized for their production of structurally diverse bioactive secondary metabolites, but the rare actinobacterial genera have been underexploited for such potential. To search for new sources of active compounds, an experiment combining genomic analysis and tandem mass spectrometry (MS/MS) screening was designed to isolate and characterize actinobacterial strains from a mangrove environment in Macau. Fourteen actinobacterial strains were isolated from the collected samples. Partial 16S sequences indicated that they were from six genera, including Brevibacterium, Curtobacterium, Kineococcus, Micromonospora, Mycobacterium, and Streptomyces. The isolate sp.01 showing 99.28% sequence similarity with a reference rare actinobacterial species Micromonospora aurantiaca ATCC 27029T was selected for whole genome sequencing. Organization of its gene clusters for secondary metabolite biosynthesis revealed 21 clusters encoded to antibiotic production, which is higher than other Micromonospora species. Of the genome-predicted antibiotics, kanamycin was found through guided MS/MS analysis producible by the M. aurantiaca strain for the first time. The present study highlighted that genomic analysis combined with MS/MS screening is a promising method to discover potential of antibiotic production from rare actinobacteria.
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Affiliation(s)
- Dini Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Chenghang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Jin
- Beijing Genomics Institute, Shenzhen, China
| | | | - Kai Meng Mok
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
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Mining the Biosynthetic Potential for Specialized Metabolism of a Streptomyces Soil Community. Antibiotics (Basel) 2020; 9:antibiotics9050271. [PMID: 32456220 PMCID: PMC7277575 DOI: 10.3390/antibiotics9050271] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/22/2022] Open
Abstract
The diversity and distribution of specialized metabolite gene clusters within a community of bacteria living in the same soil habitat are poorly documented. Here we analyzed the genomes of 8 Streptomyces isolated at micro-scale from a forest soil that belong to the same species or to different species. The results reveal high levels of diversity, with a total of 261 biosynthesis gene clusters (BGCs) encoding metabolites such as terpenes, polyketides (PKs), non-ribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs) with potential bioactivities. A significant part of these BGCs (n = 53) were unique to only one strain when only 5 were common to all strains. The metabolites belong to very diverse chemical families and revealed that a large diversity of metabolites can potentially be produced in the community. Although that analysis of the global metabolome using GC-MS revealed that most of the metabolites were shared between the strains, they exhibited a specific metabolic pattern. We also observed that the presence of these accessory pathways might result from frequent loss and gain of genes (horizontal transfer), showing that the potential of metabolite production is a dynamic phenomenon in the community. Sampling Streptomyces at the community level constitutes a good frame to discover new biosynthetic pathways and it appears as a promising reservoir for the discovery of new bioactive compounds.
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Saygin H, Ay H, Guven K, Cetin D, Sahin N. Micromonospora deserti sp. nov., isolated from the Karakum Desert. Int J Syst Evol Microbiol 2019; 70:282-291. [PMID: 31596193 DOI: 10.1099/ijsem.0.003752] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An isolate, 13K206T, with typical morphological characteristics of the genus Micromonospora was obtained during a study searching for novel actinobacteria with biosynthetic potential from the Karakum Desert. A polyphasic approach was adopted to determine taxonomic affiliation of the strain. The strain showed chemotaxonomical properties consistent with its classification in the genus Micromonospora such as meso- and 3-OH-A2pm in the cell-wall peptidoglycan, xylose in whole-cell hydrolysate and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain was closely related to 'Micromonospora spongicola' S3-1T, Micromonospora nigra DSM 43818T and Micromonospora yasonensis DS3186T with sequence similarities of 98.6, 98.5 and 98.4 %, respectively. Digital DNA-DNA hybridization and average nucleotide identity analyses in addition to gyrB gene analysis confirmed the assignment of the strain to a novel species within the genus Micromonospora for which the name Micromonospora deserti sp. nov. is proposed. The type strain is 13K206T (=JCM 32583T=DSM 107532T). The DNA G+C content of the type strain is 72.4 mol%.
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Affiliation(s)
- Hayrettin Saygin
- Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
| | - Hilal Ay
- Department of Molecular Biology and Genetics, 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 Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
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Genome-guided and mass spectrometry investigation of natural products produced by a potential new actinobacterial strain isolated from a mangrove ecosystem in Futian, Shenzhen, China. Sci Rep 2019; 9:823. [PMID: 30696899 PMCID: PMC6351551 DOI: 10.1038/s41598-018-37475-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/05/2018] [Indexed: 11/08/2022] Open
Abstract
Actinobacteria, a group of gram-positive bacteria, can produce plenty of valuable bioactive secondary metabolites, especially antibiotics. Hence, in order to search for new actinobacteria, actinobacterial isolates were obtained from rhizosphere soil collected from the Futian mangrove ecosystem in Shenzhen, China. According to 16S rRNA sequences, 14 actinobacterial strains of the genus Streptomyces, Rhodococcus, Microbacterium, Micromonospora, Actinoplanes and Mycobacterium were isolated and identified. Among these, strain Mycobacterium sp.13 was described as a potential new species belonging to the genus Mycobacterium within the class of actinobacteria according to the genomic analysis. The genome-based 16S rRNA sequences had 98.48% sequence similarity with Mycobacterium moriokaense DSM 44221T. Meanwhile, the genome sequences of Mycobacterium sp.13 showed an average nucleotide identity (ANI) with the Mycobacterium mageritense DSM 44476, Mycobacterium smegmatis MKD8 and Mycobacterium goodii strain X7B of only 74.79%, 76.12% and 76.42%, respectively. Furthermore, genome-mining results showed that Mycobacterium sp.13 contained 105 gene clusters encoding to the secondary metabolite biosynthesis, where many kinds of terpene, bacteriocin, T1pks, Nrps, saccharide, fatty acid, butyrolactone, ectoine and resorcinol were included. Finally, through LC-MS and HR-MS, analyzing the small molecules from ethyl acetate extract of this strain, asukamycin C and apramycin were for the first time found present to be in Mycobacterium moriokaense strain. Our study provides evidence in support of the potential new Mycobacterium sp.13 isolated from the mangrove environment as a possible novel source of natural products.
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