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Haas D, Barba M, Vicente C, Nezbedová Š, Garénaux A, Bury-Moné S, Lorenzi JN, Hôtel L, Laureti L, Thibessard A, Le Goff G, Ouazzani J, Leblond P, Aigle B, Pernodet JL, Lespinet O, Lautru S. Synteruptor: mining genomic islands for non-classical specialized metabolite gene clusters. NAR Genom Bioinform 2024; 6:lqae069. [PMID: 38915823 PMCID: PMC11195616 DOI: 10.1093/nargab/lqae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/26/2024] Open
Abstract
Microbial specialized metabolite biosynthetic gene clusters (SMBGCs) are a formidable source of natural products of pharmaceutical interest. With the multiplication of genomic data available, very efficient bioinformatic tools for automatic SMBGC detection have been developed. Nevertheless, most of these tools identify SMBGCs based on sequence similarity with enzymes typically involved in specialised metabolism and thus may miss SMBGCs coding for undercharacterised enzymes. Here we present Synteruptor (https://bioi2.i2bc.paris-saclay.fr/synteruptor), a program that identifies genomic islands, known to be enriched in SMBGCs, in the genomes of closely related species. With this tool, we identified a SMBGC in the genome of Streptomyces ambofaciens ATCC23877, undetected by antiSMASH versions prior to antiSMASH 5, and experimentally demonstrated that it directs the biosynthesis of two metabolites, one of which was identified as sphydrofuran. Synteruptor is also a valuable resource for the delineation of individual SMBGCs within antiSMASH regions that may encompass multiple clusters, and for refining the boundaries of these SMBGCs.
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Affiliation(s)
- Drago Haas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Matthieu Barba
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | | | - Šarká Nezbedová
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Amélie Garénaux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Stéphanie Bury-Moné
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jean-Noël Lorenzi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Laurence Hôtel
- Université de Lorraine, INRAE, DynAMic, Nancy 54000, France
| | - Luisa Laureti
- Université de Lorraine, INRAE, DynAMic, Nancy 54000, France
| | | | - Géraldine Le Goff
- Institut de Chimie des Substances Naturelles ICSN, CNRS, Gif-sur-Yvette 91198, France
| | - Jamal Ouazzani
- Institut de Chimie des Substances Naturelles ICSN, CNRS, Gif-sur-Yvette 91198, France
| | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, Nancy 54000, France
| | - Bertrand Aigle
- Université de Lorraine, INRAE, DynAMic, Nancy 54000, France
| | - Jean-Luc Pernodet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Olivier Lespinet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sylvie Lautru
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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Zheng S, Zhao H, Yuan Z, Si X, Li Z, Song J, Zhu Y, Wu H. The Analysis of the Glycosyltransferase Gene Function From a Novel Granaticin Producer, Streptomyces Vilmorinianum. YP1. Curr Microbiol 2023; 80:103. [PMID: 36781498 DOI: 10.1007/s00284-023-03192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 12/15/2022] [Indexed: 02/15/2023]
Abstract
Glycosylation is common among the synthesis of natural product and imparts the bioactivity for natural product. As for granaticin, a natural product with great bioactivity, glycosylation is an unusual sugar attachment and remains enigmatic. Orf14 in the gra cluster is the predicted glycosyltransferase but without being identified. Recently, we isolated and identified a novel granaticin producer Streptomyces vilmorinianum YP1. Orf14 gene in gra cluster of YP1 is knocked out and complemented. The instrumental analysis of the blue product synthesized by orf14-deficient mutant exhibits the none-granaticin detection and deglycosylated intermediates accumulation. The bioactivity and stability test suggests the weaker or none antibacterial activity and cytotoxicity of this blue product with greater ultraviolet stability and thermostability than granaticin and derivatives produced by YP1. All the result indicates that orf14 encodes glycosyltransferase and glycosylation played an important role in the bioactivity of granaticin. Meanwhile, the blue pigment, deglycosylated intermediates, has favorable processing characteristics. Our finding supplies the function of orf14 and glycosylation, but also indicates a promising candidate of edible blue pigment applicated in food industry.
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Affiliation(s)
- Shenglan Zheng
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Hongling Zhao
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Zuoyun Yuan
- Department of Science Technology and Innovation, Future Science and Technology Park South, COFCO Nutrition and Health Research Institute, BeiQiJia, ChangPing, BeiJing, 102209, China
| | - Xuechen Si
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Zongxian Li
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Jingyi Song
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, No.33, Fucheng Road, Beijing, 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, 100048, China
| | - Yunping Zhu
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, 100048, China.
- College of Food and Health, Beijing Technology and Business University, No. 33, Fucheng Road, Haidian District, Beijing, 100048, China.
| | - Hua Wu
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, No.33, Fucheng Road, Beijing, 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, 100048, China
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3
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Deng MR, Chik SY, Li Y, Zhu H. An in-cluster Sfp-type phosphopantetheinyl transferase instead of the holo-ACP synthase activates the granaticin biosynthesis under natural physiological conditions. Front Chem 2022; 10:1112362. [PMID: 36618868 PMCID: PMC9813960 DOI: 10.3389/fchem.2022.1112362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial aromatic polyketides are mainly biosynthesized by type II polyketide synthases (PKSs). The PKSs cannot be functional unless their acyl carrier proteins (ACPs) are phosphopantetheinylated by phosphopantetheinyl transferases (PPTases). Gra-ORF32 was identified as an in-cluster PPTase dedicated for granaticin biosynthesis in Streptomyces vietnamensis and the Arg- and Pro-rich N terminus was found to be crucial for catalytic activity. Overexpression of the encoding genes of the holo-ACP synthases of fatty acid synthases (FAS ACPSs) of both E. coli and S. vietnamensis could efficiently activate the production of granaticins in the Δgra-orf32 mutant, suggesting the ACP of granaticin (graACP) is an efficient substrate for FAS ACPSs. However, Gra-ORF32, the cognate PPTase of the graACP, could not compensate the conditional deficiency of ACPS in E. coli HT253, indicating that it has evolved to be functionally segregated from fatty acid biosynthesis. Nine out of eleven endogenous and all the tested exogenous non-cognate PPTases could activate the production of granaticins to varied extents when overexpressed in the Δgra-orf32 mutant, indicating that ACPs of type II PKSs could also be widely recognized as effective substrates by the Sfp-type PPTases. The exogenous PPTases of type II PKSs activated the production of granaticins with much higher efficiency, suggesting that the phylogenetically distant in-cluster PPTases of type II PKSs could share substrate preferences for the ACPs of type II PKSs. A significantly elevated production of granaticins was observed when the mutant Δgra-orf32 was cultivated on ISP2 plates, which was a consequence of crosstalk between the granaticin pathway and a kinamycin-like pathway as revealed by transcriptome analysis and pathway inactivations. Although the host FAS ACPS could efficiently activate the production of granaticins when overexpressed, only Gra-ORF32 activated the efficient production of granaticins under natural physiological conditions, indicating that the activity of the host FAS ACPS was strictly regulated, possibly by binding the FAS holo-ACP product with high affinity. Our findings would contribute to a more comprehensive understanding of how the ACPs of type II PKSs are activated and facilitate the future functional reconstitutions of type II PKSs in E. coli.
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Affiliation(s)
- Ming-Rong Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | | | | | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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4
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Nishiyama T, Enomoto N, Nagayasu R, Ueda K. Organocatalytic activity of granaticin and its involvement in bactericidal function. Sci Rep 2022; 12:7046. [PMID: 35487928 PMCID: PMC9054759 DOI: 10.1038/s41598-022-10877-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/14/2022] [Indexed: 11/10/2022] Open
Abstract
We previously discovered that actinorhodin, a benzoisochromanequinone antibiotic produced by Streptomyces coelicolor A3(2), serves as a catalyst facilitating the oxidation of ascorbic acid and cysteine (PNAS 48:17,152, 2014). In the present study, we screened for similar ascorbic acid-oxidizing activity in the culture broth of various Streptomyces spp., and discovered marked activity in the culture broth of Streptomyces vietnamensis. The principle active compound was granaticin, a pigmented antibiotic that is structurally related to actinorhodin. The absence of any metals in the purified granaticin fraction indicated that granaticin was an organocatalyst. Granaticin catalyzed the oxidation of L-ascorbic acid, generating L-dehydroascorbic acid and hydrogen peroxide (H2O2) at a 1:1 stoichiometric ratio, with 15 times higher reactivity than that of actinorhodin at an optimum pH of 7.0. Granaticin also oxidizes sulfhydryl compounds, including L-cysteine and glutathione. Growth inhibitory assays demonstrated that knockout mutants of the catalase gene exhibit high sensitivity to granaticin. The results suggest that the bactericidal activity of granaticin is exerted by the oxidation of sulfhydryl groups of cellular components and the toxicity of H2O2 generated during the oxidation reaction.
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Affiliation(s)
- Tatsuya Nishiyama
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252-0880, Japan
| | - Narumi Enomoto
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252-0880, Japan
| | - Reina Nagayasu
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252-0880, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252-0880, Japan.
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Deng MR, Li Y, Luo X, Zheng XL, Chen Y, Zhang YL, Zhang W, Zhou H, Zhu H. Discovery of Mycothiogranaticins from Streptomyces vietnamensis GIMV4.0001 and the Regulatory Effect of Mycothiol on the Granaticin Biosynthesis. Front Chem 2021; 9:802279. [PMID: 35004619 PMCID: PMC8733708 DOI: 10.3389/fchem.2021.802279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Granaticins are benzoisochromanequinone polyketides with remarkable antibacterial and anticancer activities. Three sulfur-containing granaticin congeners, mycothiogranaticins A (1), B (2) and granaticin MA (3) were discovered from a granaticin-producing strain of Streptomyces vietnamensis GIMV4.0001. Two of them were structurally determined with mycothiol or N-acetylcysteine moieties and found to be bio-actively reluctant. Disruption of the mshA gene (SVTN_RS20640) that encodes the D-inositol-3-phosphate glycosyltransferase crucial for mycothiol biosynthesis, fully abolished the production of mycothiogranaticins. The result substantiated that the newly discovered mycothiogranaticins are consequences of the combination of the granaticin and mycothiol biosynthetic pathways. The overall granaticin production of the ΔmshA mutant strain was unexpectedly decreased by at least more than 50%, while similar production level of granaticins to that of the wild type strain was observed in an mycothiol-S transferase gene (SVTN_RS22215) disruptant Δmst. These results indicated that the mycothiol deficiency was responsible for the decreased production of granaticins. Mycothiol may positively regulate the biosynthesis of granaticin possibly by maintaining the cellular redox balance. To the best of our knowledge, this is the first report that mycothiol can not only be a direct building block of polyketides but also play a regulatory role in the polyketide biosynthesis.
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Affiliation(s)
- Ming-Rong Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yan Li
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiao Luo
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiang-Ling Zheng
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | | | - Yu-Lian Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | | | - Hao Zhou
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application — Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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6
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Waglechner N, Culp EJ, Wright GD. Ancient Antibiotics, Ancient Resistance. EcoSal Plus 2021; 9:eESP-0027-2020. [PMID: 33734062 PMCID: PMC11163840 DOI: 10.1128/ecosalplus.esp-0027-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023]
Abstract
As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a preantibiotic era requires the discovery of new drugs. While therapeutic use of antibiotics followed by the inevitable selection of resistance is a modern phenomenon, these molecules and the genetic determinants of resistance were in use by environmental microbes long before humans discovered them. In this review, we discuss evidence that antibiotics and resistance were present in the environment before anthropogenic use, describing techniques including direct sampling of ancient DNA and phylogenetic analyses that are used to reconstruct the past. We also pay special attention to the ecological and evolutionary forces that have shaped the natural history of antibiotic biosynthesis, including a discussion of competitive versus signaling roles for antibiotics, proto-resistance, and substrate promiscuity of biosynthetic and resistance enzymes. Finally, by applying an evolutionary lens, we describe concepts governing the origins and evolution of biosynthetic gene clusters and cluster-associated resistance determinants. These insights into microbes' use of antibiotics in nature, a game they have been playing for millennia, can provide inspiration for discovery technologies and management strategies to combat the growing resistance crisis.
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Affiliation(s)
- Nicholas Waglechner
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Elizabeth J. Culp
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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7
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Deng MR, Li Y, He HH, Zhou X, Zheng XL, Wang YH, Zhu H. An aberrant metabolic flow toward early shunt products in the granaticin biosynthetic machinery of Streptomyces vietnamensis GIMV4.0001. J Antibiot (Tokyo) 2020; 73:260-264. [PMID: 31925390 DOI: 10.1038/s41429-019-0267-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/15/2019] [Accepted: 11/28/2019] [Indexed: 01/05/2023]
Abstract
A systematic study of the secondary metabolites of the wild granaticin-producing strain Streptomyces vietnamensis GIMV4.0001 led to the isolation of six known early shunt products related to actinorhodin, SEK34 (3), SEK34b (4), mutactin (5), dehydromutactin (7), EM18 (8) and GTRI-02 (9). While the other shunt products were minor or trace products, the production ratio of SEK34 (3) and SEK34b (4) to granaticins was strikingly high. Nearly 64% of the intermediate with the first ring closed went to the SEK34/SEK34b aberrant pathway. The high level of the aberrant metabolic flow toward the early shunt products SEK34 and SEK34b indicated that the second ring closure of the granaticin (1) biosynthesis is a key limiting step in the granaticin biosynthetic machinery of S. vietnamensis GIMV4.0001.
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Affiliation(s)
- Ming-Rong Deng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Yan Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Huang-Huang He
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Xiaoli Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Xiang-Ling Zheng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Yong-Hong Wang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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8
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Dominguez-Moñino I, Diaz-Herraiz M, Jurado V, Laiz L, Miller AZ, Santos JL, Alonso E, Saiz-Jimenez C. Nature and origin of the violet stains on the walls of a Roman tomb. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:889-899. [PMID: 28458206 DOI: 10.1016/j.scitotenv.2017.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
The Circular Mausoleum tomb (Roman Necropolis of Carmona, Spain) dates back from the first century AD and is characterized by a dense microbial (phototrophic) colonization on the walls and ceiling. However, some walls exhibited an important number of violet stains of unknown origin. The microbial communities of these violet stains are mainly composed of cyanobacteria, streptomycetes and fungi. A strain of Streptomyces parvus, isolated from the walls, produces a violet pigment in culture media. High performance liquid chromatography-mass spectrometry of the culture extracts obtained from this Streptomyces revealed the presence of a few granaticins, pigments with a benzoisochromanequinone structure. When metabolically active in the tomb, S. parvus synthesizes the pigments that diffuse into the mortar. During rain and/or wetting periods, the pigments are solubilized by alkaline waters and elute from the starting position to the surrounding mortar, enlarging the pigmented area and thus contributing to this exceptional biodeterioration phenomenon.
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Affiliation(s)
- Irene Dominguez-Moñino
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Marta Diaz-Herraiz
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Leonila Laiz
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Ana Z Miller
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Juan Luis Santos
- Escuela Politecnica Superior, Universidad de Sevilla, Virgen de Africa 7, 41011 Sevilla, Spain
| | - Esteban Alonso
- Escuela Politecnica Superior, Universidad de Sevilla, Virgen de Africa 7, 41011 Sevilla, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain.
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9
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Watkins AL, Ray A, R Roberts L, Caldwell KA, Olson JB. The Prevalence and Distribution of Neurodegenerative Compound-Producing Soil Streptomyces spp. Sci Rep 2016; 6:22566. [PMID: 26936423 PMCID: PMC4776106 DOI: 10.1038/srep22566] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 02/17/2016] [Indexed: 12/21/2022] Open
Abstract
Recent work from our labs demonstrated that a metabolite(s) from the soil bacterium Streptomyces venezuelae caused dopaminergic neurodegeneration in Caenorhabditis elegans and human neuroblastoma cells. To evaluate the capacity for metabolite production by naturally occurring streptomycetes in Alabama soils, Streptomyces were isolated from soils under different land uses (agriculture, undeveloped, and urban). More isolates were obtained from agricultural than undeveloped soils; there was no significant difference in the number of isolates from urban soils. The genomic diversity of the isolates was extremely high, with only 112 of the 1509 isolates considered clones. A subset was examined for dopaminergic neurodegeneration in the previously established C. elegans model; 28.3% of the tested Streptomyces spp. caused dopaminergic neurons to degenerate. Notably, the Streptomyces spp. isolates from agricultural soils showed more individual neuron damage than isolates from undeveloped or urban soils. These results suggest a common environmental toxicant(s) within the Streptomyces genus that causes dopaminergic neurodegeneration. It could also provide a possible explanation for diseases such as Parkinson's disease (PD), which is widely accepted to have both genetic and environmental factors.
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Affiliation(s)
- Anna L Watkins
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama
| | - Arpita Ray
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama
| | - Lindsay R Roberts
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama
| | - Kim A Caldwell
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama
| | - Julie B Olson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama
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10
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Andam CP, Choudoir MJ, Vinh Nguyen A, Sol Park H, Buckley DH. Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages. ISME JOURNAL 2016; 10:1731-41. [PMID: 26849310 DOI: 10.1038/ismej.2015.230] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/27/2015] [Accepted: 11/06/2015] [Indexed: 11/10/2022]
Abstract
Streptomyces species produce many important antibiotics and have a crucial role in soil nutrient cycling. However, their evolutionary history remains poorly characterized. We have evaluated the impact of homologous recombination on the evolution of Streptomyces using multi-locus sequence analysis of 234 strains that represent at least 11 species clusters. Evidence of inter-species recombination is widespread but not uniform within the genus and levels of mosaicism vary between species clusters. Most phylogenetically incongruent loci are monophyletic at the scale of species clusters and their subclades, suggesting that these recombination events occurred in shared ancestral lineages. Further investigation of two mosaic species clusters suggests that genes acquired by inter-species recombination may have become fixed in these lineages during periods of demographic expansion; implicating a role for phylogeography in determining contemporary patterns of genetic diversity. Only by examining the phylogeny at the scale of the genus is apparent that widespread phylogenetically incongruent loci in Streptomyces are derived from a far smaller number of ancestral inter-species recombination events.
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Affiliation(s)
- Cheryl P Andam
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
| | - Mallory J Choudoir
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
| | - Anh Vinh Nguyen
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
| | - Han Sol Park
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
| | - Daniel H Buckley
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
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11
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Petříčková K, Chroňáková A, Zelenka T, Chrudimský T, Pospíšil S, Petříček M, Krištůfek V. Evolution of cyclizing 5-aminolevulinate synthases in the biosynthesis of actinomycete secondary metabolites: outcomes for genetic screening techniques. Front Microbiol 2015; 6:814. [PMID: 26300877 PMCID: PMC4525017 DOI: 10.3389/fmicb.2015.00814] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/23/2015] [Indexed: 11/13/2022] Open
Abstract
A combined approach, comprising PCR screening and genome mining, was used to unravel the diversity and phylogeny of genes encoding 5-aminolevulinic acid synthases (ALASs, hemA gene products) in streptomycetes-related strains. In actinomycetes, these genes were believed to be directly connected with the production of secondary metabolites carrying the C5N unit, 2-amino-3-hydroxycyclopent-2-enone, with biological activities making them attractive for future use in medicine and agriculture. Unlike "classical" primary metabolism ALAS, the C5N unit-forming cyclizing ALAS (cALAS) catalyses intramolecular cyclization of nascent 5-aminolevulinate. Specific amino acid sequence changes can be traced by comparison of "classical" ALASs against cALASs. PCR screening revealed 226 hemA gene-carrying strains from 1,500 tested, with 87% putatively encoding cALAS. Phylogenetic analysis of the hemA homologs revealed strain clustering according to putative type of metabolic product, which could be used to select producers of specific C5N compound classes. Supporting information was acquired through analysis of actinomycete genomic sequence data available in GenBank and further genetic or metabolic characterization of selected strains. Comparison of 16S rRNA taxonomic identification and BOX-PCR profiles provided evidence for numerous horizontal gene transfers of biosynthetic genes or gene clusters within actinomycete populations and even from non-actinomycete organisms. Our results underline the importance of environmental and evolutionary data in the design of efficient techniques for identification of novel producers.
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Affiliation(s)
- Kateřina Petříčková
- Institute of Microbiology, Czech Academy of Sciences, v. v. i. Prague, Czech Republic
| | - Alica Chroňáková
- Institute of Soil Biology, Biology Centre, Czech Academy of Sciences, v. v. i. České Budějovice, Czech Republic
| | - Tomáš Zelenka
- Institute of Microbiology, Czech Academy of Sciences, v. v. i. Prague, Czech Republic
| | - Tomáš Chrudimský
- Institute of Soil Biology, Biology Centre, Czech Academy of Sciences, v. v. i. České Budějovice, Czech Republic
| | - Stanislav Pospíšil
- Institute of Microbiology, Czech Academy of Sciences, v. v. i. Prague, Czech Republic
| | - Miroslav Petříček
- Institute of Microbiology, Czech Academy of Sciences, v. v. i. Prague, Czech Republic
| | - Václav Krištůfek
- Institute of Soil Biology, Biology Centre, Czech Academy of Sciences, v. v. i. České Budějovice, Czech Republic
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12
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Maier S, Heitzler T, Asmus K, Brötz E, Hardter U, Hesselbach K, Paululat T, Bechthold A. Functional characterization of different ORFs including luciferase-like monooxygenase genes from the mensacarcin gene cluster. Chembiochem 2015; 16:1175-82. [PMID: 25907804 DOI: 10.1002/cbic.201500048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Indexed: 11/06/2022]
Abstract
The biologically active compound mensacarcin is produced by Streptomyces bottropensis. The cosmid cos2 contains a large part of the mensacarcin biosynthesis gene cluster. Heterologous expression of this cosmid in Streptomyces albus J1074 led to the production of the intermediate didesmethylmensacarcin (DDMM). In order to gain more insights into the biosynthesis, gene inactivation experiments were carried out by λ-Red/ET-mediated recombination, and the deletion mutants were introduced into the host S. albus. In total, 23 genes were inactivated. Analysis of the metabolic profiles of the mutant strains showed the complete collapse of DDMM biosynthesis, but upon overexpression of the SARP regulatory gene msnR1 in each mutant new intermediates were detected. The compounds were isolated, and their structures were elucidated. Based on the results the specific functions of several enzymes were determined, and a pathway for mensacarcin biosynthesis is proposed.
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Affiliation(s)
- Sarah Maier
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
| | - Tanja Heitzler
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
| | - Katharina Asmus
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
| | - Elke Brötz
- Organic Chemsitry II, Universität Siegen, Adolf-Reichwein-Strasse 2, 57068 Siegen (Germany).,Present address: Helmholtz Institut für Pharmazeutische Forschung Saarland, Postfach 151150, 66041 Saarbrücken (Germany)
| | - Uwe Hardter
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
| | - Katharina Hesselbach
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
| | - Thomas Paululat
- Organic Chemsitry II, Universität Siegen, Adolf-Reichwein-Strasse 2, 57068 Siegen (Germany)
| | - Andreas Bechthold
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany).
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13
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Deng MR, Guo J, Ma LY, Li YX, Feng GD, Mo CY, Zhu HH. Complete genome sequence of Streptomyces vietnamensis GIMV4.0001 T, a genetically manipulable producer of the benzoisochromanequinone antibiotic granaticin. J Biotechnol 2015; 200:6-7. [PMID: 25687102 DOI: 10.1016/j.jbiotec.2015.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 02/02/2015] [Indexed: 11/26/2022]
Abstract
We report the complete genome sequence of Streptomyces vietnamensis GIMV4.0001(T), a new and genetically manipulable producer of the benzoisochromanequinone antibiotic granaticin, whose unique sugar attachment pattern in structure has drawn much attention among chemical and biochemical researchers. The genome of S. vietnamensis GIMV4.0001(T) consists of one linear chromosome (8,867,142 bp, 72.09% G+C content) and one linear megaplasmid named pSVL1 (286,635 bp, 69.04% G+C content), encoding a total of 7356 protein coding genes. Twenty-nine gene clusters for secondary metabolites were predicted on the chromosome.
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Affiliation(s)
- Ming-Rong Deng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510075, China
| | - Jun Guo
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510075, China
| | - Lian-Ying Ma
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510075, China
| | - Yan-Xuan Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510075, China
| | - Guang-Da Feng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510075, China
| | - Cui-Yun Mo
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510075, China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510075, China.
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Jiang B, Li S, Zhao W, Li T, Zuo L, Nan Y, Wu L, Liu H, Yu L, Shan G, Zuo L. 6-Deoxy-13-hydroxy-8,11-dione-dihydrogranaticin B, an intermediate in granaticin biosynthesis, from Streptomyces sp. CPCC 200532. JOURNAL OF NATURAL PRODUCTS 2014; 77:2130-2133. [PMID: 25153802 DOI: 10.1021/np500138k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A new granaticin analogue and its hydrolysis product were isolated from Streptomyces sp. CPCC 200532. Their structures were determined to be 6-deoxy-13-hydroxy-8,11-dione-dihydrogranaticins B (1) and A (2), respectively, by detailed analysis of spectroscopic data. Compound 1 was regarded as an intermediate in granaticin biosynthesis, as it was bioconvertable to granaticin B. Compared to granaticin B, 1 showed similar cytotoxicity against cancer cell line HCT116, but decreased cytotoxicity against cancer cell lines A549, HeLa, and HepG2. Compound 2 displayed lower cytotoxicity than 1 against all four cancer cell lines tested.
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Affiliation(s)
- Bingya Jiang
- Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, 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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