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Caffrey P, Hogan M, Song Y. New Glycosylated Polyene Macrolides: Refining the Ore from Genome Mining. Antibiotics (Basel) 2022; 11:antibiotics11030334. [PMID: 35326797 PMCID: PMC8944477 DOI: 10.3390/antibiotics11030334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 01/26/2023] Open
Abstract
Glycosylated polyene macrolides include effective antifungal agents, such as pimaricin, nystatin, candicidin, and amphotericin B. For the treatment of systemic mycoses, amphotericin B has been described as a gold-standard antibiotic because of its potent activity against a broad spectrum of fungal pathogens, which do not readily become resistant. However, amphotericin B has severe toxic side effects, and the development of safer alternatives remains an important objective. One approach towards obtaining such compounds is to discover new related natural products. Advances in next-generation sequencing have delivered a wealth of microbial genome sequences containing polyene biosynthetic gene clusters. These typically encode a modular polyketide synthase that catalyzes the assembly of the aglycone core, a cytochrome P450 that oxidizes a methyl branch to a carboxyl group, and additional enzymes for synthesis and attachment of a single mycosamine sugar residue. In some cases, further P450s catalyze epoxide formation or hydroxylation within the macrolactone. Bioinformatic analyses have identified over 250 of these clusters. Some are predicted to encode potentially valuable new polyenes that have not been uncovered by traditional screening methods. Recent experimental studies have characterized polyenes with new polyketide backbones, previously unknown late oxygenations, and additional sugar residues that increase water-solubility and reduce hemolytic activity. Here we review these studies and assess how this new knowledge can help to prioritize silent polyene clusters for further investigation. This approach should improve the chances of discovering better antifungal antibiotics.
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Caffrey P, De Poire E, Sheehan J, Sweeney P. Polyene macrolide biosynthesis in streptomycetes and related bacteria: recent advances from genome sequencing and experimental studies. Appl Microbiol Biotechnol 2016; 100:3893-908. [PMID: 27023916 DOI: 10.1007/s00253-016-7474-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 02/07/2023]
Abstract
The polyene macrolide group includes important antifungal drugs, to which resistance does not arise readily. Chemical and biological methods have been used in attempts to make polyene antibiotics with fewer toxic side effects. Genome sequencing of producer organisms is contributing to this endeavour, by providing access to new compounds and by enabling yield improvement for polyene analogues obtained by engineered biosynthesis. This recent work is also enhancing bioinformatic methods for deducing the structures of cryptic natural products from their biosynthetic enzymes. The stereostructure of candicidin D has recently been determined by NMR spectroscopy. Genes for the corresponding polyketide synthase have been uncovered in several different genomes. Analysis of this new information strengthens the view that protein sequence motifs can be used to predict double bond geometry in many polyketides.Chemical studies have shown that improved polyenes can be obtained by modifying the mycosamine sugar that is common to most of these compounds. Glycoengineered analogues might be produced by biosynthetic methods, but polyene glycosyltransferases show little tolerance for donors other than GDP-α-D-mycosamine. Genome sequencing has revealed extending glycosyltransferases that add a second sugar to the mycosamine of some polyenes. NppY of Pseudonocardia autotrophica uses UDP-N-acetyl-α-D-glucosamine as donor whereas PegA from Actinoplanes caeruleus uses GDP-α-D-mannose. These two enzymes show 51 % sequence identity and are also closely related to mycosaminyltransferases. These findings will assist attempts to construct glycosyltransferases that transfer alternative UDP- or (d)TDP-linked sugars to polyene macrolactones.
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Affiliation(s)
- Patrick Caffrey
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Eimear De Poire
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - James Sheehan
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul Sweeney
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
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Kong D, Lee MJ, Lin S, Kim ES. Biosynthesis and pathway engineering of antifungal polyene macrolides in actinomycetes. ACTA ACUST UNITED AC 2013; 40:529-43. [DOI: 10.1007/s10295-013-1258-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/04/2013] [Indexed: 11/27/2022]
Abstract
Abstract
Polyene macrolides are a large family of natural products typically produced by soil actinomycetes. Polyene macrolides are usually biosynthesized by modular and large type I polyketide synthases (PKSs), followed by several steps of sequential post-PKS modifications such as region-specific oxidations and glycosylations. Although known as powerful antibiotics containing potent antifungal activities (along with additional activities against parasites, enveloped viruses and prion diseases), their high toxicity toward mammalian cells and poor distribution in tissues have led to the continuous identification and structural modification of polyene macrolides to expand their general uses. Advances in in-depth investigations of the biosynthetic mechanism of polyene macrolides and the genetic manipulations of the polyene biosynthetic pathways provide great opportunities to generate new analogues. Recently, a novel class of polyene antibiotics was discovered (a disaccharide-containing NPP) that displays better pharmacological properties such as improved water-solubility and reduced hemolysis. In this review, we summarize the recent advances in the biosynthesis, pathway engineering, and regulation of polyene antibiotics in actinomycetes.
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Affiliation(s)
- Dekun Kong
- grid.16821.3c 0000000403688293 State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology Shanghai Jiao Tong University 200240 Shanghai P. R. China
| | - Mi-Jin Lee
- grid.202119.9 0000000123648385 Department of Biological Engineering Inha University 402-751 Incheon Korea
| | - Shuangjun Lin
- grid.16821.3c 0000000403688293 State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology Shanghai Jiao Tong University 200240 Shanghai P. R. China
| | - Eung-Soo Kim
- grid.202119.9 0000000123648385 Department of Biological Engineering Inha University 402-751 Incheon Korea
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Ichikawa N, Sasagawa M, Yamamoto M, Komaki H, Yoshida Y, Yamazaki S, Fujita N. DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters. Nucleic Acids Res 2012. [PMID: 23185043 PMCID: PMC3531092 DOI: 10.1093/nar/gks1177] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This article introduces DoBISCUIT (Database of BIoSynthesis clusters CUrated and InTegrated, http://www.bio.nite.go.jp/pks/), a literature-based, manually curated database of gene clusters for secondary metabolite biosynthesis. Bacterial secondary metabolites often show pharmacologically important activities and can serve as lead compounds and/or candidates for drug development. Biosynthesis of each secondary metabolite is catalyzed by a number of enzymes, usually encoded by a gene cluster. Although many scientific papers describe such gene clusters, the gene information is not always described in a comprehensive manner and the related information is rarely integrated. DoBISCUIT integrates the latest literature information and provides standardized gene/module/domain descriptions related to the gene clusters.
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Affiliation(s)
- Natsuko Ichikawa
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-49-10 Nishihara, Shibuya-ku, Tokyo 151-0006, Japan
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Zhang H, Wang H, Wang Y, Cui H, Xie Z, Pu Y, Pei S, Li F, Qin S. Genomic sequence-based discovery of novel angucyclinone antibiotics from marine Streptomyces sp. W007. FEMS Microbiol Lett 2012; 332:105-12. [DOI: 10.1111/j.1574-6968.2012.02582.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 04/20/2012] [Accepted: 04/20/2012] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Hongbo Wang
- Department of Pharmacology; School of Pharmacy; Yantai University; Yantai; China
| | - Yipeng Wang
- Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai; China
| | - Hongli Cui
- Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai; China
| | - Zeping Xie
- Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai; China
| | - Yang Pu
- Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai; China
| | - Shiqian Pei
- Department of Pharmacology; School of Pharmacy; Yantai University; Yantai; China
| | - Fuchao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences; Qingdao; China
| | - Song Qin
- Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai; China
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Komaki H, Ichikawa N, Oguchi A, Hanamaki T, Fujita N. Genome-wide survey of polyketide synthase and nonribosomal peptide synthetase gene clusters in Streptomyces turgidiscabies NBRC 16081. J GEN APPL MICROBIOL 2012; 58:363-72. [DOI: 10.2323/jgam.58.363] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Enkh-Amgalan J, Komaki H, Daram D, Ando K, Tsetseg B. Diversity of nonribosomal peptide synthetase and polyketide synthase genes in the genus Actinoplanes found in Mongolia. J Antibiot (Tokyo) 2011; 65:103-8. [PMID: 22167156 DOI: 10.1038/ja.2011.115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Intrageneric diversity of type-I ketosynthase domain genes in the genus Nocardia. J Antibiot (Tokyo) 2011; 64:617-20. [DOI: 10.1038/ja.2011.42] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Khan ST, Komaki H, Motohashi K, Kozone I, Mukai A, Takagi M, Shin-ya K. Streptomyces associated with a marine sponge Haliclona sp.; biosynthetic genes for secondary metabolites and products. Environ Microbiol 2010; 13:391-403. [PMID: 20849448 DOI: 10.1111/j.1462-2920.2010.02337.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Terrestrial actinobacteria have served as a primary source of bioactive compounds; however, a rapid decrease in the discovery of new compounds strongly necessitates new investigational approaches. One approach is the screening of actinobacteria from marine habitats, especially the members of the genus Streptomyces. Presence of this genus in a marine sponge, Haliclona sp., was investigated using culture-dependent and -independent techniques. 16S rRNA gene clone library analysis showed the presence of diverse Streptomyces in the sponge sample. In addition to the dominant genus Streptomyces, members of six different genera were isolated using four different media. Five phylogenetically new strains, each representing a novel species in the genus Streptomyces were also isolated. Polyphasic study suggesting the classification of two of these strains as novel species is presented. Searching the strains for the production of novel compounds and the presence of biosynthetic genes for secondary metabolites revealed seven novel compounds and biosynthetic genes with unique sequences. In these compounds, JBIR-43 exhibited cytotoxic activity against cancer cell lines. JBIR-34 and -35 were particularly interesting because of their unique chemical skeleton. To our knowledge, this is the first comprehensive study detailing the isolation of actinobacteria from a marine sponge and novel secondary metabolites from these strains.
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Affiliation(s)
- Shams Tabrez Khan
- Biomedicinal Information Research Center, Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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Hutchinson E, Murphy B, Dunne T, Breen C, Rawlings B, Caffrey P. Redesign of polyene macrolide glycosylation: engineered biosynthesis of 19-(O)-perosaminyl-amphoteronolide B. ACTA ACUST UNITED AC 2010; 17:174-82. [PMID: 20189107 DOI: 10.1016/j.chembiol.2010.01.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 12/03/2009] [Accepted: 01/11/2010] [Indexed: 11/17/2022]
Abstract
Most polyene macrolide antibiotics are glycosylated with mycosamine (3,6-dideoxy-3-aminomannose). In the amphotericin B producer, Streptomyces nodosus, mycosamine biosynthesis begins with AmphDIII-catalyzed conversion of GDP-mannose to GDP-4-keto-6-deoxymannose. This is converted to GDP-3-keto-6-deoxymannose, which is transaminated to GDP-mycosamine by the AmphDII protein. The glycosyltransferase AmphDI transfers mycosamine to amphotericin aglycones (amphoteronolides). The aromatic heptaene perimycin is unusual among polyenes in that the sugar is perosamine (4,6-dideoxy-4-aminomannose), which is synthesized by direct transamination of GDP-4-keto-6-deoxymannose. Here, we use the Streptomyces aminophilus perDII perosamine synthase and perDI perosaminyltransferase genes to engineer biosynthesis of perosaminyl-amphoteronolide B in S. nodosus. Efficient production required a hybrid glycosyltransferase containing an N-terminal region of AmphDI and a C-terminal region of PerDI. This work will assist efforts to generate glycorandomized amphoteronolides for drug discovery.
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Affiliation(s)
- Eve Hutchinson
- School of Biomolecular and Biomedical Science and Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
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Multilocus sequence analysis of Streptomyces griseus isolates delineating intraspecific diversity in terms of both taxonomy and biosynthetic potential. Antonie van Leeuwenhoek 2010; 98:237-48. [PMID: 20461465 DOI: 10.1007/s10482-010-9447-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Accepted: 04/19/2010] [Indexed: 01/03/2023]
Abstract
Systematics can provide a fundamental framework for understanding the relationships and diversification of organisms. Multilocus sequence analysis (MLSA) has shown great promise for an elaborate taxonomic grouping of streptomycete diversity. To evaluate the practical significance of MLSA as a valuable systematic tool for streptomycetes, we examined six endophytic Streptomyces griseus isolates and two S. griseus reference strains possessing obvious antagonistic activities and identical 16S rRNA gene sequences, using both housekeeping genes and secondary metabolic genes. All the eight strains contained PKS-I and NRPS genes, but not PKS-II genes, and showed similar diversity in both the MLSA phylogeny based on five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) and fingerprinting of KS-AT genes. We also inferred a phylogeny based on concatenated amino acid sequences of representative KS-AT genes from the strains, which displayed a topology correlated well with those of housekeeping-gene MLSA and KS-AT fingerprinting. The good congruence observed between phylogenies based on the different datasets verified that the MLSA scheme provided robust resolution at intraspecific level and could predict the overall diversity of secondary metabolic potential within a Streptomyces species, despite somewhat of a discrepancy with antimicrobial data. It is therefore feasible to apply MLSA to dissecting natural diversity of streptomycetes for a better understanding of their evolution and ecology, as well as for facilitating their bioprospecting.
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