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Bing H, Qi C, Gu J, Zhao T, Yu X, Cai Y, Zhang Y, Li A, Wang X, Zhao J, Xiang W. Isolation and identification of NEAU-CP5: A seed-endophytic strain of B. velezensis that controls tomato bacterial wilt. Microb Pathog 2024; 192:106707. [PMID: 38777241 DOI: 10.1016/j.micpath.2024.106707] [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] [Received: 12/30/2023] [Revised: 04/29/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
Bacterial wilt of tomato caused by Ralstonia solanacearum is a critical soilborne disease that drastically reduces yield. In the current study, an endophytic strain NEAU-CP5 with strong antagonistic activity against R. solanacearum was isolated from tomato seeds and characterized. The strain was identified as Bacillus velezensis based on 16S rRNA gene and whole genome sequence analysis. NEAU-CP5 can secrete amylase, protease, and cellulase, and also produce known antibacterial metabolites, including cyclo (leucylprolyl), cyclo (phenylalanyl-prolyl), cyclo (Pro-Gly), 3-benzyl-2,5-piperazinedione, pentadecanoic acid, eicosane, 2-methyoic acid, isovaleric acid, dibuty phthalate, and esters of fatty acids (HFDU), which may be responsible for its strong antibacterial activity. Fourteen gene clusters associated with antibacterial properties were also identified in the whole genome sequence of NEAU-CP5. Pot experiment demonstrated that the application of 108 CFU/mL NEAU-CP5 on tomato plants significantly reduced the incidence of tomato bacterial wilt by 68.36 ± 1.67 %. NEAU-CP5 also increased the activity of defense-related enzymes (CAT, POD, PPO, SOD, and PAL) in tomato plants. This is the first report of an effective control of bacterial wilt on tomato plants by B. velezensis and highlights the potential of NEAU-CP5 as a potential biocontrol agent for the management of tomato bacterial wilt.
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Affiliation(s)
- Hui Bing
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Cuiping Qi
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Jinzhao Gu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Tianxin Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Xiaoyan Yu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Yang Cai
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Yance Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Ailin Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, PR China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.
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Zhao J, Li Q, Zeeshan M, Zhang G, Wang C, Han X, Yang D. Integrative Genomics and Bioactivity-Guided Isolation of Novel Antimicrobial Compounds from Streptomyces sp. KN37 in Agricultural Applications. Molecules 2024; 29:2040. [PMID: 38731531 PMCID: PMC11085741 DOI: 10.3390/molecules29092040] [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: 03/20/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Actinomycetes have long been recognized as an important source of antibacterial natural products. In recent years, actinomycetes in extreme environments have become one of the main research directions. Streptomyces sp. KN37 was isolated from the cold region of Kanas in Xinjiang. It demonstrated potent antimicrobial activity, but the primary active compounds remained unclear. Therefore, we aimed to combine genomics with traditional isolation methods to obtain bioactive compounds from the strain KN37. Whole-genome sequencing and KEGG enrichment analysis indicated that KN37 possesses the potential for synthesizing secondary metabolites, and 41 biosynthetic gene clusters were predicted, some of which showed high similarity to known gene clusters responsible for the biosynthesis of antimicrobial antibiotics. The traditional isolation methods and activity-guided fractionation were employed to isolate and purify seven compounds with strong bioactivity from the fermentation broth of the strain KN37. These compounds were identified as 4-(Diethylamino)salicylaldehyde (1), 4-Nitrosodiphenylamine (2), N-(2,4-Dimethylphenyl)formamide (3), 4-Nitrocatechol (4), Methylsuccinic acid (5), Phenyllactic acid (6) and 5,6-Dimethylbenzimidazole (7). Moreover, 4-(Diethylamino)salicylaldehyde exhibited the most potent inhibitory effect against Rhizoctonia solani, with an EC50 value of 14.487 mg/L, while 4-Nitrosodiphenylamine showed great antibacterial activity against Erwinia amylovora, with an EC50 value of 5.715 mg/L. This study successfully isolated several highly active antimicrobial compounds from the metabolites of the strain KN37, which could contribute as scaffolds for subsequent chemical synthesis. On the other hand, the newly predicted antibiotic-like substances have not yet been isolated, but they still hold significant research value. They are instructive in the study of active natural product biosynthetic pathways, activation of silent gene clusters, and engineering bacteria construction.
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Affiliation(s)
| | | | | | - Guoqiang Zhang
- The Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Utilization, College of Agriculture, Shihezi University, Shihezi 832003, China; (J.Z.); (Q.L.); (M.Z.); (X.H.); (D.Y.)
| | - Chunjuan Wang
- The Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Utilization, College of Agriculture, Shihezi University, Shihezi 832003, China; (J.Z.); (Q.L.); (M.Z.); (X.H.); (D.Y.)
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Liu Z, Sun W, Hu Z, Wang W, Zhang H. Marine Streptomyces-Derived Novel Alkaloids Discovered in the Past Decade. Mar Drugs 2024; 22:51. [PMID: 38276653 PMCID: PMC10821133 DOI: 10.3390/md22010051] [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: 12/18/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 01/27/2024] Open
Abstract
Natural alkaloids originating from actinomycetes and synthetic derivatives have always been among the important suppliers of small-molecule drugs. Among their biological sources, Streptomyces is the highest and most extensively researched genus. Marine-derived Streptomyces strains harbor unconventional metabolic pathways and have been demonstrated to be efficient producers of biologically active alkaloids; more than 60% of these compounds exhibit valuable activity such as antibacterial, antitumor, anti-inflammatory activities. This review comprehensively summarizes novel alkaloids produced by marine Streptomyces discovered in the past decade, focusing on their structural features, biological activity, and pharmacological mechanisms. Future perspectives on the discovery and development of novel alkaloids from marine Streptomyces are also provided.
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Affiliation(s)
| | | | | | | | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (Z.L.); (W.S.); (Z.H.); (W.W.)
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Li M, Lu Y, Gao Z, Yue D, Hong J, Wu J, Xi D, Deng W, Chong Y. Pan-Omics in Sheep: Unveiling Genetic Landscapes. Animals (Basel) 2024; 14:273. [PMID: 38254442 PMCID: PMC10812798 DOI: 10.3390/ani14020273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies. The comprehensive insights obtained through this approach shed light on diverse facets of sheep development, including growth, reproduction, disease resistance, and the quality of livestock products. This review primarily focuses on the application of principal omics analysis technologies in sheep, emphasizing correlation studies between multiomics data and specific traits such as meat quality, wool characteristics, and reproductive features. Additionally, this paper anticipates forthcoming trends and potential developments in this field.
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Affiliation(s)
- Mengfei Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Ying Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Zhendong Gao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Dan Yue
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
- Faculty of Animal Science and Technology, Yuxi Agricultural Vocational and Technical College, Yuxi 653106, China
| | - Jieyun Hong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Jiao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Yuqing Chong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
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Banerjee A, Brisco TA, Zhang Z, Busse AA, Sumida K, Smith MW. Modular Total Synthesis of the 5/5-Spirocyclic Spiroindimicins. Org Lett 2023; 25:8413-8418. [PMID: 37983572 DOI: 10.1021/acs.orglett.3c03131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Total syntheses of the 5/5-spirocyclic indoline alkaloids (±)-spiroindimicins B, C, D, E, F, and G have been achieved via a modular approach. Our route features direct coupling of halogenated pyrrolemetal and isatin partners, Suzuki coupling to append the indole unit, Lewis acid-mediated spirocyclization, and divergent functionalization to give various family members. These syntheses are concise (six or seven steps from commercial materials) and highly amenable to analogue synthesis.
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Affiliation(s)
- Ankush Banerjee
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Tiffany A Brisco
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Zhen Zhang
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Alexander A Busse
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Krissty Sumida
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Myles W Smith
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
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Molina Ayala KM, Kim SB. Description of Microcella humidisoli sp. nov. and Microcella daejeonensis sp. nov., isolated from riverside soil, reclassification of Marinisubtilis pacificus as Microcella pacifica comb. nov., and emended description of the genus Microcella. Int J Syst Evol Microbiol 2023; 73. [PMID: 37930354 DOI: 10.1099/ijsem.0.006150] [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: 11/07/2023] Open
Abstract
Three Gram-positive, aerobic and rod shaped actinobacteria, designated strains MMS21-STM10T, MMS21-STM12T and MMS21-STM26, were isolated from riverside soil and subjected to polyphasic taxonomic analysis. The strains grew optimally at mesophilic temperatures (25-30 °C) and neutral to slightly alkaline pH (7-8), and NaCl was not required for growth. Best growth was observed on nutrient agar or marine agar media. The strains contained diphosphatidylglycerol, phosphatidylglycerol and a series of unidentified phospholipids, glycolipids and aminolipids, and anteiso-C15 : 0 and iso-C16 : 0 as the main fatty acids in common. The genome sizes ranged between 2.65 and 2.78 Mbp, and the DNA G+C contents between 70.4 and 72.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS21-STM10T showed highest sequence similarity of 98.3 % to Microcella putealis CV-2T, and MMS21-STM12T and MMS21-STM26 of 99.2-99.3 % to Microcella flavibacter WY83T, respectively. In the whole genome-based comparison using the orthologous average nucleotide identity and digital DNA-DNA hybridization, each of strains MMS21-STM10T and MMS21-STM12T could be separated from other species of Microcella. The genome analysis also indicated that both strains contained gene clusters involved in the biosynthesis of alkylresorcinol, microansamycin and carotenoids. The phenotypic characteristics again differentiated the strains from related species, and two new species of Microcella, Microcella humidisoli sp. nov. (type strain, MMS21-STM10T=KCTC 49773T=LMG 32522T) and Microcella daejeonensis sp. nov. (type strain, MMS21-STM12T=KCTC 49750T=LMG 32523T) are proposed accordingly. It was also evident that Marinisubtilis pacificus KN1116T should be reclassified as a new species of Microcella, and Microcella pacifica comb. nov. (type strain, KN1116T=CGMCC 1.17143T=KCTC 49299T) is proposed. In addition, an emended description of Microcella is proposed based on this study.
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Affiliation(s)
- Katya Michelle Molina Ayala
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
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Chukwudulue UM, Barger N, Dubovis M, Luzzatto Knaan T. Natural Products and Pharmacological Properties of Symbiotic Bacillota (Firmicutes) of Marine Macroalgae. Mar Drugs 2023; 21:569. [PMID: 37999393 PMCID: PMC10672036 DOI: 10.3390/md21110569] [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] [Received: 10/06/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
The shift from the terrestrial to the marine environment to discover natural products has given rise to novel bioactive compounds, some of which have been approved for human medicine. However, the ocean, which makes up nearly three-quarters of the Earth's surface, contains macro- and microorganisms whose natural products are yet to be explored. Among these underexplored marine organisms are macroalgae and their symbiotic microbes, such as Bacillota, a phylum of mostly Gram-positive bacteria previously known as Firmicutes. Macroalgae-associated Bacillota often produce chemical compounds that protect them and their hosts from competitive and harmful rivals. Here, we summarised the natural products made by macroalgae-associated Bacillota and their pharmacological properties. We discovered that these Bacillota are efficient producers of novel biologically active molecules. However, only a few macroalgae had been investigated for chemical constituents of their Bacillota: nine brown, five red and one green algae. Thus, Bacillota, especially from the marine habitat, should be investigated for potential pharmaceutical leads. Moreover, additional diverse biological assays for the isolated molecules of macroalgae Bacillota should be implemented to expand their bioactivity profiles, as only antibacterial properties were tested for most compounds.
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Affiliation(s)
| | | | | | - Tal Luzzatto Knaan
- Department of Marine Biology, The Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa 103301, Israel; (U.M.C.); (N.B.); (M.D.)
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Manochkumar J, Cherukuri AK, Kumar RS, Almansour AI, Ramamoorthy S, Efferth T. A critical review of machine-learning for "multi-omics" marine metabolite datasets. Comput Biol Med 2023; 165:107425. [PMID: 37696182 DOI: 10.1016/j.compbiomed.2023.107425] [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] [Received: 05/30/2023] [Revised: 07/12/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
During the last decade, genomic, transcriptomic, proteomic, metabolomic, and other omics datasets have been generated for a wide range of marine organisms, and even more are still on the way. Marine organisms possess unique and diverse biosynthetic pathways contributing to the synthesis of novel secondary metabolites with significant bioactivities. As marine organisms have a greater tendency to adapt to stressed environmental conditions, the chance to identify novel bioactive metabolites with potential biotechnological application is very high. This review presents a comprehensive overview of the available "-omics" and "multi-omics" approaches employed for characterizing marine metabolites along with novel data integration tools. The need for the development of machine-learning algorithms for "multi-omics" approaches is briefly discussed. In addition, the challenges involved in the analysis of "multi-omics" data and recommendations for conducting "multi-omics" study were discussed.
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Affiliation(s)
- Janani Manochkumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Aswani Kumar Cherukuri
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, 632014, India
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Siva Ramamoorthy
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany.
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Widada J, Damayanti E, Mustofa M, Dinoto A, Febriansah R, Hertiani T. Marine-Derived Streptomyces sennicomposti GMY01 with Anti-Plasmodial and Anticancer Activities: Genome Analysis, In Vitro Bioassay, Metabolite Profiling, and Molecular Docking. Microorganisms 2023; 11:1930. [PMID: 37630491 PMCID: PMC10458361 DOI: 10.3390/microorganisms11081930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
To discover novel antimalarial and anticancer compounds, we carried out a genome analysis, bioassay, metabolite profiling, and molecular docking of marine sediment actinobacteria strain GMY01. The whole-genome sequence analysis revealed that Streptomyces sp. GMY01 (7.9 Mbp) is most similar to Streptomyces sennicomposti strain RCPT1-4T with an average nucleotide identity (ANI) and ANI based on BLAST+ (ANIb) values of 98.09 and 97.33% (>95%). An in vitro bioassay of the GMY01 bioactive on Plasmodium falciparum FCR3, cervical carcinoma of HeLa cell and lung carcinoma of HTB cells exhibited moderate activity (IC50 value of 46.06; 27.31 and 33.75 µg/mL) with low toxicity on Vero cells as a normal cell (IC50 value of 823.3 µg/mL). Metabolite profiling by LC-MS/MS analysis revealed that the active fraction of GMY01 contained carbohydrate-based compounds, C17H29NO14 (471.15880 Da) as a major compound (97.50%) and mannotriose (C18H32O16; 504.16903 Da, 1.96%) as a minor compound. Molecular docking analysis showed that mannotriose has a binding affinity on glutathione reductase (GR) and glutathione-S-transferase (GST) of P. falciparum and on autophagy proteins (mTORC1 and mTORC2) of cancer cells. Streptomyces sennicomposti GMY01 is a potential bacterium producing carbohydrate-based bioactive compounds with anti-plasmodial and anticancer activities and with low toxicity to normal cells.
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Affiliation(s)
- Jaka Widada
- Department of Agricultural Microbiology, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Ema Damayanti
- Research Center for Food Technology and Processing, National Research and Innovation Agency (BRIN), Gunungkidul 55861, Indonesia;
| | - Mustofa Mustofa
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gajah Mada, Yogyakarta 55281, Indonesia;
| | - Achmad Dinoto
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia;
| | - Rifki Febriansah
- Faculty of Medicine and Health Sciences, Universitas Muhammadiyah, Yogyakarta 55183, Indonesia;
| | - Triana Hertiani
- Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia;
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Widada J, Damayanti E, Herdini C, Wijayanti N, Hosoyama A, Yamazoe A, Suzuki-Minakuchi C, Hariwiyanto B, Mubarika S, Dinoto A, Nojiri H. Draft Genome Sequence of the Marine-Derived, Anticancer Compound-Producing Bacterium Streptomyces sp. Strain GMY01. Microbiol Resour Announc 2023:e0136620. [PMID: 37140375 DOI: 10.1128/mra.01366-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
The marine Streptomyces sp. strain GMY01 was isolated from Indonesian marine sediment. Genome mining analysis revealed that GMY01 has 28 biosynthetic gene clusters, dominated by genes encoding nonribosomal peptide synthetase and polyketide synthase.
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Affiliation(s)
- Jaka Widada
- Department of Agricultural Microbiology, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ema Damayanti
- Research Center for Food Technology and Processing, National Research and Innovation Agency, Yogyakarta, Indonesia
| | - Camelia Herdini
- Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Akira Hosoyama
- Biological Resource Center, National Institute of Technology and Evaluation, Nishihara, Shibuya-ku, Tokyo, Japan
| | - Atsushi Yamazoe
- Biological Resource Center, National Institute of Technology and Evaluation, Nishihara, Shibuya-ku, Tokyo, Japan
| | - Chiho Suzuki-Minakuchi
- Biological Resource Center, National Institute of Technology and Evaluation, Nishihara, Shibuya-ku, Tokyo, Japan
| | - Bambang Hariwiyanto
- Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sofia Mubarika
- Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Achmad Dinoto
- Research Center for Applied Microbiology, National Research and Innovation Agency, Cibinong, Indonesia
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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In Silico Prediction of Secondary Metabolites and Biosynthetic Gene Clusters Analysis of Streptomyces thinghirensis HM3 Isolated from Arid Soil. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Natural products produced by microorganisms are considered an important resource of bioactive secondary metabolites, such as anticancer, antifungal, antibiotic, and immunosuppressive molecules. Streptomyces are the richest source of bioactive natural products via possessing a wide number of secondary metabolite biosynthetic gene clusters (SM-BGCs). Based on rapid development in sequencing technologies with advances in genome mining, exploring the newly isolated Streptomyces species for possible new secondary metabolites is mandatory to find novel natural products. The isolated Streptomyces thinghirensis strain HM3 from arid and sandy texture soil in Qassim, SA, exerted inhibition activity against tested animal pathogenic Gram-positive bacteria and pathogenic fungal species. In this study, we report the draft genome of S. thinghirensis strain HM3, which consists of 7,139,324 base pairs (bp), with an average G+C content of 71.49%, predicting 7949 open reading frames, 12 rRNA operons (5S, 16S, 23S) and 60 tRNAs. An in silico analysis of strain HM3 genome by the antiSMASH and PRISM 4 online software for SM-BGCs predicted 16 clusters, including four terpene, one lantipeptide, one siderophore, two polyketide synthase (PKS), two non-ribosomal peptide synthetase (NRPS) cluster)/NRPS-like fragment, two RiPP/RiPP-like (ribosomally synthesised and post-translationally modified peptide product), two butyrolactone, one CDPS (tRNA-dependent cyclodipeptide synthases), and one other (cluster containing a secondary metabolite-related protein that does not fit into any other category) BGC. The presented BGCs inside the genome, along with antibacterial and antifungal activity, indicate that HM3 may represent an invaluable source for new secondary metabolites.
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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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13
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Maimone NM, Junior MCP, de Oliveira LFP, Rojas-Villalta D, de Lira SP, Barrientos L, Núñez-Montero K. Metabologenomics analysis of Pseudomonas sp. So3.2b, an Antarctic strain with bioactivity against Rhizoctonia solani. Front Microbiol 2023; 14:1187321. [PMID: 37213498 PMCID: PMC10192879 DOI: 10.3389/fmicb.2023.1187321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/06/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Phytopathogenic fungi are a considerable concern for agriculture, as they can threaten the productivity of several crops worldwide. Meanwhile, natural microbial products are acknowledged to play an important role in modern agriculture as they comprehend a safer alternative to synthetic pesticides. Bacterial strains from underexplored environments are a promising source of bioactive metabolites. Methods We applied the OSMAC (One Strain, Many Compounds) cultivation approach, in vitro bioassays, and metabolo-genomics analyses to investigate the biochemical potential of Pseudomonas sp. So3.2b, a strain isolated from Antarctica. Crude extracts from OSMAC were analyzed through HPLC-QTOF-MS/MS, molecular networking, and annotation. The antifungal potential of the extracts was confirmed against Rhizoctonia solani strains. Moreover, the whole-genome sequence was studied for biosynthetic gene clusters (BGCs) identification and phylogenetic comparison. Results and Discussion Molecular networking revealed that metabolite synthesis has growth media specificity, and it was reflected in bioassays results against R. solani. Bananamides, rhamnolipids, and butenolides-like molecules were annotated from the metabolome, and chemical novelty was also suggested by several unidentified compounds. Additionally, genome mining confirmed a wide variety of BGCs present in this strain, with low to no similarity with known molecules. An NRPS-encoding BGC was identified as responsible for producing the banamides-like molecules, while phylogenetic analysis demonstrated a close relationship with other rhizosphere bacteria. Therefore, by combining -omics approaches and in vitro bioassays, our study demonstrates that Pseudomonas sp. So3.2b has potential application to agriculture as a source of bioactive metabolites.
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Affiliation(s)
- Naydja Moralles Maimone
- 'Luiz de Queiroz' Superior College of Agriculture, Department of Math, Chemistry, and Statistics, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Mario Cezar Pozza Junior
- 'Luiz de Queiroz' Superior College of Agriculture, Department of Math, Chemistry, and Statistics, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Lucianne Ferreira Paes de Oliveira
- 'Luiz de Queiroz' Superior College of Agriculture, Department of Math, Chemistry, and Statistics, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Dorian Rojas-Villalta
- Biotechnology Research Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Simone Possedente de Lira
- 'Luiz de Queiroz' Superior College of Agriculture, Department of Math, Chemistry, and Statistics, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Leticia Barrientos
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
- *Correspondence: Leticia Barrientos, ; Kattia Núñez-Montero,
| | - Kattia Núñez-Montero
- Facultad Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Temuco, Chile
- *Correspondence: Leticia Barrientos, ; Kattia Núñez-Montero,
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The Diversity of Deep-Sea Actinobacteria and Their Natural Products: An Epitome of Curiosity and Drug Discovery. DIVERSITY 2022. [DOI: 10.3390/d15010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bioprospecting of novel antibiotics has been the conventional norm of research fostered by researchers worldwide to combat drug resistance. With the exhaustion of incessant leads, the search for new chemical entities moves into uncharted territories such as the deep sea. The deep sea is a furthermost ecosystem with much untapped biodiversity thriving under extreme conditions. Accordingly, it also encompasses a vast pool of ancient natural products. Actinobacteria are frequently regarded as the bacteria of research interest due to their inherent antibiotic-producing capabilities. These interesting groups of bacteria occupy diverse ecological habitats including a multitude of different deep-sea habitats. In this review, we provide a recent update on the novel species and compounds of actinomycetes from the deep-sea environments within a period of 2016–2022. Within this period, a total of 24 new species of actinomycetes were discovered and characterized as well as 101 new compounds of various biological activities. The microbial communities of various deep-sea ecosystems are the emerging frontiers of bioprospecting.
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Zheng X, Li Y, Guan M, Wang L, Wei S, Li YC, Chang CY, Xu Z. Biomimetic Total Synthesis of the Spiroindimicin Family of Natural Products. Angew Chem Int Ed Engl 2022; 61:e202208802. [PMID: 35904849 DOI: 10.1002/anie.202208802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Indexed: 12/24/2022]
Abstract
A unified strategy for the biomimetic total synthesis of the spiroindimicin family of natural products was reported. Key transformations include a one-pot two-enzyme-catalyzed oxidative dimerization of L-tryptophan/5-chloro-L-tryptophan to afford the bis-indole precursors chromopyrrolic acid/5',5''-dichloro-chromopyrrolic acid, and regioselective C3'-C2'' and C3'-C4'' bond formation converting a common bis-indole skeleton to two skeletally different natural products, including (±)-spiroindimicins D and G with a [5,5] spiro-ring skeleton, and (±)-spiroindimicins A and H with a [5,6] spiro-ring skeleton, respectively.
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Affiliation(s)
- Xikang Zheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Yan Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Mengtie Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Lingyue Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Shilong Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Yi-Cheng Li
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, P. R. China
| | - Chin-Yuan Chang
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, P. R. China
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
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Zhou W, Alharbi HA, Hummingbird E, Keatinge-Clay AT, Mahmud T. Functional Studies and Revision of the NFAT-133/TM-123 Biosynthetic Pathway in Streptomyces pactum. ACS Chem Biol 2022; 17:2039-2045. [PMID: 35904416 PMCID: PMC9391300 DOI: 10.1021/acschembio.2c00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biosynthetic gene cluster of NFAT-133, an inhibitor of the nuclear factor of activated T cells, was recently identified in Streptomyces pactum ATCC 27456. This cluster is conspicuous by its highly disordered noncollinear type I modular polyketide synthase (PKS) genes that encode PKSs with one module more than those expected for the heptaketide NFAT-133 biosynthesis. Thus, the major metabolite NFAT-133 was proposed to derive from an octaketide analogue, TM-123. Here, we report that further bioinformatic analysis and gene inactivation studies suggest that NFAT-133 is not derived from TM-123 but rather a product of programmed KS7 extension skipping of a nascent heptaketide from the PKS assembly line that produces TM-123. Furthermore, identification of NFAT-133/TM-123 analogues from mutants of the ATCC 27456 strain suggests that NftN (a putative dehydrogenase), NftE (a cytochrome P450), and NftG (a putative hydrolase/decarboxylase) function "in trans" during the polyketide chain assembly processes.
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Affiliation(s)
- Wei Zhou
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Hattan A. Alharbi
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Eshe Hummingbird
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | | | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
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Zheng X, Li Y, Guan M, Wang L, Wei S, Li YC, Chang CY, Xu Z. Biomimetic Total Synthesis of the Spiroindimicin Family of Natural Products. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xikang Zheng
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Yan Li
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Mengtie Guan
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Lingyue Wang
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Shilong Wei
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences CHINA
| | - Yi-Cheng Li
- National Yang Ming Chiao Tung University Department of Biological Sciences and Technology TAIWAN
| | - Chin-Yuan Chang
- National Yang Ming Chiao Tung University Department of Biological Sciences and Technology TAIWAN
| | - Zhengren Xu
- Peking University State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences 38 Xueyuan Road, Haidian District 100191 Beijing CHINA
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18
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Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13030031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp.
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Complete genome analysis reveals secondary metabolite biosynthetic capabilities of Streptomyces sp. R527F isolated from the Arctic Ocean. Mar Genomics 2022; 63:100949. [DOI: 10.1016/j.margen.2022.100949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/19/2022] [Accepted: 03/20/2022] [Indexed: 11/20/2022]
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20
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Kaari M, Manikkam R, Baskaran A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:448-467. [PMID: 35394575 DOI: 10.1007/s10126-022-10118-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: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.
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Affiliation(s)
- Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India.
| | - Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
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Sedeek AM, Ismail MM, Elsayed TR, Ramadan MA. Recent methods for discovering novel bioactive metabolites, specifically antimicrobial agents, from marine-associated microorganisms. Lett Appl Microbiol 2022; 75:511-525. [PMID: 35485872 DOI: 10.1111/lam.13728] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/08/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022]
Abstract
Marine microorganisms are a promising source for novel natural compounds with many medical and biotechnological applications. Here we demonstrate limitations and recent strategies for investigating the marine microbial community for novel bioactive metabolites, specifically those of antimicrobial potential. These strategies include culture-dependent methods such as modifying the standard culture media, including changing the gelling agent, dissolving vehicle, media supplementation, and preparation to access a broader range of bacterial diversity from marine samples. Furthermore, we discuss strategies like in situ cultivation, dilution-to-extinction cultivation, and long-term incubation. We are presenting recent applications of culture-independent methods such as genome mining, proteomics profiling, and the application of metagenomics as a novel strategy for structure confirmation in the discovery of the marine microorganism for novel antimicrobial metabolites. We present this review as a simple guide and a helpful resource for those who seek to enter the challenging field of applied marine microbiology.
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Affiliation(s)
- Abdelrahman M Sedeek
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismaillia, 41522, Egypt
| | - Maha M Ismail
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Tarek R Elsayed
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Egypt, Giza, 12613, Egypt
| | - Mohamed A Ramadan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
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22
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Hosseini H, Al-Jabri HM, Moheimani NR, Siddiqui SA, Saadaoui I. Marine microbial bioprospecting: Exploitation of marine biodiversity towards biotechnological applications-a review. J Basic Microbiol 2022; 62:1030-1043. [PMID: 35467037 DOI: 10.1002/jobm.202100504] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 11/09/2022]
Abstract
The increase in the human population causes an increase in the demand for nutritional supplies and energy resources. Thus, the novel, natural, and renewable resources became of great interest. Here comes the optimistic role of bioprospecting as a promising tool to isolate novel and interesting molecules and microorganisms from the marine environment as alternatives to the existing resources. Bioprospecting of marine metabolites and microorganisms with high biotechnological potentials has gained wide interest due to the variability and richness of the marine environment. Indeed, the existence of extreme conditions that increases the adaptability of marine organisms, especially planktons, allow the presence of interesting biological species that are able to produce novel compounds with multiple health benefits and high economical value. This review aims to provide a comprehensive overview of marine microbial bioprospecting as a growing field of interest. It emphasizes functional bioprospecting that facilitates the discovery of interesting metabolites. Marine bioprospecting was also discussed from a legal aspect for the first time, focusing on the shortcomings of international law. We also summarized the challenges facing bioprospecting in the marine environment including economic feasibility issues.
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Affiliation(s)
- Hoda Hosseini
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Hareb M Al-Jabri
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Navid R Moheimani
- Algae R&D Centre, Harry Buttler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Simil A Siddiqui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Imen Saadaoui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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23
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Erdenetsogt U, Nadmid S, Paetz C, Dahse HM, Voigt K, Gotov C, Boland W, Dagvadorj E. New Guaianolide Sesquiterpene Lactones and Other Constituents from Pyrethrum pulchrum. PLANTA MEDICA 2022; 88:380-388. [PMID: 34352920 DOI: 10.1055/a-1554-2866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Pyrethrum pulchrum is a rare Mongolian plant species that has been traditionally used as an ingredient in various remedies. Bioactivity-guided fractionation performed on the methanol extract of its aerial parts led to the isolation of 2 previously undescribed guaianolide-type sesquiterpene lactones, namely 1β,10β-epoxy-8α-hydroxyguaia-3,11(13)-dien-6,12-olide (1: ) and 1,8,10-trihydroxyguaia-3,11(13)-dien-6,12-olide (2: ), along with the isolation or chromatographic identification of 11 compounds, arglabin (3: ), 3β-hydroxycostunolide (4: ), isocostic acid (5: ), (E)-9-(2-thienyl)-6-nonen-8-yn-3-ol (6: ), (Z)-9-(2-thienyl)-6-nonen-8-yn-3-ol (7: ), N 1,N 5,N 10,N 14-tetra-p-coumaroyl spermine (8: ), chlorogenic acid (9: ), 3,5-di-O-caffeoylquinic acid (10: ), 3,5-di-O-caffeoylquinic acid methyl ester (11: ), 3,4-di-O-caffeoylquinic acid (12: ), and tryptophan (13: ). Their structures were assigned based on spectroscopic and spectrometric data. The antimicrobial, antiproliferative and cytotoxic activities of selected compounds were evaluated. The new compounds showed weak to moderate antimicrobial activity. Arglabin (3: ), the major sesquiterpene lactone found in the methanol extract of P. pulchrum, exhibited the highest activity against human cancer lines, while compound 1: also possesses significant antiproliferative activity against leukemia cells.
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Affiliation(s)
| | - Suvd Nadmid
- Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | | | - Hans-Martin Dahse
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Jena, Germany
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Jena, Germany
| | - Choijamts Gotov
- Otoch Manramba University of Mongolia, Ulaanbaatar, Mongolia
| | - Wilhelm Boland
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Enkhmaa Dagvadorj
- Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
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Wang J, Pang X, Chen C, Gao C, Zhou X, Liu Y, Luo X. Chemistry, Biosynthesis, and Biological Activity of Halogenated Compounds Produced by Marine Microorganisms. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jiamin Wang
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Xiaoyan Pang
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
| | - Chunmei Chen
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Chenghai Gao
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
| | - Xuefeng Zhou
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Xiaowei Luo
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
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De Rop AS, Rombaut J, Willems T, De Graeve M, Vanhaecke L, Hulpiau P, De Maeseneire SL, De Mol ML, Soetaert WK. Novel Alkaloids from Marine Actinobacteria: Discovery and Characterization. Mar Drugs 2021; 20:md20010006. [PMID: 35049861 PMCID: PMC8777666 DOI: 10.3390/md20010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 01/03/2023] Open
Abstract
The marine environment is an excellent resource for natural products with therapeutic potential. Its microbial inhabitants, often associated with other marine organisms, are specialized in the synthesis of bioactive secondary metabolites. Similar to their terrestrial counterparts, marine Actinobacteria are a prevalent source of these natural products. Here, we discuss 77 newly discovered alkaloids produced by such marine Actinobacteria between 2017 and mid-2021, as well as the strategies employed in their elucidation. While 12 different classes of alkaloids were unraveled, indoles, diketopiperazines, glutarimides, indolizidines, and pyrroles were most dominant. Discoveries were mainly based on experimental approaches where microbial extracts were analyzed in relation to novel compounds. Although such experimental procedures have proven useful in the past, the methodologies need adaptations to limit the chance of compound rediscovery. On the other hand, genome mining provides a different angle for natural product discovery. While the technology is still relatively young compared to experimental screening, significant improvement has been made in recent years. Together with synthetic biology tools, both genome mining and extract screening provide excellent opportunities for continued drug discovery from marine Actinobacteria.
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Affiliation(s)
- Anne-Sofie De Rop
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (A.-S.D.R.); (J.R.); (T.W.); (M.L.D.M.); (W.K.S.)
| | - Jeltien Rombaut
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (A.-S.D.R.); (J.R.); (T.W.); (M.L.D.M.); (W.K.S.)
| | - Thomas Willems
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (A.-S.D.R.); (J.R.); (T.W.); (M.L.D.M.); (W.K.S.)
| | - Marilyn De Graeve
- Laboratory of Chemical Analysis (LCA), Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (M.D.G.); (L.V.)
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis (LCA), Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (M.D.G.); (L.V.)
| | - Paco Hulpiau
- BioInformatics Knowledge Center (BiKC), Campus Station Brugge, Howest University of Applied Sciences, Rijselstraat 5, 8200 Bruges, Belgium;
| | - Sofie L. De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (A.-S.D.R.); (J.R.); (T.W.); (M.L.D.M.); (W.K.S.)
- Correspondence:
| | - Maarten L. De Mol
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (A.-S.D.R.); (J.R.); (T.W.); (M.L.D.M.); (W.K.S.)
| | - Wim K. Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (A.-S.D.R.); (J.R.); (T.W.); (M.L.D.M.); (W.K.S.)
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Petruncio G, Shellnutt Z, Elahi-Mohassel S, Alishetty S, Paige M. Skipped dienes in natural product synthesis. Nat Prod Rep 2021; 38:2187-2213. [PMID: 34913051 DOI: 10.1039/d1np00012h] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Covering: 2000-2020The 1,4-diene motif, also known as a skipped diene, is widespread across various classes of natural products including alkaloids, fatty acids, terpenoids, and polyketides as part of either the finalized structure or a biosynthetic intermediate. The prevalence of this nonconjugated diene system in nature has resulted in numerous encounters in the total synthesis literature. However, skipped dienes have not been extensively reviewed, which could be attributed to overshadowing by the more recognized 1,3-diene system. In this review, we aim to highlight the relevance of skipped dienes in natural products through the lens of total synthesis. Subjects that will be covered include nomenclature, structural properties, prevalence in natural products, synthetic strategies and the future direction of the field.
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Affiliation(s)
- Greg Petruncio
- Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, Virginia 20110, USA.
| | - Zachary Shellnutt
- Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, Virginia 20110, USA.
| | - Synah Elahi-Mohassel
- Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, Virginia 20110, USA.
| | - Suman Alishetty
- Department of Bioengineering, George Mason University, 10920 George Mason Circle, Manassas, Virginia 20110, USA
| | - Mikell Paige
- Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, Virginia 20110, USA.
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Hu Y, Chen S, Yang F, Dong S. Marine Indole Alkaloids-Isolation, Structure and Bioactivities. Mar Drugs 2021; 19:658. [PMID: 34940657 PMCID: PMC8708922 DOI: 10.3390/md19120658] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 11/30/2022] Open
Abstract
Indole alkaloids are heterocyclic natural products with extensive pharmacological activities. As an important source of lead compounds, many clinical drugs have been derived from natural indole compounds. Marine indole alkaloids, from unique marine environments with high pressure, high salt and low temperature, exhibit structural diversity with various bioactivities, which attracts the attention of drug researchers. This article is a continuation of the previous two comprehensive reviews and covers the literature on marine indole alkaloids published from 2015 to 2021, with 472 new or structure-revised compounds categorized by sources into marine microorganisms, invertebrates, and plant-derived. The structures and bioactivities demonstrated in this article will benefit the synthesis and pharmacological activity study for marine indole alkaloids on their way to clinical drugs.
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Affiliation(s)
| | | | | | - Shuai Dong
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (Y.H.); (S.C.); (F.Y.)
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28
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Seipp K, Geske L, Opatz T. Marine Pyrrole Alkaloids. Mar Drugs 2021; 19:514. [PMID: 34564176 PMCID: PMC8471394 DOI: 10.3390/md19090514] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 12/13/2022] Open
Abstract
Nitrogen heterocycles are essential parts of the chemical machinery of life and often reveal intriguing structures. They are not only widespread in terrestrial habitats but can also frequently be found as natural products in the marine environment. This review highlights the important class of marine pyrrole alkaloids, well-known for their diverse biological activities. A broad overview of the marine pyrrole alkaloids with a focus on their isolation, biological activities, chemical synthesis, and derivatization covering the decade from 2010 to 2020 is provided. With relevant structural subclasses categorized, this review shall provide a clear and timely synopsis of this area.
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Affiliation(s)
| | | | - Till Opatz
- Department of Chemistry, Organic Chemistry Section, Johannes Gutenberg University, Duesbergweg 10–14, 55128 Mainz, Germany; (K.S.); (L.G.)
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29
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Krause J. Applications and Restrictions of Integrated Genomic and Metabolomic Screening: An Accelerator for Drug Discovery from Actinomycetes? Molecules 2021; 26:5450. [PMID: 34576921 PMCID: PMC8471533 DOI: 10.3390/molecules26185450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 02/07/2023] Open
Abstract
Since the golden age of antibiotics in the 1950s and 1960s actinomycetes have been the most prolific source for bioactive natural products. However, the number of discoveries of new bioactive compounds decreases since decades. New procedures (e.g., activating strategies or innovative fermentation techniques) were developed to enhance the productivity of actinomycetes. Nevertheless, compound identification remains challenging among others due to high rediscovery rates. Rapid and cheap genome sequencing as well as the advent of bioinformatical analysis tools for biosynthetic gene cluster identification in combination with mass spectrometry-based molecular networking facilitated the tedious process of dereplication. In recent years several studies have been dedicated to accessing the biosynthetic potential of Actinomyces species, especially streptomycetes, by using integrated genomic and metabolomic screening in order to boost the discovery rate of new antibiotics. This review aims to present the various possible applications of this approach as well as the newly discovered molecules, covering studies between 2014 and 2021. Finally, the effectiveness of this approach with regard to find new bioactive agents from actinomycetes will be evaluated.
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Affiliation(s)
- Janina Krause
- Abteilung Biomedizinische Grundlagen 1, Institut für Gesundheitsforschung und Bildung, Universität Osnabrück, 49076 Osnabrück, Germany
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30
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Králová S, Sandoval-Powers M, Fawwal DV, Degnes KF, Lewin AS, Klinkenberg G, Nguyen GS, Liles MR, Wentzel A. Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord. Front Microbiol 2021; 12:714233. [PMID: 34421874 PMCID: PMC8371330 DOI: 10.3389/fmicb.2021.714233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
Marine environments are home to an extensive number of microorganisms, many of which remain unexplored for taxonomic novelty and functional capabilities. In this study, a slow-growing Streptomyces strain expressing unique genomic and phenotypic characteristics, P38-E01T, was described using a polyphasic taxonomic approach. This strain is part of a collection of over 8,000 marine Actinobacteria isolates collected in the Trondheim fjord of Norway by SINTEF Industry (Trondheim, Norway) and the Norwegian University of Science and Technology (NTNU, Trondheim, Norway). Strain P38-E01T was isolated from the sediments of the Trondheim fjord, and phylogenetic analyses affiliated this strain with the genus Streptomyces, but it was not closely affiliated with other described species. The closest related type strains were Streptomyces daliensis YIM 31724T (98.6%), Streptomyces rimosus subsp. rimosus ATCC 10970T (98.4%), and Streptomyces sclerotialus NRRL ISP-5269T (98.3%). Predominant fatty acids were C16:0 iso, C16:0, and Summed Feature 3, and the predominant respiratory quinones were MK-10(H6), MK-10(H4), and MK9(H4). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphoglycolipid. The whole-cell sugars were glucose, ribose, and in minor amounts, mannose. The cell wall peptidoglycan contained LL-diaminopimelic acid. The draft genome has a size of 6.16 Mb, with a %G + C content of 71.4% and is predicted to contain at least 19 biosynthetic gene clusters encoding diverse secondary metabolites. Strain P38-E01T was found to inhibit the growth of the pathogenic yeast Candida albicans ATCC 90028 and a number of Gram-positive bacterial human and plant pathogens. Metabolites extracted from cultures of P38-E01T were analyzed by mass spectrometry, and it was found that the isolate produced the antifungal compound candicidin. Phenotypic and chemotaxonomic signatures, along with phylogenetic analyses, distinguished isolate P38-E01T from its closest neighbors; thus, this isolate represents a novel species of the genus Streptomyces for which the name Streptomyces tardus sp. nov. (P38-E01T = CCM 9049T = DSM 111582T) is proposed.
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Affiliation(s)
- Stanislava Králová
- Department of Biological Sciences, Auburn University, Auburn, AL, United States.,Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Dorelle V Fawwal
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Kristin F Degnes
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Anna Sofia Lewin
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Geir Klinkenberg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Giang-Son Nguyen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
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Al-shaibani MM, Radin Mohamed RMS, Sidik NM, Enshasy HAE, Al-Gheethi A, Noman E, Al-Mekhlafi NA, Zin NM. Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications. Molecules 2021; 26:molecules26154504. [PMID: 34361657 PMCID: PMC8347454 DOI: 10.3390/molecules26154504] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/14/2021] [Accepted: 07/22/2021] [Indexed: 12/08/2022] Open
Abstract
The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities' well-being.
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Affiliation(s)
- Muhanna Mohammed Al-shaibani
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Center for Diagnostic, Therapeutic and Investigative Studies, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia;
| | - Radin Maya Saphira Radin Mohamed
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Nik Marzuki Sidik
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli 17600, Kelantan, Malaysia
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Hesham Ali El Enshasy
- Institute of Bioproducts Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai 81310, Johor, Malaysia;
- City of Scientific Research and Technology Applications (SRTA), 21934 New Burg Al Arab, Alexandria, Egypt
| | - Adel Al-Gheethi
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Efaq Noman
- Applied Microbiology Department, Faculty of Applied Sciences, Taiz University, Taiz 6803, Yemen;
| | - Nabil Ali Al-Mekhlafi
- Atta-ur-Rahman Institute for Natural Product Discovery, UiTM, Puncak Alam Campus, Bandar Puncak Alam 42300, Selangor, Malaysia;
- Biochemical Technology Program, Department of Chemistry Faculty of Applied Science, Thamar University, Thamar P.O. Box 87246, Yemen
| | - Noraziah Mohamad Zin
- Center for Diagnostic, Therapeutic and Investigative Studies, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia;
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Zhang Z, Ray S, Imlay L, Callaghan LT, Niederstrasser H, Mallipeddi PL, Posner BA, Wetzel DM, Phillips MA, Smith MW. Total synthesis of (+)-spiroindimicin A and congeners unveils their antiparasitic activity. Chem Sci 2021; 12:10388-10394. [PMID: 34377425 PMCID: PMC8336461 DOI: 10.1039/d1sc02838c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/25/2021] [Indexed: 12/02/2022] Open
Abstract
The spiroindimicins are a unique class of chlorinated indole alkaloids characterized by three heteroaromatic rings structured around a congested spirocyclic stereocenter. Here, we report the first total synthesis of (+)-spiroindimicin A, which bears a challenging C-3′/C-5′′-linked spiroindolenine. We detail our initial efforts to effect a biomimetic oxidative spirocyclization from its proposed natural precursor, lynamicin D, and describe how these studies shaped our final abiotic 9-step solution to this complex alkaloid built around a key Pd-catalyzed asymmetric spirocyclization. Scalable access to spiroindimicins A, H, and their congeners has enabled discovery of their activity against several parasites relevant to human health, providing potential starting points for new therapeutics for the neglected tropical diseases leishmaniasis and African sleeping sickness. Spiroindimicins A and H have been synthesized for the first time via a key palladium-catalyzed spirocyclization. Access to these alkaloids and several congeners has allowed the discovery of their antiparasitic properties.![]()
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Affiliation(s)
- Zhen Zhang
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Sneha Ray
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Leah Imlay
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Lauren T Callaghan
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA .,Department of Pediatrics, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Hanspeter Niederstrasser
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Prema Latha Mallipeddi
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Bruce A Posner
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Dawn M Wetzel
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA .,Department of Pediatrics, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Myles W Smith
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
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Chanson A, Moreau CS, Duplais C. Assessing Biosynthetic Gene Cluster Diversity of Specialized Metabolites in the Conserved Gut Symbionts of Herbivorous Turtle Ants. Front Microbiol 2021; 12:678100. [PMID: 34267736 PMCID: PMC8277422 DOI: 10.3389/fmicb.2021.678100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
Cephalotes are herbivorous ants (>115 species) feeding on low-nitrogen food sources, and they rely on gut symbionts to supplement their diet by recycling nitrogen food waste into amino acids. These conserved gut symbionts, which encompass five bacterial orders, have been studied previously for their primary nitrogen metabolism; however, little is known about their ability to biosynthesize specialized metabolites which can play a role in bacterial interactions between communities living in close proximity in the gut. To evaluate the biosynthetic potential of their gut symbionts, we mine 14 cultured isolate genomes and gut metagenomes across 17 Cephalotes species to explore the biodiversity of biosynthetic gene clusters (BGCs) producing specialized metabolites. The diversity of BGCs across Cephalotes phylogeny was analyzed using sequence similarity networking and BGC phylogenetic reconstruction. Our results reveal that the conserved gut symbionts involved in the nutritional symbiosis possess 80% of all the 233 BGCs retrieved in this work. Furthermore, the phylogenetic analysis of BGCs reveals different patterns of distribution, suggesting different mechanisms of conservation. A siderophore BGC shows high similarity in a single symbiont across different ant host species, whereas a BGC encoding the production of non-ribosomal peptides (NRPs) found different symbionts within a single host species. Additionally, BGCs were abundant in four of the five bacterial orders of conserved symbionts co-occurring in the hindgut. However, one major symbiont localized alone in the midgut lack BGCs. Because the spatial isolation prevents direct interaction with other symbionts, this result supports the idea that BGCs are maintained in bacteria living in close proximity but are dispensable for an alone-living symbiont. These findings together pave the way for studying the mechanisms of BGC conservation and evolution in gut bacterial genomes associated with Cephalotes. This work also provides a genetic background for further study, aiming to characterize bacterial specialized metabolites and to understand their functional role in multipartite mutualisms between conserved gut symbionts and Cephalotes turtle ants.
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Affiliation(s)
- Anaïs Chanson
- Université de Guyane, UMR 8172 EcoFoG, AgroParisTech, CNRS, Cirad, INRAE, Université des Antilles, Kourou, France
| | - Corrie S. Moreau
- Department of Entomology and Ecology & Evolutionary Biology, Cornell University, Ithaca, NY, United States
| | - Christophe Duplais
- CNRS, UMR 8172 EcoFoG, AgroParisTech, Cirad, INRAE, Université des Antilles, Université de Guyane, Kourou, France
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Yun T, Zhang M, Zhou D, Jing T, Zang X, Qi D, Chen Y, Li K, Zhao Y, Tang W, Huang J, Wang W, Xie J. Anti-Foc RT4 Activity of a Newly Isolated Streptomyces sp. 5-10 From a Medicinal Plant ( Curculigo capitulata). Front Microbiol 2021; 11:610698. [PMID: 33552022 PMCID: PMC7862724 DOI: 10.3389/fmicb.2020.610698] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/21/2020] [Indexed: 01/25/2023] Open
Abstract
Fusarium wilt of banana caused by Fusarium oxysporum f. sp. cubense (Foc) is a disastrous soil-borne fungal disease. Foc tropical race 4 (Foc TR4) can infect almost all banana cultivars. Until now, there is a shortage of safety and effective control methods and commercial banana cultivars with a resistance against Foc TR4. Biocontrol using environmentally friendly microbes is a promising strategy for the management of Foc TR4. Here, a strain 5-10, newly isolated from a medicinal plant (Curculigo capitulata), exhibited a high antifungal activity against Foc TR4. Combing the morphological characteristics and molecular identification, strain 5-10 was classified as a Streptomyces genus. The sequenced genome revealed that more than 39 gene clusters were involved in the biosynthesis of secondary metabolites. Some multidrug resistance gene clusters were also identified such as mdtD, vatB, and vgaE. To improve the anti-Foc TR4 activity of the strain 5-10 extracts, an optimization method of fermentation broth was established. Antifungal activity increased by 72.13% under the fermentation system containing 2.86 g/L of NaCl and 11.57% of inoculation amount. After being treated with the strain 5-10 extracts, the Foc TR4 hyphae shrinked, deformed, and ruptured. The membrane integrity and cell ultrastructure incurred irreversible damage. Streptomyces sp. 5-10 extracts play a fungicidal role in Foc TR4. Hence, Streptomyces sp. 5-10 will be a potential biocontrol agent to manage fungal diseases by exploring the microbial fertilizer.
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Affiliation(s)
- Tianyan Yun
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Miaoyi Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
| | - Dengbo Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
| | - Tao Jing
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiaoping Zang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Dengfeng Qi
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
| | - Yufeng Chen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
| | - Kai Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
| | - Yankun Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
| | - Wen Tang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
| | - Jiaquan Huang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Wei Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
| | - Jianghui Xie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
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Desert Environments Facilitate Unique Evolution of Biosynthetic Potential in Streptomyces. Molecules 2021; 26:molecules26030588. [PMID: 33499369 PMCID: PMC7865587 DOI: 10.3390/molecules26030588] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 12/19/2022] Open
Abstract
Searching for new bioactive metabolites from the bacterial genus Streptomyces is a challenging task. Combined genomic tools and metabolomic screening of Streptomyces spp. native to extreme environments could be a promising strategy to discover novel compounds. While Streptomyces of desertic origin have been proposed as a source of new metabolites, their genome mining, phylogenetic analysis, and metabolite profiles to date are scarcely documented. Here, we hypothesized that Streptomyces species of desert environments have evolved with unique biosynthetic potential. To test this, along with an extensive characterization of biosynthetic potential of a desert isolate Streptomyces sp. SAJ15, we profiled phylogenetic relationships among the closest and previously reported Streptomyces of desert origin. Results revealed that Streptomyces strains of desert origin are closer to each other and relatively distinct from Streptomyces of other environments. The draft genome of strain SAJ15 was 8.2 Mb in size, which had 6972 predicted genes including 3097 genes encoding hypothetical proteins. Successive genome mining and phylogenetic analysis revealed the presence of putative novel biosynthetic gene clusters (BGCs) with low incidence in another Streptomyces. In addition, high-resolution metabolite profiling indicated the production of arylpolyene, terpenoid, and macrolide compounds in an optimized medium by strain SAJ15. The relative abundance of different BGCs in arid Streptomyces differed from the non-arid counterparts. Collectively, the results suggested a distinct evolution of desert Streptomyces with a unique biosynthetic potential.
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36
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Exometabolites of endospore-forming bacteria of Bacillus genus identified by genomic-metabolomic profiling. UKRAINIAN BIOCHEMICAL JOURNAL 2020. [DOI: 10.15407/ubj92.06.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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37
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Zhou W, Posri P, Abugrain ME, Weisberg AJ, Chang JH, Mahmud T. Biosynthesis of the Nuclear Factor of Activated T Cells Inhibitor NFAT-133 in Streptomyces pactum. ACS Chem Biol 2020; 15:3217-3226. [PMID: 33284588 DOI: 10.1021/acschembio.0c00775] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NFAT-133 is a Streptomyces-derived aromatic polyketide compound with immunosuppressive, antidiabetic, and antitrypanosomal activities. It inhibits transcription mediated by nuclear factor of activated T cells (NFAT), leading to the suppression of interleukin-2 expression and T cell proliferation. It also activates the AMPK pathway in L6 myotubes and increases glucose uptake. In addition to NFAT-133, a number of its congeners, e.g., panowamycins and benwamycins, have been identified. However, little is known about their modes of formation in the producing organisms. Through genome sequencing of Streptomyces pactum ATCC 27456, gene inactivation, and genetic complementation experiments, the biosynthetic gene cluster of NFAT-133 and its congeners has been identified. The cluster contains a highly disordered genetic organization of type I modular polyketide synthase genes with several genes that are necessary for the formation of the aromatic core unit and tailoring processes. In addition, a number of new analogs of NFAT-133 were isolated and their chemical structures elucidated. It is suggested that the heptaketide NFAT-133 is derived from an octaketide intermediate, TM-123. The current study shows yet another unusual biosynthetic pathway involving a noncanonical polyketide synthase assembly line to produce a group of small molecules with valuable bioactivities.
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Lee Y, Lee N, Hwang S, Kim K, Kim W, Kim J, Cho S, Palsson BO, Cho BK. System-level understanding of gene expression and regulation for engineering secondary metabolite production in Streptomyces. ACTA ACUST UNITED AC 2020; 47:739-752. [DOI: 10.1007/s10295-020-02298-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022]
Abstract
Abstract
The gram-positive bacterium, Streptomyces, is noticed for its ability to produce a wide array of pharmaceutically active compounds through secondary metabolism. To discover novel bioactive secondary metabolites and increase the production, Streptomyces species have been extensively studied for the past decades. Among the cellular components, RNA molecules play important roles as the messengers for gene expression and diverse regulations taking place at the RNA level. Thus, the analysis of RNA-level regulation is critical to understanding the regulation of Streptomyces’ metabolism and secondary metabolite production. A dramatic advance in Streptomyces research was made recently, by exploiting high-throughput technology to systematically understand RNA levels. In this review, we describe the current status of the system-wide investigation of Streptomyces in terms of RNA, toward expansion of its genetic potential for secondary metabolite synthesis.
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Affiliation(s)
- Yongjae Lee
- grid.37172.30 0000 0001 2292 0500 Department of Biological Sciences and KI for the BioCentury Korea Advanced Institute of Science and Technology 34141 Daejeon Republic of Korea
| | - Namil Lee
- grid.37172.30 0000 0001 2292 0500 Department of Biological Sciences and KI for the BioCentury Korea Advanced Institute of Science and Technology 34141 Daejeon Republic of Korea
| | - Soonkyu Hwang
- grid.37172.30 0000 0001 2292 0500 Department of Biological Sciences and KI for the BioCentury Korea Advanced Institute of Science and Technology 34141 Daejeon Republic of Korea
| | - Kangsan Kim
- grid.37172.30 0000 0001 2292 0500 Department of Biological Sciences and KI for the BioCentury Korea Advanced Institute of Science and Technology 34141 Daejeon Republic of Korea
| | - Woori Kim
- grid.37172.30 0000 0001 2292 0500 Department of Biological Sciences and KI for the BioCentury Korea Advanced Institute of Science and Technology 34141 Daejeon Republic of Korea
| | - Jihun Kim
- grid.37172.30 0000 0001 2292 0500 Department of Biological Sciences and KI for the BioCentury Korea Advanced Institute of Science and Technology 34141 Daejeon Republic of Korea
| | - Suhyung Cho
- grid.37172.30 0000 0001 2292 0500 Department of Biological Sciences and KI for the BioCentury Korea Advanced Institute of Science and Technology 34141 Daejeon Republic of Korea
| | - Bernhard O Palsson
- grid.266100.3 0000 0001 2107 4242 Department of Bioengineering University of California San Diego 92093 La Jolla CA USA
- grid.266100.3 0000 0001 2107 4242 Department of Pediatrics University of California San Diego 92093 La Jolla CA USA
- grid.5170.3 0000 0001 2181 8870 Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark 2800 Lyngby Denmark
| | - Byung-Kwan Cho
- grid.37172.30 0000 0001 2292 0500 Department of Biological Sciences and KI for the BioCentury Korea Advanced Institute of Science and Technology 34141 Daejeon Republic of Korea
- Intelligent Synthetic Biology Center 34141 Daejeon Republic of Korea
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Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces. Comput Struct Biotechnol J 2020; 18:1548-1556. [PMID: 32637051 PMCID: PMC7327026 DOI: 10.1016/j.csbj.2020.06.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 01/04/2023] Open
Abstract
Streptomyces are a large and valuable resource of bioactive and complex secondary metabolites, many of which have important clinical applications. With the advances in high throughput genome sequencing methods, various in silico genome mining strategies have been developed and applied to the mapping of the Streptomyces genome. These studies have revealed that Streptomyces possess an even more significant number of uncharacterized silent secondary metabolite biosynthetic gene clusters (smBGCs) than previously estimated. Linking smBGCs to their encoded products has played a critical role in the discovery of novel secondary metabolites, as well as, knowledge-based engineering of smBGCs to produce altered products. In this mini review, we discuss recent progress in Streptomyces genome sequencing and the application of genome mining approaches to identify and characterize smBGCs. Furthermore, we discuss several challenges that need to be overcome to accelerate the genome mining process and ultimately support the discovery of novel bioactive compounds.
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Chu L, Huang J, Muhammad M, Deng Z, Gao J. Genome mining as a biotechnological tool for the discovery of novel marine natural products. Crit Rev Biotechnol 2020; 40:571-589. [PMID: 32308042 DOI: 10.1080/07388551.2020.1751056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Compared to terrestrial environments, the oceans harbor a variety of environments, creating higher biodiversity, which gives marine natural products a high occurrence of significant biology and novel chemistry. However, traditional bioassay-guided isolation and purification strategies are severely limiting the discovery of additional novel natural products from the ocean. With an increasing number of marine microorganisms being sequenced, genome mining is gradually becoming a powerful tool to retrieve novel marine natural products. In this review, we have summarized genome mining approaches used to analyze key enzymes of biosynthetic pathways and predict the chemical structure of new gene clusters by introducing successful stories that used genome mining strategy to identify new marine-derived compounds. Furthermore, we also put forward challenges for genome mining techniques and their proposed solutions. The detailed analysis of the genome mining strategy will help researchers to understand this novel technique and its application. With the development of a genome sequence, genome mining strategies will be applied more widely, which will drive rapid development in the field of marine natural product development.
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Affiliation(s)
- Leixia Chu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinping Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mustafa Muhammad
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangtao Gao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Odekina PA, Agbo MO, Omeje EO. Antimicrobial and Antioxidant Activities of Novel Marine Bacteria (Bacillus 2011SOCCUF3) Isolated from Marine Sponge (Spongia officinalis). PHARMACEUTICAL SCIENCES 2020. [DOI: 10.34172/ps.2019.59] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background
: Bacillus species represent a rich source of new bioactive metabolites that can combat diseases. Methods: Bacillus strain was isolated from the marine sponge Spongia officinalis and routinely maintained on marine broth. The bacteria strain was identified as Bacillus 2011SOCCUF3 using 16S rDNA sequencing. The strain was cultured on Tryptone Casein Oat Soluble Starch (TCOATSS) media with continuous agitation for 4 days. The fermented broth was centrifuged, and the supernatant was mixed with 10% (w/v) of adsorbent resin (XAD-7HP and XAD-16N, 1:1) and shaken continuously at a reduced speed for 7 h; and the resin was collected by filtration through sintered glass funnel and washed with MilliQ water, and then eluted with methanol to obtain the extract. The extract was evaporated in vacuo at reduced temperature and pressure to obtain the dry extract. The dry extract was purified by vacuum liquid chromatography, eluting with methanol in acetone gradient. The in vitro antimicrobial and antioxidant activities were investigated using the agar-well diffusion, DPPH scavenging and the phosphomolybdate methods respectively. Results: The extract and fractions showed good antimicrobial activities with minimum inhibitory concentration range of <1.0 mg/mL. The extract and fractions also exhibited good antioxidant activities with their IC50 values been comparable to the standard. Conclusion: Thus, a novel Bacillus strain isolated from the marine sponge (Spongia officinalis) obtained from Cortiou and Riou, France, exhibited promising antimicrobial and antioxidant activities.
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Affiliation(s)
- Peter Adukwu Odekina
- Natural Products Unit, Department of Pharmaceutical & Medicinal Chemistry, University of Nigeria Nsukka 410001, Enugu State, Nigeria
| | - Matthias Onyebuchi Agbo
- Natural Products Unit, Department of Pharmaceutical & Medicinal Chemistry, University of Nigeria Nsukka 410001, Enugu State, Nigeria
- School of Chemistry, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Edwin Ogochukwu Omeje
- Natural Products Unit, Department of Pharmaceutical & Medicinal Chemistry, University of Nigeria Nsukka 410001, Enugu State, Nigeria
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Enhancement of Antibacterial Activity of Paludifilum halophilum and Identification of N-(1-Carboxy-ethyl)-phthalamic Acid as the Main Bioactive Compound. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4805706. [PMID: 32104693 PMCID: PMC7038168 DOI: 10.1155/2020/4805706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/03/2019] [Accepted: 12/12/2019] [Indexed: 11/17/2022]
Abstract
The aim of this study was to determine the combined effect of fermentation parameters and enhance the production of cellular biomass and antibacterial compounds from Paludifilum halophilum SMBg3 using the response surface methodology (RSM). Eight variables were screened to assess the effects of fermentation parameters on growth and metabolite production by Taguchi experimental design. Among these, the initial pH, temperature, and the percentage of MgSO4·7H2O in the medium were found to be most influential. The Box-Behnken design was applied to derive a statistical model for the optimization of these three fermentation parameters. The optimal parameters were initial pH: 8.3, temperature growth: 44°C, and MgSO4·7H2O: 1.6%, respectively. The maximum yield of biomass and metabolite production were, respectively, 11 mg/mL dry weight and 15.5 mm inhibition zone diameter against Salmonella enterica, which were in agreement with predicted values. The bioactive compounds were separated by the thick-layer chromatography technique and analyzed by GC/MS, NMR (1D and 2D), and Fourier-transform infrared spectroscopy (FT-IR). In addition to several fatty acids, N-(1-carboxy-ethyl)-phthalamic acid was identified as the main antibacterial compound. This element exhibited a potent activity against the ciprofloxacin-resistant Salmonella enterica CIP 8039 and Pseudomonas aeruginosa ATCC 9027 with a minimum inhibitory concentration (MIC) value range of 12.5-25 μg/mL. Results demonstrated that P. halophilum strain SMBg3 is a promising resource for novel antibacterial production due to its high-level yield potential and the capacity for large-scale fermentation.
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Stuart KA, Welsh K, Walker MC, Edrada-Ebel R. Metabolomic tools used in marine natural product drug discovery. Expert Opin Drug Discov 2020; 15:499-522. [PMID: 32026730 DOI: 10.1080/17460441.2020.1722636] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: The marine environment is a very promising resource for natural product research, with many of these reaching the market as new drugs, especially in the field of cancer therapy as well as the drug discovery pipeline for new antimicrobials. Exploitation for bioactive marine compounds with unique structures and novel bioactivity such as the isoquinoline alkaloid; trabectedin, the polyether macrolide; halichondrin B, and the peptide; dolastatin 10, requires the use of analytical techniques, which can generate unbiased, quantitative, and qualitative data to benefit the biodiscovery process. Metabolomics has shown to bridge this understanding and facilitate the development of new potential drugs from marine sources and particularly their microbial symbionts.Areas covered: In this review, articles on applied secondary metabolomics ranging from 1990-2018 as well as to the last quarter of 2019 were probed to investigate the impact of metabolomics on drug discovery for new antibiotics and cancer treatment.Expert opinion: The current literature review highlighted the effectiveness of metabolomics in the study of targeting biologically active secondary metabolites from marine sources for optimized discovery of potential new natural products to be made accessible to a R&D pipeline.
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Affiliation(s)
- Kevin Andrew Stuart
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Keira Welsh
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Molly Clare Walker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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Rodríguez Estévez M, Gummerlich N, Myronovskyi M, Zapp J, Luzhetskyy A. Benzanthric Acid, a Novel Metabolite From Streptomyces albus Del14 Expressing the Nybomycin Gene Cluster. Front Chem 2020; 7:896. [PMID: 31998688 PMCID: PMC6965495 DOI: 10.3389/fchem.2019.00896] [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: 09/04/2019] [Accepted: 12/12/2019] [Indexed: 11/17/2022] Open
Abstract
Streptomycetes constitute a diverse bacterial group able to produce a wide variety of secondary metabolites with potential applications in the pharmacy industry. However, the genes responsible for the biosynthesis of these compounds are very frequently inactive or expressed at very low levels under standard laboratory cultivation conditions. Therefore, the activation or upregulation of secondary metabolite biosynthesis genes is a crucial step for the discovery of new bioactive natural products. We have recently reported the discovery of the biosynthetic genes for the antibiotic nybomycin (nyb genes) in Streptomyces albus subsp. chlorinus. The nyb genes were expressed in the heterologous host Streptomyces albus Del14, which produces not only nybomycin, but also a novel compound. In this study, we describe the isolation, purification, and structure elucidation of the new substance named benzanthric acid.
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Affiliation(s)
| | - Nils Gummerlich
- Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Josef Zapp
- Department of Pharmacy, Institute of Pharmaceutical Biology, University of Saarland, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany.,Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
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Ahmed Y, Rebets Y, Estévez MR, Zapp J, Myronovskyi M, Luzhetskyy A. Engineering of Streptomyces lividans for heterologous expression of secondary metabolite gene clusters. Microb Cell Fact 2020; 19:5. [PMID: 31918711 PMCID: PMC6950998 DOI: 10.1186/s12934-020-1277-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/02/2020] [Indexed: 12/04/2022] Open
Abstract
Background Heterologous expression of secondary metabolite gene clusters is used to achieve increased production of desired compounds, activate cryptic gene clusters, manipulate clusters from genetically unamenable strains, obtain natural products from uncultivable species, create new unnatural pathways, etc. Several Streptomyces species are genetically engineered for use as hosts for heterologous expression of gene clusters. S. lividans TK24 is one of the most studied and genetically tractable actinobacteria, which remain untapped. It was therefore important to generate S. lividans chassis strains with clean metabolic backgrounds. Results In this study, we generated a set of S. lividans chassis strains by deleting endogenous gene clusters and introducing additional φC31 attB loci for site-specific integration of foreign DNA. In addition to the simplified metabolic background, the engineered S. lividans strains had better growth characteristics than the parental strain in liquid production medium. The utility of the developed strains was validated by expressing four secondary metabolite gene clusters responsible for the production of different classes of natural products. Engineered strains were found to be superior to the parental strain in production of heterologous natural products. Furthermore, S. lividans-based strains were better producers of amino acid-based natural products than other tested common hosts. Expression of a Streptomyces albus subsp. chlorinus NRRL B-24108 genomic library in the modified S. lividans ΔYA9 and S. albus Del14 strains resulted in the production of 7 potentially new compounds, only one of which was produced in both strains. Conclusion The constructed S. lividans-based strains are a great complement to the panel of heterologous hosts for actinobacterial secondary metabolite gene expression. The expansion of the number of such engineered strains will contribute to an increased success rate in isolation of new natural products originating from the expression of genomic and metagenomic libraries, thus raising the chance to obtain novel biologically active compounds.
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Affiliation(s)
- Yousra Ahmed
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Yuriy Rebets
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Josef Zapp
- Pharmazeutische Biologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany. .,Helmholtz-Institut für Pharmazeutische Forschung Saarland, Saarbrücken, Germany.
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Exploitation of Potentially New Antibiotics from Mangrove Actinobacteria in Maowei Sea by Combination of Multiple Discovery Strategies. Antibiotics (Basel) 2019; 8:antibiotics8040236. [PMID: 31783564 PMCID: PMC6963217 DOI: 10.3390/antibiotics8040236] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/05/2022] Open
Abstract
Rediscovery of known antibiotics from actinobacteria, especially Streptomyces, has become a bottleneck issue. Nowadays, more specific identification and dereplication could be acquired by a combination of modern analytic techniques with various databases. In this study, 261 actinobacterial strains were isolated from 8 mangrove soil samples by culture-dependent method. A total of 83 strains were selected to evaluate antibacterial activities and mechanisms by disc diffusion method and a unique double fluorescent protein reporter system (pDualrep2), respectively. Thirty-two strains exhibited antagonistic activity against at least one of the “ESKAPE” pathogens. Four Streptomyces strains (B475, B486, B353, and B98) showed strong inhibitory activity against Gram-positive bacteria and induced DNA damage SOS response. One Micromonospora strain (B704) exhibited inhibitory activity against several pathogens and induced attenuation-based translational inhibitors reporter. Seven members of quinoxaline-type antibiotics including quinomycin A, quinomycin monosulfoxide, and other five putative new analogues were found from the culture broth of strain B475 by a combination of anti-MRSA guide, HPTLC, HPLC-UV, and UPLC-UV-HRESIMS/MS analysis, Chemspider searching, and MS/MS-based molecular networking analysis. In conclusion, this study not only demonstrated that mangrove is a rich source of actinobacteria with the potentially new antibiotics but showed rapid dereplication of known antibiotics in the early stage can improve efficiency for the discovery of new antibiotics.
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Bader CD, Panter F, Müller R. In depth natural product discovery - Myxobacterial strains that provided multiple secondary metabolites. Biotechnol Adv 2019; 39:107480. [PMID: 31707075 DOI: 10.1016/j.biotechadv.2019.107480] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/28/2022]
Abstract
In recognition of many microorganisms ability to produce a variety of secondary metabolites in parallel, Zeeck and coworkers introduced the term "OSMAC" (one strain many compounds) around the turn of the century. Since then, additional efforts focused on the systematic characterization of a single bacterial species ability to form multiple secondary metabolite scaffolds. With the beginning of the genomic era mainly initiated by a dramatic reduction of sequencing costs, investigations of the genome encoded biosynthetic potential and especially the exploitation of biosynthetic gene clusters of undefined function gained attention. This was seen as a novel means to extend range and diversity of bacterial secondary metabolites. Genome analyses showed that even for well-studied bacterial strains, like the myxobacterium Myxococcus xanthus DK1622, many biosynthetic gene clusters are not yet assigned to their corresponding hypothetical secondary metabolites. In contrast to the results from emerging genome and metabolome mining techniques that show the large untapped biosynthetic potential per strain, many newly isolated bacterial species are still used for the isolation of only one target compound class and successively abandoned in the sense that no follow up studies are published from the same species. This work provides an overview about myxobacterial bacterial strains, from which not just one but multiple different secondary metabolite classes were successfully isolated. The underlying methods used for strain prioritization and natural product discovery such as biological characterization of crude extracts against a panel of pathogens, in-silico prediction of secondary metabolite abundance from genome data and state of the art instrumental analytics required for new natural product scaffold discovery in comparative settings are summarized and classified according to their output. Furthermore, for each approach selected studies performed with actinobacteria are shown to underline especially innovative methods used for natural product discovery.
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Affiliation(s)
- Chantal D Bader
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Fabian Panter
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany.
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Heinrichs L, Aytur SA, Bucci JP. Whole metagenomic sequencing to characterize the sediment microbial community within the Stellwagen Bank National Marine Sanctuary and preliminary biosynthetic gene cluster screening of Streptomyces scabrisporus. Mar Genomics 2019; 50:100718. [PMID: 31680056 DOI: 10.1016/j.margen.2019.100718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 08/28/2019] [Accepted: 09/19/2019] [Indexed: 10/25/2022]
Abstract
Understanding the marine sediment microbial community structure is of increasing importance to microbiologists since little is known of the diverse taxonomy that exists within this environment. Quantifying microbial species distribution patterns within marine sanctuaries is necessary to address conservation requirements. The objectives of this study were to characterize the relative abundance and biodiversity of metagenome samples of the sediment microbial community in the Stellwagen Bank National Marine Sanctuary (SBNMS). Related to the need for a comprehensive assessment of the microbial habitat within marine sanctuaries is the increased threat of antibiotic-resistant pathogens, coupled with multi-resistant bacterial strains. This has necessitated a renewed search for bioactive compounds in marine benthic habitat. An additional aim was to initiate quantification of biosynthetic gene clusters in species that have potential for natural product and drug discovery relevant to human health. Surficial sediment from 18 samples was collected in the summer and fall of 2017 from three benthic sites in the SBNMS. Microbial DNA was extracted from samples, and sequencing libraries were prepared for taxonomic analysis. Whole metagenome sequencing (WMGS) in combination with a bioinformatics pipeline was employed to delineate the taxa of bacteria present in each sample. Among all sampling sites, biodiversity was higher for summer compared to fall for class (p = 0.0013; F = 4.5) and genus (p = 0.0219; F = 4.4). Actinobacteria was the fifth most abundant class in both seasons (7.81%). Streptomyces was observed to be the fourth most abundant genus in both seasons with significantly higher prevalence in summer compared to fall samples. In summer, site 3 had the highest percentage of Streptomyces (1.71%) compared to sites 2 (1.62%) and 1 (1.37%). The results enabled preliminary quantification of the sequenced hits from the SBNMS sites with the highest potential for harboring secondary metabolite biosynthetic gene clusters for Streptomyces scabrisporus strain (NF3) genomic regions. This study is one of the first to use a whole metagenomics approach to characterize sediment microbial biodiversity in partnership with the SBNMS and demonstrates the potential for future ecological and biomedical research.
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Affiliation(s)
- Lina Heinrichs
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824, United States of America
| | - Semra A Aytur
- Department of Health Management and Policy, University of New Hampshire, 4 Library Way, Durham, NH 03824, United States of America
| | - John P Bucci
- Marine Microverse Institute, PO Box 59, Kittery Point, ME 03905, and the School of Marine Science and Ocean Engineering, University of New Hampshire, 8 College Road, Durham, NH 03824, United States of America.
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Almeida EL, Carrillo Rincón AF, Jackson SA, Dobson ADW. Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential. Front Microbiol 2019; 10:1713. [PMID: 31404169 PMCID: PMC6676996 DOI: 10.3389/fmicb.2019.01713] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/11/2019] [Indexed: 12/28/2022] Open
Abstract
The emergence of antibiotic resistant microorganisms has led to an increased need for the discovery and development of novel antimicrobial compounds. Frequent rediscovery of the same natural products (NPs) continues to decrease the likelihood of the discovery of new compounds from soil bacteria. Thus, efforts have shifted toward investigating microorganisms and their secondary metabolite biosynthesis potential, from diverse niche environments, such as those isolated from marine sponges. Here we investigated at the genomic level two Streptomyces spp. strains, namely SM17 and SM18, isolated from the marine sponge Haliclona simulans, with previously reported antimicrobial activity against clinically relevant pathogens; using single molecule real-time (SMRT) sequencing. We performed a series of comparative genomic analyses on SM17 and SM18 with their closest terrestrial relatives, namely S. albus J1074 and S. pratensis ATCC 33331 respectively; in an effort to provide further insights into potential environmental niche adaptations (ENAs) of marine sponge-associated Streptomyces, and on how these adaptations might be linked to their secondary metabolite biosynthesis potential. Prediction of secondary metabolite biosynthetic gene clusters (smBGCs) indicated that, even though the marine isolates are closely related to their terrestrial counterparts at a genomic level; they potentially produce different compounds. SM17 and SM18 displayed a better ability to grow in high salinity medium when compared to their terrestrial counterparts, and further analysis of their genomes indicated that they possess a pool of 29 potential ENA genes that are absent in S. albus J1074 and S. pratensis ATCC 33331. This ENA gene pool included functional categories of genes that are likely to be related to niche adaptations and which could be grouped based on potential biological functions such as osmotic stress, defense; transcriptional regulation; symbiotic interactions; antimicrobial compound production and resistance; ABC transporters; together with horizontal gene transfer and defense-related features.
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Affiliation(s)
| | | | - Stephen A. Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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JAKUBIEC-KRZESNIAK KATARZYNA, RAJNISZ-MATEUSIAK ALEKSANDRA, GUSPIEL ADAM, ZIEMSKA JOANNA, SOLECKA JOLANTA. Secondary Metabolites of Actinomycetes and their Antibacterial, Antifungal and Antiviral Properties. Pol J Microbiol 2019; 67:259-272. [PMID: 30451442 PMCID: PMC7256786 DOI: 10.21307/pjm-2018-048] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/01/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022] Open
Abstract
The growing resistance of microorganisms towards antibiotics has become a serious global problem. Therapeutics with novel chemical scaffolds and/or mechanisms of action are urgently needed to combat infections caused by multidrug resistant pathogens, including bacteria, fungi and viruses. Development of novel antimicrobial agents is still highly dependent on the discovery of new natural products. At present, most antimicrobial drugs used in medicine are of natural origin. Among the natural producers of bioactive substances, Actinobacteria continue to be an important source of novel secondary metabolites for drug application. In this review, the authors report on the bioactive antimicrobial secondary metabolites of Actinobacteria that were described between 2011 and April 2018. Special attention is paid to the chemical scaffolds, biological activities and origin of these novel antibacterial, antifungal and antiviral compounds. Arenimycin C, chromopeptide lactone RSP 01, kocurin, macrolactins A1 and B1, chaxamycin D as well as anthracimycin are regarded as the most effective compounds with antibacterial activity. In turn, the highest potency among selected antifungal compounds is exhibited by enduspeptide B, neomaclafungins A-I and kribelloside D, while ahmpatinin i Bu, antimycin A1a, and pentapeptide 4862F are recognized as the strongest antiviral agents.
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Affiliation(s)
- KATARZYNA JAKUBIEC-KRZESNIAK
- National Institute of Public Health – National Institute of Hygiene, Department of Environmental Health and Safety, Warsaw, Poland
| | - ALEKSANDRA RAJNISZ-MATEUSIAK
- National Institute of Public Health – National Institute of Hygiene, Department of Environmental Health and Safety, Warsaw, Poland
| | - ADAM GUSPIEL
- National Institute of Public Health – National Institute of Hygiene, Department of Environmental Health and Safety, Warsaw, Poland
| | - JOANNA ZIEMSKA
- National Institute of Public Health – National Institute of Hygiene, Department of Environmental Health and Safety, Warsaw, Poland
| | - JOLANTA SOLECKA
- National Institute of Public Health – National Institute of Hygiene, Department of Environmental Health and Safety, Warsaw, Poland
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