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de Souza Rodrigues R, de Souza AQL, Feitoza MDO, Alves TCL, Barbosa AN, da Silva Santiago SRS, de Souza ADL. Biotechnological potential of actinomycetes in the 21st century: a brief review. Antonie Van Leeuwenhoek 2024; 117:82. [PMID: 38789815 DOI: 10.1007/s10482-024-01964-y] [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: 08/31/2023] [Accepted: 04/07/2024] [Indexed: 05/26/2024]
Abstract
This brief review aims to draw attention to the biotechnological potential of actinomycetes. Their main uses as sources of antibiotics and in agriculture would be enough not to neglect them; however, as we will see, their biotechnological application is much broader. Far from intending to exhaust this issue, we present a short survey of the research involving actinomycetes and their applications published in the last 23 years. We highlight a perspective for the discovery of new active ingredients or new applications for the known metabolites of these microorganisms that, for approximately 80 years, since the discovery of streptomycin, have been the main source of antibiotics. Based on the collected data, we organize the text to show how the cosmopolitanism of actinomycetes and the evolutionary biotic and abiotic ecological relationships of actinomycetes translate into the expression of metabolites in the environment and the richness of biosynthetic gene clusters, many of which remain silenced in traditional laboratory cultures. We also present the main strategies used in the twenty-first century to promote the expression of these silenced genes and obtain new secondary metabolites from known or new strains. Many of these metabolites have biological activities relevant to medicine, agriculture, and biotechnology industries, including candidates for new drugs or drug models against infectious and non-infectious diseases. Below, we present significant examples of the antimicrobial spectrum of actinomycetes, which is the most commonly investigated and best known, as well as their non-antimicrobial spectrum, which is becoming better known and increasingly explored.
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Affiliation(s)
- Rafael de Souza Rodrigues
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil.
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil.
| | - Antonia Queiroz Lima de Souza
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
- Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | | | | | - Anderson Nogueira Barbosa
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
| | - Sarah Raquel Silveira da Silva Santiago
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
| | - Afonso Duarte Leão de Souza
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
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Xue Y, Zhou Z, Feng F, Zhao H, Tan S, Li J, Wu S, Ju Z, He S, Ding L. Genomic Analysis of Kitasatospora setae to Explore Its Biosynthetic Potential Regarding Secondary Metabolites. Antibiotics (Basel) 2024; 13:459. [PMID: 38786187 PMCID: PMC11117518 DOI: 10.3390/antibiotics13050459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Actinomycetes have long been recognized as important sources of clinical antibiotics. However, the exploration of rare actinomycetes, despite their potential for producing bioactive molecules, has remained relatively limited compared to the extensively studied Streptomyces genus. The extensive investigation of Streptomyces species and their natural products has led to a diminished probability of discovering novel bioactive compounds from this group. Consequently, our research focus has shifted towards less explored actinomycetes, beyond Streptomyces, with particular emphasis on Kitasatospora setae (K. setae). The genome of K. setae was annotated and analyzed through whole-genome sequencing using multiple bio-informatics tools, revealing an 8.6 Mbp genome with a 74.42% G + C content. AntiSMASH analysis identified 40 putative biosynthetic gene clusters (BGCs), approximately half of which were recessive and unknown. Additionally, metabolomic mining utilizing mass spectrometry demonstrated the potential for this rare actinomycete to generate numerous bioactive compounds such as glycosides and macrolides, with bafilomycin being the major compound produced. Collectively, genomics- and metabolomics-based techniques confirmed K. setae's potential as a bioactive secondary metabolite producer that is worthy of further exploration.
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Affiliation(s)
- Yutong Xue
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
| | - Zhiyan Zhou
- School of Pharmacy, Ningbo University, Ningbo 315211, China;
| | - Fangjian Feng
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
| | - Hang Zhao
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
| | - Shuangling Tan
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
| | - Jinling Li
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
| | - Sitong Wu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (S.W.); (Z.J.)
| | - Zhiran Ju
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (S.W.); (Z.J.)
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
- School of Pharmacy, Ningbo University, Ningbo 315211, China;
| | - Lijian Ding
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
- School of Pharmacy, Ningbo University, Ningbo 315211, China;
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Wang A, Li S, Wei Y, Wang G, Shi W, Shang Y, Yu L, Chen S, Li Y, Gan M. Quinomycins with an unusual N-methyl-3-methylsulfinyl-alanine residue from a Streptomyces sp. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00736-0. [PMID: 38745102 DOI: 10.1038/s41429-024-00736-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Four new echinomycin congeners, quinomycins M-P (1-4) were isolated from the cultures of the soil-derived Streptomyces sp. CPCC205575. The planar structures were determined by comprehensive analyses of NMR and HRESIMS/MS data. The absolute configurations were elucidated by the advanced Marfey's method combined with biosynthetic gene analysis. Compounds 1-4 represent the first examples of quinomycin-type natural products with the sulfur atom at the N,S-dimethylcysteine residue oxidized as a sulfoxide group forming the unusual N-methyl-3-methylsulfinyl-alanine residue. Bioassay results revealed that the oxidation of the sulfur atom at the Cys or Cys' residues led to dramatic decrease of cytotoxicity and antimicrobial activity.
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Affiliation(s)
- Anqi Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China
| | - Shasha Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China
| | - Yuanjuan Wei
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China
| | - Guiyang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China
| | - Wenjing Shi
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China
| | - Yue Shang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China
| | - Shuzhen Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China.
| | - Yan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China.
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China.
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Owens SL, Ahmed SR, Lang Harman RM, Stewart LE, Mori S. Natural Products That Contain Higher Homologated Amino Acids. Chembiochem 2024; 25:e202300822. [PMID: 38487927 DOI: 10.1002/cbic.202300822] [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: 12/04/2023] [Revised: 03/13/2024] [Indexed: 04/11/2024]
Abstract
This review focuses on discussing natural products (NPs) that contain higher homologated amino acids (homoAAs) in the structure as well as the proposed and characterized biosynthesis of these non-proteinogenic amino acids. Homologation of amino acids includes the insertion of a methylene group into its side chain. It is not a very common modification found in NP biosynthesis as approximately 450 homoAA-containing NPs have been isolated from four bacterial phyla (Cyanobacteria, Actinomycetota, Myxococcota, and Pseudomonadota), two fungal phyla (Ascomycota and Basidiomycota), and one animal phylum (Porifera), except for a few examples. Amino acids that are found to be homologated and incorporated in the NP structures include the following ten amino acids: alanine, arginine, cysteine, isoleucine, glutamic acid, leucine, phenylalanine, proline, serine, and tyrosine, where isoleucine, leucine, phenylalanine, and tyrosine share the comparable enzymatic pathway. Other amino acids have their individual homologation pathway (arginine, proline, and glutamic acid for bacteria), likely utilize the primary metabolic pathway (alanine and glutamic acid for fungi), or have not been reported (cysteine and serine). Despite its possible high potential in the drug discovery field, the biosynthesis of homologated amino acids has a large room to explore for future combinatorial biosynthesis and metabolic engineering purpose.
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Affiliation(s)
- Skyler L Owens
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shopno R Ahmed
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Rebecca M Lang Harman
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Laura E Stewart
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shogo Mori
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
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Hao X, Li S, Li J, Wang G, Li J, Peng Z, Gan M. Acremosides A-G, Sugar Alcohol-Conjugated Acyclic Sesquiterpenes from a Sponge-Derived Acremonium Species. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38561238 DOI: 10.1021/acs.jnatprod.4c00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Seven new sugar alcohol-conjugated acyclic sesquiterpenes, acremosides A-G (1-7), were isolated from the cultures of the sponge-associated fungus Acremonium sp. IMB18-086 cultivated with heat-killed Pseudomonas aeruginosa. The structures were determined by comprehensive analyses of 1D and 2D NMR spectroscopic data. The relative configurations were established by J-based configuration analysis and acetonide derivatization. The absolute configurations were elucidated by the Mosher ester method and ECD calculations. The structures of acremosides E-G (5-7) featured the linear sesquiterpene skeleton with a tetrahydrofuran moiety attached to a sugar alcohol. Acremosides A (1) and C-E (3-5) showed significant inhibitory activities against hepatitis C virus (EC50 values of 4.8-8.8 μM) with no cytotoxicity (CC50 of >200 μM).
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Affiliation(s)
- Xiaomeng Hao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Shasha Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Jianrui Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Guiyang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Jiao Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Zonggen Peng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
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Zhang Y, Feng L, Hemu X, Tan NH, Wang Z. OSMAC Strategy: A promising way to explore microbial cyclic peptides. Eur J Med Chem 2024; 268:116175. [PMID: 38377824 DOI: 10.1016/j.ejmech.2024.116175] [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: 09/18/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Microbial secondary metabolites are pivotal for the development of novel drugs. However, conventional culture techniques, have left a vast array of unexpressed biosynthetic gene clusters (BGCs) in microorganisms, hindering the discovery of metabolites with distinct structural features and diverse biological functions. To address this limitation, several innovative strategies have been emerged. The "One Strain Many Compounds" (OSMAC) strategy, which involves altering microbial culture conditions, has proven to be particularly effective in mining numerous novel secondary metabolites for the past few years. Among these, microbial cyclic peptides stand out. These peptides often comprise rare amino acids, unique chemical structures, and remarkable biological function. With the advancement of the OSMAC strategy, a plethora of new cyclic peptides have been identified from diverse microbial genera. This work reviews the progress in mining novel compounds using the OSMAC strategy and the applications of this strategy in discovering 284 microbial cyclic peptides from 63 endophytic strains, aiming to offer insights for the further explorations into novel active cyclic peptides.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li Feng
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xinya Hemu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Ning-Hua Tan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Zhe Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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Zhao JH, Wang YW, Yang J, Tong ZJ, Wu JZ, Wang YB, Wang QX, Li QQ, Yu YC, Leng XJ, Chang L, Xue X, Sun SL, Li HM, Ding N, Duan JA, Li NG, Shi ZH. Natural products as potential lead compounds to develop new antiviral drugs over the past decade. Eur J Med Chem 2023; 260:115726. [PMID: 37597436 DOI: 10.1016/j.ejmech.2023.115726] [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: 04/13/2023] [Revised: 05/22/2023] [Accepted: 08/13/2023] [Indexed: 08/21/2023]
Abstract
Virus infection has been one of the main causes of human death since the ancient times. Even though more and more antiviral drugs have been approved in clinic, long-term use can easily lead to the emergence of drug resistance and side effects. Fortunately, there are many kinds of metabolites which were produced by plants, marine organisms and microorganisms in nature with rich structural skeletons, and they are natural treasure house for people to find antiviral active substances. Aiming at many types of viruses that had caused serious harm to human health in recent years, this review summarizes the natural products with antiviral activity that had been reported for the first time in the past ten years, we also sort out the source, chemical structure and safety indicators in order to provide potential lead compounds for the research and development of new antiviral drugs.
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Affiliation(s)
- Jing-Han Zhao
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yue-Wei Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Jin Yang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Zhen-Jiang Tong
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Jia-Zhen Wu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yi-Bo Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Qing-Xin Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Qing-Qing Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yan-Cheng Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Xue-Jiao Leng
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Liang Chang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - He-Min Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Jin-Ao Duan
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Zhi-Hao Shi
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
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Zhong W, Aiosa N, Deutsch JM, Garg N, Agarwal V. Pseudobulbiferamides: Plasmid-Encoded Ureidopeptide Natural Products with Biosynthetic Gene Clusters Shared Among Marine Bacteria of Different Genera. JOURNAL OF NATURAL PRODUCTS 2023; 86:2414-2420. [PMID: 37713418 PMCID: PMC10616845 DOI: 10.1021/acs.jnatprod.3c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/17/2023]
Abstract
Ureidopeptidic natural products possess a wide variety of favorable pharmacological properties. In addition, they have been shown to mediate core physiological functions in producer bacteria. Here, we report that similar ureidopeptidic natural products with conserved biosynthetic gene clusters are produced by different bacterial genera that coinhabit marine invertebrate microbiomes. We demonstrate that a Microbulbifer strain isolated from a marine sponge can produce two different classes of ureidopeptide natural products encoded by two different biosynthetic gene clusters that are positioned on the bacterial chromosome and on a plasmid. The plasmid encoded ureidopeptide natural products, which we term the pseudobulbiferamides (5-8), resemble the ureidopeptide natural products produced by Pseudovibrio, a different marine bacterial genus that is likewise present in marine sponge commensal microbiomes. Using imaging mass spectrometry, we find that the two classes of Microbulbifer-derived ureidopeptides occupy different physical spaces relative to the bacterial colony, perhaps implying different roles for these two compound classes in Microbulbifer physiology and environmental interactions.
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Affiliation(s)
- Weimao Zhong
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Nicole Aiosa
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Jessica M. Deutsch
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Neha Garg
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- Center
for Microbial Dynamics and Infection, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vinayak Agarwal
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
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9
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Absolute Stereochemistry Determination of Bioactive Marine-Derived Cyclopeptides by Liquid Chromatography Methods: An Update Review (2018-2022). MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020615. [PMID: 36677673 PMCID: PMC9867211 DOI: 10.3390/molecules28020615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
Cyclopeptides are considered as one of the most important classes of compounds derived from marine sources, due to their structural diversity and a myriad of their biological and pharmacological activities. Since marine-derived cyclopeptides consist of different amino acids, many of which are non-proteinogenic, they possess various stereogenic centers. In this respect, the structure elucidation of new molecular scaffolds obtained from natural sources, including marine-derived cyclopeptides, can become a very challenging task. The determination of the absolute configurations of the amino acid residues is accomplished, in most cases, by performing acidic hydrolysis, followed by analyses by liquid chromatography (LC). In a continuation with the authors' previous publication, and to analyze the current trends, the present review covers recently published works (from January 2018 to November 2022) regarding new cyclopeptides from marine organisms, with a special focus on their biological/pharmacological activities and the absolute stereochemical assignment of the amino acid residues. Ninety-one unreported marine-derived cyclopeptides were identified during this period, most of which displayed anticancer or antimicrobial activities. Marfey's method, which involves LC, was found to be the most frequently used for this purpose.
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10
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Wu C, Tang J, Limlingan Malit JJ, Wang R, Sung HHY, Williams ID, Qian PY. Bathiapeptides: Polythiazole-Containing Peptides from a Marine Biofilm-Derived Bacillus sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:1751-1762. [PMID: 35703501 DOI: 10.1021/acs.jnatprod.2c00290] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacteria in marine biofilms are a rich reservoir of natural products. To facilitate novel secondary metabolite discovery, we investigated the metabolic profile of a marine biofilm-derived Bacillus sp. B19-2 by combining bioinformatics and LC-UV-MS analyses. After dereplication and purification of putatively unknown compounds, a new family of compounds 1-8 was uncovered and named bathiapeptides. Structural elucidation using NMR, HRESIMS, ozonolysis, advanced Marfey's analysis, and X-ray diffraction revealed that bathiapeptides are polypeptides that contain a rare polythiazole moiety. These compounds exhibited strong cytotoxicity against Hep G2, HeLa, MCF-7, and MGC-803 cell lines, and the lowest IC50 value was 0.5 μM. An iterative biosynthesis logic in bathiapeptides' biosynthesis was proposed based on the identified chemical structures and putative gene cluster analysis.
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Affiliation(s)
- Chuanhai Wu
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, 511458 People's Republic of China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Jianwei Tang
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, 511458 People's Republic of China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Jessie James Limlingan Malit
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, 511458 People's Republic of China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Ruojun Wang
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, 511458 People's Republic of China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Herman H-Y Sung
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, 511458 People's Republic of China
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Ian D Williams
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, 511458 People's Republic of China
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, 511458 People's Republic of China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
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11
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Hao X, Li S, Wang G, Li J, Peng Z, Zhang Y, Yu L, Gan M. Zelkovamycins F and G, Cyclopeptides with Cα-Methyl-threonine Residues, from an Endophytic Kitasatospora sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:1715-1722. [PMID: 35715218 DOI: 10.1021/acs.jnatprod.2c00174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Zelkovamycins F and G (1 and 2), two new natural cyclic octapeptides possessing the unprecedented nonproteinogenic amino acid residues l-α-methyl-threonine and l-α-methyl-allo-threonine, respectively, along with four new analogues, zelkovamycins H-K (3-6), were identified from the endophytic Kitasatospora sp. CPCC 204717. Their structures were elucidated by detailed analysis of NMR and HRESIMS/MS spectroscopic data. The configurations of amino acid residues were determined by Marfey's analysis combined with NMR calculations. Compounds 1, 2, and 4 showed potent antibacterial activity against methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis. The structure-activity relationship study revealed that the 2-methyl-3-oxobutyrine and sarcosine residues played important roles in their antibacterial activities. Zelkovamycin (7) and zelkovamycin E (8) exhibited significant antiviral activity against the hepatitis C virus.
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Affiliation(s)
- Xiaomeng Hao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shasha Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Guiyang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Jianrui Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Zonggen Peng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
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12
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Tian MY, Bao J, Li X, Zhang QR, Li SS, Gan ML, Wang SJ. Antimicrobial alkaloids from the root bark of Dictamnus dasycarpus. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2022; 24:483-489. [PMID: 34190010 DOI: 10.1080/10286020.2021.1939311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
Two new furoquinoline alkaloids, named 1'-oxo-isoplatydesmine (1) and demethoxyacrophylline (2), as well as 11 known alkaloids (3-13) were isolated from the root bark of Dictamnus dasycarpus Turcz. The structures of 1 and 2 were established by detailed spectroscopic elucidation, such as 1 D & 2 D NMR and HRMS, etc. The unexpected autoracemization of 1 was discussed based on the stereochemistry of reported dihydrofuroquinolines. Compounds 3-5 exhibited moderate inhibitory activities against Bacillus subtilis, Candida albicans, and Pseudomonas aeruginosa with MICs 32-64 μg/ml, revealing the active principles of D. dasycarpus for treating skin diseases in its traditional usage.
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Affiliation(s)
- Meng-Yin Tian
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jie Bao
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xin Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Qian-Ru Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Sha-Sha Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mao-Luo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Su-Juan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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13
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Tarantini FS, Brunati M, Taravella A, Carrano L, Parenti F, Hong KW, Williams P, Chan KG, Heeb S, Chan WC. Actinomadura graeca sp. nov.: A novel producer of the macrocyclic antibiotic zelkovamycin. PLoS One 2021; 16:e0260413. [PMID: 34847153 PMCID: PMC8631618 DOI: 10.1371/journal.pone.0260413] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/09/2021] [Indexed: 11/18/2022] Open
Abstract
As part of a screening programme for antibiotic-producing bacteria, a novel Actinomadura species was discovered from a soil sample collected in Santorini, Greece. Preliminary 16S rRNA gene sequence comparisons highlighted Actinomadura macra as the most similar characterised species. However, whole-genome sequencing revealed an average nucleotide identity (ANI) value of 89% with A. macra, the highest among related species. Further phenotypic and chemotaxonomic analyses confirmed that the isolate represents a previously uncharacterised species in the genus Actinomadura, for which the name Actinomadura graeca sp. nov. is proposed (type strain 32-07T). The G+C content of A. graeca 32-07 is 72.36%. The cell wall contains DL-diaminopimelic acid, intracellular sugars are glucose, ribose and galactose, the predominant menaquinone is MK-9(H6), the major cellular lipid is phosphatidylinositol and fatty acids consist mainly of hexadecanoic acid. No mycolic acid was detected. Furthermore, A. graeca 32-07 has been confirmed as a novel producer of the non-ribosomal peptide antibiotic zelkovamycin and we report herein a provisional description of the unique biosynthetic gene cluster.
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Affiliation(s)
- Francesco Saverio Tarantini
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Mara Brunati
- Fondazione Istituto Insubrico di Ricerca per la Vita (FIIRV), Gerenzano, Italy
| | - Anna Taravella
- Fondazione Istituto Insubrico di Ricerca per la Vita (FIIRV), Gerenzano, Italy
| | - Lucia Carrano
- Fondazione Istituto Insubrico di Ricerca per la Vita (FIIRV), Gerenzano, Italy
| | - Francesco Parenti
- Fondazione Istituto Insubrico di Ricerca per la Vita (FIIRV), Gerenzano, Italy
| | - Kar Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
- Institute of Marine Sciences, Shantou University, Shantou, China
| | - Paul Williams
- Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang, China
| | - Stephan Heeb
- Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- * E-mail: (SH); (WCC)
| | - Weng C. Chan
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
- * E-mail: (SH); (WCC)
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14
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Hao X, Li S, Ni J, Wang G, Li F, Li Q, Chen S, Shu J, Gan M. Acremopeptaibols A-F, 16-Residue Peptaibols from the Sponge-Derived Acremonium sp. IMB18-086 Cultivated with Heat-Killed Pseudomonas aeruginosa. JOURNAL OF NATURAL PRODUCTS 2021; 84:2990-3000. [PMID: 34781681 DOI: 10.1021/acs.jnatprod.1c00834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Six new 16-residue peptaibols, acremopeptaibols A-F (1-6), along with five known compounds, were isolated from the cultures of the sponge-associated fungus Acremonium sp. IMB18-086 grown in the presence of the autoclaved bacterium Pseudomonas aeruginosa on solid rice medium. The peptaibol sequences were established based on comprehensive analysis of 1D and 2D NMR spectroscopic data in conjunction with HRESIMS/MS experiments. The configurations of the amino acid residues were determined by advanced Marfey's analysis. Compounds 1-6 feature the lack of the highly conserved Thr6 and Hyp10 residues in comparison with other members of the SF3 subfamily peptaibols. A plausible biosynthetic pathway of compounds 1-6 was proposed on the basis of genomic analysis. Compounds 1, 5, 7, and 10 exhibited significant antimicrobial activity against Staphylococcus aureus, methicillin-resistant S. aureus, Bacillus subtilis, and Candida albicans. Compounds 7-10 showed potent cytotoxicities against the A549 and/or HepG2 cancer cell lines.
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Affiliation(s)
- Xiaomeng Hao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shasha Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Jun Ni
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Guiyang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Fang Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Qin Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
- Key Laboratory of Modern Preparation of Traditional Chinese Medicines, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, People's Republic of China
| | - Shuzhen Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Jicheng Shu
- Key Laboratory of Modern Preparation of Traditional Chinese Medicines, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, People's Republic of China
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
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15
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Li Y, Wang M, Sun ZZ, Xie BB. Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces. Front Microbiol 2021; 12:683814. [PMID: 34194415 PMCID: PMC8236941 DOI: 10.3389/fmicb.2021.683814] [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: 03/22/2021] [Accepted: 05/20/2021] [Indexed: 11/25/2022] Open
Abstract
While the genus Streptomyces (family Streptomycetaceae) has been studied as a model for bacterial secondary metabolism and genetics, its close relatives have been less studied. The genus Kitasatospora is the second largest genus in the family Streptomycetaceae. However, its taxonomic position within the family remains under debate and the secondary metabolic potential remains largely unclear. Here, we performed systematic comparative genomic and phylogenomic analyses of Kitasatospora. Firstly, the three genera within the family Streptomycetaceae (Kitasatospora, Streptomyces, and Streptacidiphilus) showed common genomic features, including high G + C contents, high secondary metabolic potentials, and high recombination frequencies. Secondly, phylogenomic and comparative genomic analyses revealed phylogenetic distinctions and genome content differences among these three genera, supporting Kitasatospora as a separate genus within the family. Lastly, the pan-genome analysis revealed extensive genetic diversity within the genus Kitasatospora, while functional annotation and genome content comparison suggested genomic differentiation among lineages. This study provided new insights into genomic characteristics of the genus Kitasatospora, and also uncovered its previously underestimated and complex secondary metabolism.
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Affiliation(s)
- Yisong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Meng Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zhong-Zhi Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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16
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Hill RA, Sutherland A. Hot off the Press. Nat Prod Rep 2021. [DOI: 10.1039/d1np90005f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as pedrolide from Euphorbia pedroi.
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Affiliation(s)
- Robert A. Hill
- School of Chemistry, Glasgow University, Glasgow, G12 8QQ, UK
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