1
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Elsayed SS, van der Heul HU, Xiao X, Nuutila A, Baars LR, Wu C, Metsä-Ketelä M, van Wezel GP. Unravelling key enzymatic steps in C-ring cleavage during angucycline biosynthesis. Commun Chem 2023; 6:281. [PMID: 38110491 PMCID: PMC10728087 DOI: 10.1038/s42004-023-01059-1] [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: 06/30/2023] [Accepted: 11/08/2023] [Indexed: 12/20/2023] Open
Abstract
Angucyclines are type II polyketide natural products, often characterized by unusual structural rearrangements through B- or C-ring cleavage of their tetracyclic backbone. While the enzymes involved in B-ring cleavage have been extensively studied, little is known of the enzymes leading to C-ring cleavage. Here, we unravel the function of the oxygenases involved in the biosynthesis of lugdunomycin, a highly rearranged C-ring cleaved angucycline derivative. Targeted deletion of the oxygenase genes, in combination with molecular networking and structural elucidation, showed that LugOI is essential for C12 oxidation and maintaining a keto group at C6 that is reduced by LugOII, resulting in a key intermediate towards C-ring cleavage. An epoxide group is then inserted by LugOIII, and stabilized by the novel enzyme LugOV for the subsequent cleavage. Thus, for the first time we describe the oxidative enzymatic steps that form the basis for a wide range of rearranged angucycline natural products.
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Affiliation(s)
- Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands.
| | - Helga U van der Heul
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands
| | - Xiansha Xiao
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Aleksi Nuutila
- Department of Life Technologies, University of Turku, Tykistökatu 6, FIN-20014, Turku, Finland
| | - Laura R Baars
- Department of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237, Qingdao, P.R. China
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, Tykistökatu 6, FIN-20014, Turku, Finland
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands.
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708PB, Wageningen, The Netherlands.
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2
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Schaenzer AJ, Rodriguez Hernandez A, Tsai K, Hobson C, Fujimori DG, Wright GD. Angucyclinones rescue PhLOPS A antibiotic activity by inhibiting Cfr-dependent antibiotic resistance. mBio 2023; 14:e0179123. [PMID: 38014974 PMCID: PMC10746278 DOI: 10.1128/mbio.01791-23] [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: 07/10/2023] [Accepted: 10/16/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Cfr is an antibiotic resistance enzyme that inhibits five clinically important antibiotic classes, is genetically mobile, and has a minimal fitness cost, making Cfr a serious threat to antibiotic efficacy. The significance of our work is in discovering molecules that inhibit Cfr-dependent methylation of the ribosome, thus protecting the efficacy of the PhLOPSA antibiotics. These molecules are the first reported inhibitors of Cfr-mediated ribosome methylation and, as such, will guide the further discovery of chemical scaffolds against Cfr-mediated antibiotic resistance. Our work acts as a foundation for further development of molecules that safeguard the PhLOPSA antibiotics from Cfr.
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Affiliation(s)
- Adam J. Schaenzer
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Annia Rodriguez Hernandez
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | - Kaitlyn Tsai
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Christian Hobson
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, California, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Gerard D. Wright
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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3
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Sarmiento-Vizcaíno A, Martín J, Ortiz-López FJ, Reyes F, García LA, Blanco G. Natural products, including a new caboxamycin, from Streptomyces and other Actinobacteria isolated in Spain from storm clouds transported by Northern winds of Arctic origin. Front Chem 2022; 10:948795. [DOI: 10.3389/fchem.2022.948795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Actinobacteria, mostly Streptomyces species, are the main source of natural products essential in medicine. While the majority of producer microorganisms of secondary metabolite are reported from terrestrial or marine environments, there are limited reports of their isolation from atmospheric precipitations. Clouds are considered as atmospheric oases for microorganisms and there is a recent paradigm shift whereby atmospheric-derived Actinobacteria emerge as an alternative source for drug discovery. In this context, we studied a total of 18 bioactive Actinobacteria strains, isolated by sampling nine precipitation events with prevailing Northern winds in the Cantabrian Sea coast, Northern Spain. Backward trajectories meteorological analyses indicate that air masses were originated mostly in the Arctic Ocean, and their trajectory to downwind areas involved the Atlantic Ocean and also terrestrial sources from continental Europe, and in some events from Canada, Greenland, Mauritania and Canary Islands. Taxonomic identification of the isolates, by 16S rRNA gene sequencing and phylogenetic analyses, revealed that they are members of three Actinobacteria genera. Fifteen of the isolates are Streptomyces species, thus increasing the number of bioactive species of this genus in the atmosphere to a 6.8% of the total currently validated species. In addition, two of the strains belong to the genus Micromonospora and one to genus Nocardiopsis. These findings reinforce a previous atmospheric dispersal model, extended herein to the genus Micromonospora. Production of bioactive secondary metabolites was screened in ethyl acetate extracts of the strains by LC-UV-MS and a total of 94 secondary metabolites were detected after LC/MS dereplication. Comparative analyses with natural products databases allowed the identification of 69 structurally diverse natural products with contrasted biological activities, mostly as antibiotics and antitumor agents, but also anti-inflammatory, antiviral, antiparasitic, immunosuppressant and neuroprotective among others. The molecular formulae of the 25 remaining compounds were determined by HRMS. None of these molecules had been previously reported in natural product databases indicating potentially novel metabolites. As a proof of concept, a new metabolite caboxamycin B (1) was isolated from the culture broth of Streptomyces sp. A-177 and its structure was determined by various spectrometric methods. To the best of our knowledge, this is the first novel natural product obtained from an atmospheric Streptomyces, thus pointing out precipitations as an innovative source for discovering new pharmaceutical natural products.
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4
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Shen Q, Dai G, Li A, Liu Y, Zhong G, Li X, Ren X, Sui H, Fu J, Jiao N, Zhang Y, Bian X, Zhou H. Genome-Guided Discovery of Highly Oxygenated Aromatic Polyketides, Saccharothrixins D-M, from the Rare Marine Actinomycete Saccharothrix sp. D09. JOURNAL OF NATURAL PRODUCTS 2021; 84:2875-2884. [PMID: 34784196 DOI: 10.1021/acs.jnatprod.1c00617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Angucyclines and angucyclinones are aromatic polyketides with intriguing structures and therapeutic value. Genome mining of the rare marine actinomycete Saccharothrix sp. D09 led to the identification of a type II polyketide synthase biosynthetic gene cluster, sxn, which encodes several distinct subclasses of oxidoreductases, implying that this strain has the potential to produce novel polycyclic aromatic polyketides with unusual redox modifications. The "one strain-many compounds" (OSMAC) strategy and comparative metabolite analysis facilitated the discovery of 20 angucycline derivatives from the D09 strain, including six new highly oxygenated saccharothrixins D-I (1-6), four new glycosylated saccharothrixins J-M (7-10), and 10 known analogues (11-20). Their structures were elucidated based on detailed HRESIMS, NMR spectroscopic, and X-ray crystallographic analysis. With the help of gene disruption and heterologous expression, we proposed their plausible biosynthetic pathways. In addition, compounds 3, 4, and 8 showed antibacterial activity against Helicobacter pylori with MIC values ranging from 16 to 32 μg/mL. Compound 3 also revealed anti-inflammatory activity by inhibiting the production of NO with an IC50 value of 28 μM.
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Affiliation(s)
- Qiyao Shen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Aiying Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yang Liu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Guannan Zhong
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaoju Li
- Core Facilities for Life and Environmental Sciences, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiangmei Ren
- Core Facilities for Life and Environmental Sciences, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Haiyan Sui
- Core Facilities for Life and Environmental Sciences, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jun Fu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Nianzhi Jiao
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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5
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Cao M, Zheng C, Yang D, Kalkreuter E, Adhikari A, Liu YC, Rateb ME, Shen B. Cryptic Sulfur Incorporation in Thioangucycline Biosynthesis. Angew Chem Int Ed Engl 2021; 60:7140-7147. [PMID: 33465268 PMCID: PMC7969429 DOI: 10.1002/anie.202015570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/30/2020] [Indexed: 12/16/2022]
Abstract
Sulfur incorporation into natural products is a critical area of biosynthetic studies. Recently, a subset of sulfur-containing angucyclines has been discovered, and yet, the sulfur incorporation step is poorly understood. In this work, a series of thioether-bridged angucyclines were discovered, and a cryptic epoxide Michael acceptor intermediate was revealed en route to thioangucyclines (TACs) A and B. However, systematic gene deletion of the biosynthetic gene cluster (BGC) by CRISPR/Cas9 could not identify any gene responsible for the conversion of the epoxide intermediate to TACs. Instead, a series of in vitro and in vivo experiments conclusively showed that the conversion is the result of two non-enzymatic steps, possibly mediated by endogenous hydrogen sulfide. Therefore, the TACs are proposed to derive from a detoxification process. These results are expected to contribute to the study of both angucyclines and the utilization of inorganic sulfur in natural product biosynthesis.
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Affiliation(s)
| | | | - Dong Yang
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Edward Kalkreuter
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ajeeth Adhikari
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yu-Chen Liu
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Mostafa E. Rateb
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ben Shen
- Department of Chemistry, Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, Florida 33458, United States
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6
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Cao M, Zheng C, Yang D, Kalkreuter E, Adhikari A, Liu Y, Rateb ME, Shen B. Cryptic Sulfur Incorporation in Thioangucycline Biosynthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mingming Cao
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Chengjian Zheng
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Dong Yang
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Edward Kalkreuter
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Ajeeth Adhikari
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Yu‐Chen Liu
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Mostafa E. Rateb
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
| | - Ben Shen
- Department of Chemistry Department of Molecular Medicine Natural Products Discovery Center at Scripps Research The Scripps Research Institute Jupiter FL 33458 USA
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7
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Mikhaylov AA, Ikonnikova VA, Solyev PN. Disclosing biosynthetic connections and functions of atypical angucyclinones with a fragmented C-ring. Nat Prod Rep 2021; 38:1506-1517. [PMID: 33480893 DOI: 10.1039/d0np00082e] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review on atypical angucyclinones possessing an aromatic cleavage of the C-ring covers literature between 1995 and early 2020.The unusual framework of the middle C-ring, "broken" as a result of biotransformations and oxidations in vivo and bearing an sp3-C connection, is of interest for biosynthetic investigations. The reported 39 natural compounds (55 including stereoisomers) have been analyzed and arranged into three structural groups. The biosynthetic origin of all these compounds has been thoroughly reviewed and revised, based on the found connections with oxidized angucyclinone structures. The data on biological activities has been summarized. Careful consideration of the origin of the structure allowed us to outline a hypothesis on the biological function as well as prospective applications of such atypical angucyclinones.
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Affiliation(s)
- Andrey A Mikhaylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, 117997, Russia.
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8
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Safaei N, Mast Y, Steinert M, Huber K, Bunk B, Wink J. Angucycline-like Aromatic Polyketide from a Novel Streptomyces Species Reveals Freshwater Snail Physa acuta as Underexplored Reservoir for Antibiotic-Producing Actinomycetes. Antibiotics (Basel) 2020; 10:antibiotics10010022. [PMID: 33383910 PMCID: PMC7823578 DOI: 10.3390/antibiotics10010022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/23/2020] [Accepted: 12/25/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The current study shows that freshwater snails can be considered as new sources for bioactive metabolites, since a novel Streptomyces species 7NS3 produced four active compounds against Gram-positive bacteria. One of the compounds was an angucycline-like aromatic polyketide matched with a known compound, emycin A. Genome mining studies based on the whole-genome sequence of 7NS3 resulted in the identification of a gene cluster potentially coding for emycin A biosynthesis. Abstract Antibiotic producers have mainly been isolated from soil, which often has led to the rediscovery of known compounds. In this study, we identified the freshwater snail Physa acuta as an unexplored source for new antibiotic producers. The bacterial diversity associated with the snail was characterized by a metagenomic approach using cultivation-independent high-throughput sequencing. Although Actinobacteria represented only 2% of the bacterial community, the focus was laid on the isolation of the genus Streptomyces due to its potential to produce antibiotics. Three Streptomyces strains (7NS1, 7NS2 and 7NS3) were isolated from P. acuta, and the antimicrobial activity of the crude extracts were tested against a selection of Gram-positive and Gram-negative bacteria and fungi. 7NS3 showed the strongest activity against Gram-positive bacteria and, thus, was selected for genome sequencing and a phylogenomic analysis. 7NS3 represents a novel Streptomyces species, which was deposited as Streptomyces sp. DSM 110735 at the Leibniz Institute-German Collection of Microorganisms and Cell Cultures (DSMZ). Bioassay-guided high-performance liquid chromatography (HPLC) and high-resolution electrospray ionization-mass spectrometry (HR-ESI-MS) analyses of crude extract fractions resulted in the detection of four compounds, one of which matched the compound characteristics of emycin A, an angucycline-like aromatic polyketide. Genome mining studies based on the whole-genome sequence of 7NS3 resulted in the identification of a gene cluster potentially coding for emycin A biosynthesis. Our study demonstrates that freshwater snails like P. acuta can represent promising reservoirs for the isolation of new antibiotic-producing actinobacterial species.
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Affiliation(s)
- Nasim Safaei
- Helmholtz Centre for Infection Research, Department of microbial Strain Collection, Inhoffenstrasse 7, D-38124 Braunschweig, Germany;
| | - Yvonne Mast
- German Center for Infection Research (DZIF), Leibniz Institute DSMZ, Inhoffenstrasse 7, D-38124 Braunschweig, Germany; (Y.M.); (K.H.); (B.B.)
| | - Michael Steinert
- Technical University of Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany;
| | - Katharina Huber
- German Center for Infection Research (DZIF), Leibniz Institute DSMZ, Inhoffenstrasse 7, D-38124 Braunschweig, Germany; (Y.M.); (K.H.); (B.B.)
| | - Boyke Bunk
- German Center for Infection Research (DZIF), Leibniz Institute DSMZ, Inhoffenstrasse 7, D-38124 Braunschweig, Germany; (Y.M.); (K.H.); (B.B.)
| | - Joachim Wink
- Helmholtz Centre for Infection Research, Department of microbial Strain Collection, Inhoffenstrasse 7, D-38124 Braunschweig, Germany;
- Correspondence: ; Tel.: +49-531-6181-4223
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9
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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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10
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Baikalomycins A-C, New Aquayamycin-Type Angucyclines Isolated from Lake Baikal Derived Streptomyces sp. IB201691-2A. Microorganisms 2020; 8:microorganisms8050680. [PMID: 32392775 PMCID: PMC7284819 DOI: 10.3390/microorganisms8050680] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 01/06/2023] Open
Abstract
Natural products produced by bacteria found in unusual and poorly studied ecosystems, such as Lake Baikal, represent a promising source of new valuable drug leads. Here we report the isolation of a new Streptomyces sp. strain IB201691-2A from the Lake Baikal endemic mollusk Benedictia baicalensis. In the course of an activity guided screening three new angucyclines, named baikalomycins A–C, were isolated and characterized, highlighting the potential of poorly investigated ecological niches. Besides that, the strain was found to accumulate large quantities of rabelomycin and 5-hydroxy-rabelomycin, known shunt products in angucyclines biosynthesis. Baikalomycins A–C demonstrated varying degrees of anticancer activity. Rabelomycin and 5-hydroxy-rabelomycin further demonstrated antiproliferative activities. The structure elucidation showed that baikalomycin A is a modified aquayamycin with β-d-amicetose and two additional hydroxyl groups at unusual positions (6a and 12a) of aglycone. Baikalomycins B and C have alternating second sugars attached, α-l-amicetose and α-l-aculose, respectively. The gene cluster for baikalomycins biosynthesis was identified by genome mining, cloned using a transformation-associated recombination technique and successfully expressed in S. albus J1074. It contains a typical set of genes responsible for an angucycline core assembly, all necessary genes for the deoxy sugars biosynthesis, and three genes coding for the glycosyltransferase enzymes. Heterologous expression and deletion experiments allowed to assign the function of glycosyltransferases involved in the decoration of baikalomycins aglycone.
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11
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Dan VM, J S V, C J S, Sanawar R, Lekshmi A, Kumar RA, Santhosh Kumar TR, Marelli UK, Dastager SG, Pillai MR. Molecular Networking and Whole-Genome Analysis Aid Discovery of an Angucycline That Inactivates mTORC1/C2 and Induces Programmed Cell Death. ACS Chem Biol 2020; 15:780-788. [PMID: 32058690 DOI: 10.1021/acschembio.0c00026] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rediscovery of known compounds and time consumed in identification, especially high molecular weight compounds with complex structure, have let down interest in drug discovery. In this study, whole-genome analysis of microbe and Global Natural Products Social (GNPS) molecular networking helped in initial understanding of possible compounds produced by the microbe. Genome data revealed 10 biosythethic gene clusters that encode for secondary metabolites with anticancer potential. NMR analysis of the pure compound revealed the presence of a four-ringed benz[a]anthracene, thus confirming angucycline; molecular networking further confirmed production of this class of compounds. The type II polyketide synthase gene identified in the microbial genome was matched with the urdamycin cluster by BLAST analysis. This information led to ease in identification of urdamycin E and a novel natural derivative, urdamycin V, purified from Streptomyces sp. OA293. Urdamycin E (Urd E) induced apoptosis and autophagy in cancer cell lines. Urd E exerted anticancer action through inactivation of the mTOR complex by preventing phosphorylation at Ser 2448 and Ser 2481 of mTORC1 and mTORC2, respectively. Significant reduction in phosphorylation of the major downstream regulators of both mTORC1 (p70s6k and 4e-bp1) and mTORC2 (Akt) were observed, thus further confirming complete inhibition of the mTOR pathway. Urd E presents itself as a novel mTOR inhibitor that employs a novel mechanism in mTOR pathway inhibition.
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Affiliation(s)
- Vipin Mohan Dan
- Microbiology Division, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Palode, Thiruvananthapuram, Kerala, India
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala, India
| | - Vinodh J S
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala, India
- NCIM Resource Centre, Division of Biochemical Sciences, CSIR - National Chemical Laboratory, Pune, Maharashtra, India
| | - Sandesh C J
- Central NMR Facility, CSIR - National Chemical Laboratory, Pune, Maharashtra, India
| | - Rahul Sanawar
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala, India
| | - Asha Lekshmi
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala, India
| | - R. Ajay Kumar
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala, India
| | - T. R. Santhosh Kumar
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala, India
| | - Uday Kiran Marelli
- Central NMR Facility, CSIR - National Chemical Laboratory, Pune, Maharashtra, India
| | - Syed G. Dastager
- NCIM Resource Centre, Division of Biochemical Sciences, CSIR - National Chemical Laboratory, Pune, Maharashtra, India
| | - M. Radhakrishna Pillai
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala, India
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12
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Comparative Genomic Insights into Secondary Metabolism Biosynthetic Gene Cluster Distributions of Marine Streptomyces. Mar Drugs 2019; 17:md17090498. [PMID: 31454987 PMCID: PMC6780079 DOI: 10.3390/md17090498] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial secondary metabolites have huge application potential in multiple industries. Biosynthesis of bacterial secondary metabolites are commonly encoded in a set of genes that are organized in the secondary metabolism biosynthetic gene clusters (SMBGCs). The development of genome sequencing technology facilitates mining bacterial SMBGCs. Marine Streptomyces is a valuable resource of bacterial secondary metabolites. In this study, 87 marine Streptomyces genomes were obtained and carried out into comparative genomic analysis, which revealed their high genetic diversity due to pan-genomes owning 123,302 orthologous clusters. Phylogenomic analysis indicated that the majority of Marine Streptomyces were classified into three clades named Clade I, II, and III, containing 23, 38, and 22 strains, respectively. Genomic annotations revealed that SMBGCs in the genomes of marine Streptomyces ranged from 16 to 84. Statistical analysis pointed out that phylotypes and ecotypes were both associated with SMBGCs distribution patterns. The Clade I and marine sediment-derived Streptomyces harbored more specific SMBGCs, which consisted of several common ones; whereas the Clade II and marine invertebrate-derived Streptomyces have more SMBGCs, acting as more plentiful resources for mining secondary metabolites. This study is beneficial for broadening our knowledge about SMBGC distribution patterns in marine Streptomyces and developing their secondary metabolites in the future.
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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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Liu T, Jin J, Yang X, Song J, Yu J, Geng T, Zhang Z, Ma X, Wang G, Xiao H, Ge Y, Sun X, Xing B, Ma X, Chi C, Kuang Y, Ye M, Wang H, Zhang Y, Yang D, Ma M. Discovery of a Phenylamine-Incorporated Angucyclinone from Marine Streptomyces sp. PKU-MA00218 and Generation of Derivatives with Phenylamine Analogues. Org Lett 2019; 21:2813-2817. [PMID: 30924671 DOI: 10.1021/acs.orglett.9b00800] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A new phenylamine-incorporated angucyclinone (1) featuring a unique 1-phenylbenzo[ cd]indol-3(1 H)-one moiety was discovered from marine Streptomyces sp. PKU-MA00218. A series of experimental investigations identified that 1 was produced from the nonenzymatic conversion of a C-ring-cleaved angucyclinone (2) with phenylamine. Utilizing the nonenzymatic conversion, 18 phenylamine-incorporated angucyclinone derivatives with halogen, methyl, methoxy, and carboxy substitutions were efficiently generated under mild conditions. These results highlighted the impressive roles of nonenzymatic reactions in expanding the structural diversity of angucyclinones.
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Affiliation(s)
- Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Jing Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Xiaoyan Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Juan Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Jiahui Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Tongtong Geng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Zhongyi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Xueyang Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Guiyang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Hua Xiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Yuanjie Ge
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Xiaoxu Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Baiying Xing
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Xiaojie Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Changbiao Chi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Yi Kuang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science , Shandong University , Qingdao 266237 , China
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science , Shandong University , Qingdao 266237 , China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
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Seghal Kiran G, Ramasamy P, Sekar S, Ramu M, Hassan S, Ninawe A, Selvin J. Synthetic biology approaches: Towards sustainable exploitation of marine bioactive molecules. Int J Biol Macromol 2018; 112:1278-1288. [DOI: 10.1016/j.ijbiomac.2018.01.149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/18/2018] [Accepted: 01/21/2018] [Indexed: 12/18/2022]
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16
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Zhang S, Yang Q, Guo L, Zhang Y, Feng L, Zhou L, Yang S, Yao Q, Pescitelli G, Xie Z. Isolation, structure elucidation and racemization of (+)- and (-)-pratensilins A-C: unprecedented spiro indolinone-naphthofuran alkaloids from a marine Streptomyces sp. Chem Commun (Camb) 2018; 53:10066-10069. [PMID: 28840219 DOI: 10.1039/c7cc04983h] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three pairs of new enantiomeric alkaloids with an unprecedented spiro indolinone-naphthofuran skeleton were isolated from a marine Streptomyces sp. The pure enantiomers had a marked difference in the enantiomerization processes for the three compounds. DFT calculations in combination with chemical derivatization were performed to corroborate the racemization process via a keto-enol-type tautomerism.
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Affiliation(s)
- Shumin Zhang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
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Jiang S, Piao C, Yu Y, Cao P, Li C, Yang F, Li M, Xiang W, Liu C. Streptomyces capitiformicae sp. nov., a novel actinomycete producing angucyclinone antibiotics isolated from the head of Camponotus japonicus Mayr. Int J Syst Evol Microbiol 2017; 68:118-124. [PMID: 29111972 DOI: 10.1099/ijsem.0.002468] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated strain 1H-SSA4T, was isolated from the head of an ant (Camponotus japonicus Mayr) and was found to produce angucyclinone antibiotics. A polyphasic approach was used to determine the taxonomic status of strain 1H-SSA4T. The DNA G+C content of the draft genome sequence, consisting of 11.4 Mbp, was 70.0 mol%. 16S rRNA gene sequence similarity studies showed that strain 1H-SSA4T belongs to the genus Streptomyces with the highest sequence similarity to Streptomyces hygroscopicus subsp. ossamyceticus NBRC 13983T (98.9 %), and phylogenetically clustered with this species, Streptomyces torulosus LMG 20305T (98.8 %), Streptomyces ipomoeae NBRC 13050T (98.5 %) and Streptomyces decoyicus NRRL 2666T (98.4 %). The morphological and chemotaxonomic properties of the strain were also consistent with those members of the genus Streptomyces. A combination of DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 1H-SSA4T and the above-mentioned strains, which further clarified their relatedness and demonstrated that strain 1H-SSA4T could be distinguished from these strains. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces capitiformicae sp. nov. is proposed. The type strain is 1H-SSA4T (=CGMCC 4.7403T=DSM 104537T).
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Affiliation(s)
- Shanwen Jiang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Chenyu Piao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Yang Yu
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Peng Cao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Chenxu Li
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Fan Yang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Mutong Li
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, 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
| | - Chongxi Liu
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
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Undabarrena A, Ugalde JA, Seeger M, Cámara B. -Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis. PeerJ 2017; 5:e2912. [PMID: 28229018 PMCID: PMC5312570 DOI: 10.7717/peerj.2912] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/14/2016] [Indexed: 12/25/2022] Open
Abstract
Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.
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Affiliation(s)
- Agustina Undabarrena
- Departmento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María , Valparaiso , Chile
| | - Juan A Ugalde
- Centro de Genética y Genómica, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo , Santiago , Chile
| | - Michael Seeger
- Departmento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María , Valparaiso , Chile
| | - Beatriz Cámara
- Departmento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María , Valparaiso , Chile
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19
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He Q, Li L, Yang T, Li R, Li A. Functional Characterization of a Ketoreductase-Encoding Gene med-ORF12 Involved in the Formation of a Stereospecific Pyran Ring during the Biosynthesis of an Antitumor Antibiotic Medermycin. PLoS One 2015; 10:e0132431. [PMID: 26162081 PMCID: PMC4498746 DOI: 10.1371/journal.pone.0132431] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 06/16/2015] [Indexed: 01/27/2023] Open
Abstract
Medermycin, a polyketide antibiotic, possesses strong bioactivity against a variety of tumors through a novel mechanism and is structurally featured with a pyran ring containing two chiral centers (3S and 15R). By far the biosynthetic origin of such enantiomerical conformations still remains obscure. In the present study, we reported the functional characterization of a proposed ketoreductase Med-ORF12 encoded by medermycin biosynthetic cluster and revealed its involvement in the stereochemical control at C3 center of medermycin. Firstly, bioinformatics analysis of Med-ORF12 suggested that it belongs to a group of stereospecific ketoreductases. Next, a Med-ORF12-deficient mutant was obtained and LC/MS measurements demonstrated that medermycin production was completely abolished in this mutant. Meanwhile, it was found that two shunt products were accumulated at the absence of Med-ORF12. Finally, the reintroduction of Med-ORF12 into this mutant could restore the production of medermycin. In a conclusion, these data supported that Med-ORF12 is essential for the biosynthesis of medermycin and performs its role as a stereospecifc ketoreductase in the tailoring steps of medermycin biosynthetic pathway.
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Affiliation(s)
- Qiang He
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Jinan, China
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Le Li
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Tingting Yang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Jinan, China
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Ruijuan Li
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Jinan, China
| | - Aiying Li
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Jinan, China
- School of Life Sciences, Central China Normal University, Wuhan, China
- * E-mail:
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Accumulation of a bioactive benzoisochromanequinone compound kalafungin by a wild type antitumor-medermycin-producing streptomycete strain. PLoS One 2015; 10:e0117690. [PMID: 25695632 PMCID: PMC4335000 DOI: 10.1371/journal.pone.0117690] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 12/17/2014] [Indexed: 11/19/2022] Open
Abstract
Medermycin and kalafungin, two antibacterial and antitumor antibiotics isolated from different streptomycetes, share an identical polyketide skeleton core. The present study reported the discovery of kalafungin in a medermycin-producing streptomycete strain for the first time. A mutant strain obtained through UV mutagenesis showed a 3-fold increase in the production of this antibiotic, compared to the wild type strain. Heterologous expression experiments suggested that its production was severely controlled by the gene cluster for medermycin biosynthesis. In all, these findings suggested that kalafungin and medermycin could be accumulated by the same streptomycete and share their biosynthetic pathway to some extent in this strain.
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Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar Drugs 2014; 12:3516-59. [PMID: 24918453 PMCID: PMC4071589 DOI: 10.3390/md12063516] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 12/30/2022] Open
Abstract
Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.
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Abstract
The most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a DNA-binding domain. Among the >20 classes of one-component systems, the TetR family of regulators (TFRs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. However, TFRs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and many other aspects of prokaryotic physiology. There are several well-established model systems for understanding these important proteins, and structural studies have begun to unveil the mechanisms by which they bind DNA and recognize small-molecule ligands. The sequences for more than 200,000 TFRs are available in the public databases, and genomics studies are identifying their target genes. Three-dimensional structures have been solved for close to 200 TFRs. Comparison of these structures reveals a common overall architecture of nine conserved α helices. The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.
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Donkor ES. Sequencing of bacterial genomes: principles and insights into pathogenesis and development of antibiotics. Genes (Basel) 2013; 4:556-72. [PMID: 24705262 PMCID: PMC3927574 DOI: 10.3390/genes4040556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/24/2013] [Accepted: 08/27/2013] [Indexed: 11/17/2022] Open
Abstract
The impact of bacterial diseases on public health has become enormous, and is partly due to the increasing trend of antibiotic resistance displayed by bacterial pathogens. Sequencing of bacterial genomes has significantly improved our understanding about the biology of many bacterial pathogens as well as identification of novel antibiotic targets. Since the advent of genome sequencing two decades ago, about 1,800 bacterial genomes have been fully sequenced and these include important aetiological agents such as Streptococcus pneumoniae, Mycobacterium tuberculosis, Escherichia coli O157:H7, Vibrio cholerae, Clostridium difficile and Staphylococcus aureus. Very recently, there has been an explosion of bacterial genome data and is due to the development of next generation sequencing technologies, which are evolving so rapidly. Indeed, the field of microbial genomics is advancing at a very fast rate and it is difficult for researchers to be abreast with the new developments. This highlights the need for regular updates in microbial genomics through comprehensive reviews. This review paper seeks to provide an update on bacterial genome sequencing generally, and to analyze insights gained from sequencing in two areas, including bacterial pathogenesis and the development of antibiotics.
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Affiliation(s)
- Eric S Donkor
- Department of Microbiology, University of Ghana Medical School, P. O. Box 4236, Accra, Ghana.
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