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Kirita K, Matsumoto H, Endo G, Hosokawa S. Total Syntheses of Borolithochromes A, D and G. Angew Chem Int Ed Engl 2024; 63:e202400586. [PMID: 38369567 DOI: 10.1002/anie.202400586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
Total syntheses of borolithochromes A, D and G, red pigments isolated from fossils of Jurassic putative red alga Solenopora jurassica, have been achieved. The benzo[gh]tetraphene skeletons of the borate ligands in these substances were constructed using Diels-Alder reactions of aryl dienes with naphthoquinone, followed by intramolecular Corey-Chaykovsky reactions. Complexation of these ligands with trimethyl borate generated homocomplexes, which upon sequential O-demethylation produced borolithochromes A and G. In the route to borolithochrome D, a heterocomplex was prepared by stepwise complexation of the ligands with 2-(dimethylamino)ethyl dimethyl borate. The strategy devised to accomplish the first total synthesis of borolithochromes A, D and G should be applicable to the preparation of other borolithochromes as well as spiroborates possessing two fused polycyclic aromatic ligands.
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Affiliation(s)
- Kanade Kirita
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Hirotake Matsumoto
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Gaku Endo
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Seijiro Hosokawa
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan
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2
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Jung SH, Riu M, Lee S, Kim JS, Jeon JS, Ryu CM. An anaerobic rhizobacterium primes rice immunity. THE NEW PHYTOLOGIST 2023; 238:1755-1761. [PMID: 36823752 DOI: 10.1111/nph.18834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 02/10/2023] [Indexed: 05/04/2023]
Affiliation(s)
- Sung-Hee Jung
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, 34141, South Korea
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
| | - Myoungjoo Riu
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
- Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, 34134, South Korea
| | - Soohyun Lee
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
| | - Jun-Seob Kim
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
| | - Je-Seung Jeon
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
| | - Choong-Min Ryu
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, 34141, South Korea
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
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3
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Yang Y, Kessler MGC, Marchán-Rivadeneira MR, Han Y. Combating Antimicrobial Resistance in the Post-Genomic Era: Rapid Antibiotic Discovery. Molecules 2023; 28:molecules28104183. [PMID: 37241928 DOI: 10.3390/molecules28104183] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Constantly evolving drug-resistant "superbugs" have caused an urgent demand for novel antimicrobial agents. Natural products and their analogs have been a prolific source of antimicrobial agents, even though a high rediscovery rate and less targeted research has made the field challenging in the pre-genomic era. With recent advancements in technology, natural product research is gaining new life. Genome mining has allowed for more targeted excavation of biosynthetic potential from natural sources that was previously overlooked. Researchers use bioinformatic algorithms to rapidly identify and predict antimicrobial candidates by studying the genome before even entering the lab. In addition, synthetic biology and advanced analytical instruments enable the accelerated identification of novel antibiotics with distinct structures. Here, we reviewed the literature for noteworthy examples of novel antimicrobial agents discovered through various methodologies, highlighting the candidates with potent effectiveness against antimicrobial-resistant pathogens.
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Affiliation(s)
- Yuehan Yang
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
| | - Mara Grace C Kessler
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Honors Tutorial College, Ohio University, Athens, OH 45701, USA
| | - Maria Raquel Marchán-Rivadeneira
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
- Center for Research on Health in Latinamerica (CISeAL)-Biological Science Department, Pontificia Universidad Católica del Ecuador (PUCE), Quito 170143, Ecuador
| | - Yong Han
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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4
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Zhao JX, Yue JM. Frontier studies on natural products: moving toward paradigm shifts. Sci China Chem 2023. [DOI: 10.1007/s11426-022-1512-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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5
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Paff A, Cockburn DW. Evaluating the efficacy of non-thermal microbial load reduction treatments of heat labile food components for in vitro fermentation experiments. PLoS One 2023; 18:e0283287. [PMID: 36943858 PMCID: PMC10030034 DOI: 10.1371/journal.pone.0283287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Increasingly, in vitro simulated colon fermentations are being used as a pre-clinical step to assess the impacts of foods and drugs on the gut microbiota in a cost-effective manner. One challenge in such systems is that they are potentially susceptible to the influences of contaminating microbes in test materials. Simulated gastric and intestinal digestion can relieve some of these concerns, however, live microbes may remain that can confound analysis. Autoclave treatment of test materials is the surest way to eliminate these microbes but presents problems when using heat labile components such as resistant starch. In this study, liquid chemical sterilant alternatives to moist heat sterilization were explored for treating pulse flours for use during in vitro simulated colon fermentation. Key attributes considered in chemical selection were accessibility, impact on treated food components, and effectiveness of the treatments for reducing microbial load. Three chemicals were selected for evaluation, bleach, alcohol, and hydrogen peroxide, at varying concentrations. Flours chosen for testing were from green lentil, field pea, chickpea, or sprouted green lentil. All treatments significantly reduced microbial loads, though there were still detectable levels of microbes after alcohol treatments. Furthermore, in vitro simulated colon fermentations of the treated pulses showed minimal difference from the untreated control both in terms of microbial composition and short chain fatty acid production. Scanning electron microscopy showed minimal impact of sterilization treatments on the gross structure of the pulse flours. Together these results suggest that bleach and hydrogen peroxide treatments can be effective nonthermal treatments to eliminate contaminating microbes in pulse flours without causing significant damage to starch and other fermentable substrates. This is thus also a promising treatment method for other starchy food substrates, though further testing is required.
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Affiliation(s)
- Andrew Paff
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Darrell W Cockburn
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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Suppression of Methicillin-Resistant Staphylococcus aureus and Reduction of Other Bacteria by Black Soldier Fly Larvae Reared on Potato Substrate. Microbiol Spectr 2022; 10:e0232122. [PMID: 36197291 PMCID: PMC9602475 DOI: 10.1128/spectrum.02321-22] [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] [Indexed: 01/04/2023] Open
Abstract
Larvae of black soldier flies, Hermetia illucens, are increasingly used for biological conversion of animal and plant wastes into ingredients of animal feeds on an industrial scale. The presence of pathogenic microorganisms in harvested larvae may be a serious problem for wide-scale adoption of this technology. Fortunately, black soldier fly larvae may have some antimicrobial properties. Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterium associated with various environments that can be pathogenic to humans and farmed animals. We tested whether black soldier fly larvae suppress MRSA on potato substrate. Autoclaved potatoes containing black soldier fly larvae (P+BSFL), potatoes inoculated with MRSA and containing black soldier fly larvae (P+MRSA+BSFL), and potatoes inoculated with MRSA (P+MRSA) were incubated in glass jars. Substrate samples were taken after 3 and 7 days of incubation and plated on Trypticase soy agar (TSA) and Staphylococcus medium 110 agar (SA) to quantify total bacteria and MRSA, respectively. DNA was extracted from potato substrates on both days and sequenced to assess bacterial and fungal diversity using 515F/806R and internal transcribed spacer (ITS) 1/2 primers, respectively, and QIIME 2.0 software. Both total bacterial and MRSA-specific CFU were reduced in the presence of black soldier fly larvae, with a larger reduction for the latter. Twenty-five bacterial genera and 3 fungal genera were detected. Twenty bacterial genera were shared among the treatments and the days, but their relative abundances often varied. Among the most abundant genera, only Enterococcus and Lactococcus were universally present. Our findings confirm antimicrobial properties of black soldier fly larvae. IMPORTANCE Larvae of black soldier flies, Hermetia illucens, may be used to provide an environmentally sustainable and economically viable method for biological conversion of animal and plant wastes into ingredients of animal feeds on an industrial scale. However, contamination of harvested larvae by pathogenic microorganisms inhabiting decaying substrates may be a serious problem for wide-scale adoption of this technology. Fortunately, black soldier fly larvae may have some antimicrobial properties, including suppression of several common pathogens. Our study showed that such a suppression applies to methicillin-resistant Staphylococcus aureus, which is a ubiquitous bacterium pathogenic to animals (including humans).
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Zhang D, Wang J, Qiao Y, Lin B, Deng Z, Kong L, You D. Genome Mining and Metabolic Profiling Reveal Cytotoxic Cyclodipeptides in Streptomyces hygrospinosus var. Beijingensis. Antibiotics (Basel) 2022; 11:1463. [PMID: 36358118 PMCID: PMC9686873 DOI: 10.3390/antibiotics11111463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 08/27/2023] Open
Abstract
Two new cyclodipeptide (CDP) derivatives (1-2) and another seven known cyclodipeptides (3-9) were isolated from Streptomyces 26D9-414 by the genome mining approach combined with genetic dereplication and the "one strain many compounds" (OSMAC) strategy. The structures of the new CDPs were established on the basis of 1D- and 2D-NMR and comparative electronic circular dichroism (ECD) spectra analysis. The biosynthetic gene clusters (BGCs) for these CDPs were identified through antiSMASH analysis. The relevance between this cdp cluster and the identified nine CDPs was established by genetic interruption manipulation. The newly discovered natural compound 2 displayed comparable cytotoxicity against MDA-MB-231 and SW480 with that of cisplatin, a widely used chemotherapeutic agent for the treatment of various cancers.
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Affiliation(s)
| | | | | | | | | | - Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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8
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Dynamic description of temporal changes of gut microbiota in broilers. Poult Sci 2022; 101:102037. [PMID: 35901643 PMCID: PMC9334346 DOI: 10.1016/j.psj.2022.102037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 12/09/2022] Open
Abstract
The diversity of bacteria and fungi in the gut microbiota of commercial broilers that raised in cages from hatch to the end of the production cycle were examined by an analysis of 3,592 and 3,899 amplicon sequence variants (ASVs), respectively. More than 90% sequences in bacterial communities were related to Firmicutes and Proteobacteria. More than 90% sequences in fungal communities were related to Ascomycota, Basidiomycota, and Glomeromycota. A statistical analysis of the microbiota composition succession showed that age was one of the main factors affecting the intestinal microbial communities of broilers. The increasingly complex community succession of transient microbiota occurred along with an increase of age. This dynamic change was observed to be similar between bacteria and fungi. The gut microbiota had a special structure in the first 3 d after birth of broiler. The microbiota structure was quite stable in the period of rapid skeletal growth (d 14–21), and then changed significantly in the period of rapid gaining weight (d 35–42), thus indicating the composition of gut microbiota in broilers had unique structures at different developmental stages. We observed that several bacteria and fungi occupied key functions in the gut microbiota of broilers, suggesting that the gut homeostasis of broilers might be affected by losses of bacteria and fungi via altering interactions between microbiota. This study aimed to provide a data basis for manipulating the microbiota at different developmental stages, in order to improve production and the intestinal health of broilers.
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Chen S, Zhang C, Zhang L. Investigation of the Molecular Landscape of Bacterial Aromatic Polyketides by Global Analysis of Type II Polyketide Synthases. Angew Chem Int Ed Engl 2022; 61:e202202286. [PMID: 35384223 DOI: 10.1002/anie.202202286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 12/17/2022]
Abstract
Aromatic polyketides biosynthesized by microorganisms are a prominent class of natural products widely used in clinical treatments. Although genome mining approaches have accelerated the discovery of these molecules, the molecular diversity, abundance, and distribution of bacterial aromatic polyketides at a global scale remain elusive. Here, we provide a global atlas of bacterial aromatic polyketides based on large-scale analysis of type II polyketide synthases. We first established the chain length factor protein as a marker that can predict both chemical class and molecular uniqueness of the biosynthetic product, and analyzed the abundance, taxonomic distribution, estimated structural diversity, and the total number of aromatic polyketides in bacteria. We further show the identification of oryzanaphthopyrans with an unprecedented angular naphthopyran scaffold from a rare actinobacterium by genome mining guided by the global atlas. These results serve as a compass for exploiting the entire type II polyketide synthase-derived aromatic polyketides in bacteria.
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Affiliation(s)
- Shanchong Chen
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang Province, China.,Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Chi Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
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10
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Shifts in the Bacterial Community Related to Quality Properties of Vacuum-Packaged Peeled Potatoes during Storage. Foods 2022; 11:foods11081147. [PMID: 35454734 PMCID: PMC9032337 DOI: 10.3390/foods11081147] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
To reveal the potential relationship between the bacterial community and quality attributes of vacuum-packaged peeled potatoes, the bacterial community dynamics, visual quality, organic acids, flavor and volatile organic compounds (VOCs) during 12 days of storage under 10 °C were studied, and a correlation analysis was performed between the bacterial community and VOCs. During the whole storage, the dominant bacteria changed from Ralstonia, Pseudomonas, Pantoea and Comamonas to Clostridia, Clostridium, Lacrimispora, Lactococcus and Leuconostoc. The visual quality and hardness deteriorated significantly on day 12; meanwhile, lactic and acetic acid content accumulated to 0.79 and 4.87 mg/g FW, respectively. Potatoes’ flavor deteriorated severely after 8 days, as evidenced by results of an electronic nose (e-nose). A total of 37 VOCs were detected, and the total content showed an increasing trend from 2164.85 to 10658.68 μg/kg during the whole storage. A correlation analysis showed that Enterobacteriaceae, Erwinia, Lacrimispora, Lactococcus, Serratia, Pantoea, Clostridium, Flavobacterium and Clostridia were positively correlated with the biosynthesis of VOCs. In addition, 10 spoilage markers were screened according to a variable importance in projection (VIP) ≥ 1. Ethanol, which was the most abundant spoilage marker, was significantly related to Enterobacteriaceae, Erwinia, Lacrimispora and Lactococcus. The results of this study have great practical significance for prolonging the shelf life of fresh-cut agricultural produce.
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11
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Chen S, Zhang C, Zhang L. Investigation of the Molecular Landscape of Bacterial Aromatic Polyketides by Global Analysis of Type II Polyketide Synthases. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shanchong Chen
- Zhejiang University Department of Chemistry Hangzhou CHINA
| | - Chi Zhang
- Westlake University School of Science Hangzhou CHINA
| | - Lihan Zhang
- Westlake University School of Science Shilongshan Rd.18Xihu District 310024 Hangzhou CHINA
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12
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Salvatore MM, Di Lelio I, DellaGreca M, Nicoletti R, Salvatore F, Russo E, Volpe G, Becchimanzi A, Mahamedi AE, Berraf-Tebbal A, Andolfi A. Secondary Metabolites, including a New 5,6-Dihydropyran-2-One, Produced by the Fungus Diplodia corticola. Aphicidal Activity of the Main Metabolite, Sphaeropsidin A. Molecules 2022; 27:molecules27072327. [PMID: 35408726 PMCID: PMC9000672 DOI: 10.3390/molecules27072327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/05/2023] Open
Abstract
An undescribed 5,6-dihydropyran-2-one, namely diplopyrone C, was isolated and characterized from the cultures of an isolate of the fungus Diplodia corticola recovered from Quercus suber in Algeria. The structure and relative stereostructure of (5S,6S,7Z,9S,10S)-5-hydroxy-6-(2-(3-methyloxiran-2-yl)vinyl)-5,6-dihydro-2H-pyran-2-one were assigned essentially based on NMR and MS data. Furthermore, ten known compounds were isolated and identified in the same cultures. The most abundant product, the tetracyclic pimarane diterpene sphaeropsidin A, was tested for insecticidal effects against the model sucking aphid, Acyrthosiphon pisum. Results showed a toxic dose-dependent oral activity of sphaeropsidin A, with an LC50 of 9.64 mM.
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Affiliation(s)
- Maria Michela Salvatore
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (M.M.S.); (M.D.); (F.S.)
- Institute for Sustainable Plant Protection, National Research Council, 80055 Portici, Italy
| | - Ilaria Di Lelio
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy; (I.D.L.); (R.N.); (E.R.); (G.V.); (A.B.)
| | - Marina DellaGreca
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (M.M.S.); (M.D.); (F.S.)
| | - Rosario Nicoletti
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy; (I.D.L.); (R.N.); (E.R.); (G.V.); (A.B.)
- Research Center for Olive, Fruit, and Citrus Crops, Council for Agricultural Research and Economics, 81100 Caserta, Italy
| | - Francesco Salvatore
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (M.M.S.); (M.D.); (F.S.)
| | - Elia Russo
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy; (I.D.L.); (R.N.); (E.R.); (G.V.); (A.B.)
| | - Gennaro Volpe
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy; (I.D.L.); (R.N.); (E.R.); (G.V.); (A.B.)
| | - Andrea Becchimanzi
- Department of Agriculture, University of Naples Federico II, 80055 Portici, Italy; (I.D.L.); (R.N.); (E.R.); (G.V.); (A.B.)
| | - Alla Eddine Mahamedi
- Department of Biology, Faculty of Natural Sciences, Life and Earth Sciences, University of Ghardaia, Ghardaia 47000, Algeria;
| | - Akila Berraf-Tebbal
- Mendeleum-Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, 69144 Lednice, Czech Republic;
| | - Anna Andolfi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (M.M.S.); (M.D.); (F.S.)
- BAT Center-Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples Federico II, 80055 Portici, Italy
- Correspondence:
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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14
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Scherlach K, Hertweck C. Mining and unearthing hidden biosynthetic potential. Nat Commun 2021; 12:3864. [PMID: 34162873 PMCID: PMC8222398 DOI: 10.1038/s41467-021-24133-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes. Natural products are an important source of bioactive compounds and have versatile applications in different fields, but their discovery is challenging. Here, the authors review the recent developments in genome mining for discovery of natural products, focusing on compounds from unconventional microorganisms and microbiomes.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
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15
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Chen L, Wang M, Feng Y, Xu X, Luo X, Zhang Z. Production of bioelectricity may play an important role for the survival of Xanthomonas campestris pv. campestris (Xcc) under anaerobic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:144335. [PMID: 33736299 DOI: 10.1016/j.scitotenv.2020.144335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
The plant pathogen Xanthomonas is commonly found in biocontaminated bioreactors; however, few studies have evaluated the growth and impacts of this microorganism on bioreactors. In this study, we examined the characteristics of Xanthomonas campestris pv. campestris (Xcc). Our results showed that Xcc could reduce metal Fe (III) and decolorise methyl orange in vitro. Moreover, I-t and cyclic voltammetry curves showed that Xcc could generate bioelectricity and had two extracellular electron transfer pathways, similar to that of Shewanella. Based on the spectral analysis of intact cells and scanning electron microscopy analysis, one pathway was speculated to involve cytochrome C by direct contact with the pili or cell surface. The other pathway may involve indirect mediators, such as redox substrates, among extracellular polymeric substances. For the direct extracellular electron transfer process, the charge transfer coefficient α, electron number n, and the electron transfer rate constant ks were determined to be 0.49, 2.6, and 2.2 × 10-3 s-1, respectively. In the indirect extracellular electron transfer processes, the values of α, n, and ks were 0.52, 4, and 1.21 s-1, respectively. Of these two transfer methods, indirect electron transfer is dominant and faster than direct electron transfer. Moreover, after mutation of the dsbD gene, which is important for indirect electron transfer, the electrochemical parameters α, n, and ks decreased. Our findings reveal a new anaerobic mechanism mediating the survival of Xcc during wastewater treatment, and may help develop new strategies for preventing Xcc growth during wastewater treatment.
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Affiliation(s)
- Lei Chen
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Mingpeng Wang
- School of Life Science, Qufu Normal University, Qufu 273165, China.
| | - Yujie Feng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiaoyu Xu
- School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiaobo Luo
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Zhaojie Zhang
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
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16
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Abstract
Anaerobic gut fungi are important members of the gut microbiome of herbivores, yet they exist in small numbers relative to bacteria. Here, we show that these early-branching fungi produce a wealth of secondary metabolites (natural products) that may act to regulate the gut microbiome. We use an integrated 'omics'-based approach to classify the biosynthetic genes predicted from fungal genomes, determine transcriptionally active genes, and verify the presence of their enzymatic products. Our analysis reveals that anaerobic gut fungi are an untapped reservoir of bioactive compounds that could be harnessed for biotechnology. Anaerobic fungi (class Neocallimastigomycetes) thrive as low-abundance members of the herbivore digestive tract. The genomes of anaerobic gut fungi are poorly characterized and have not been extensively mined for the biosynthetic enzymes of natural products such as antibiotics. Here, we investigate the potential of anaerobic gut fungi to synthesize natural products that could regulate membership within the gut microbiome. Complementary 'omics' approaches were combined to catalog the natural products of anaerobic gut fungi from four different representative species: Anaeromyces robustus (A. robustus), Caecomyces churrovis (C. churrovis), Neocallimastix californiae (N. californiae), and Piromyces finnis (P. finnis). In total, 146 genes were identified that encode biosynthetic enzymes for diverse types of natural products, including nonribosomal peptide synthetases and polyketide synthases. In addition, N. californiae and C. churrovis genomes encoded seven putative bacteriocins, a class of antimicrobial peptides typically produced by bacteria. During standard laboratory growth on plant biomass or soluble substrates, 26% of total core biosynthetic genes in all four strains were transcribed. Across all four fungal strains, 30% of total biosynthetic gene products were detected via proteomics when grown on cellobiose. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of fungal supernatants detected 72 likely natural products from A. robustus alone. A compound produced by all four strains of anaerobic fungi was putatively identified as the polyketide-related styrylpyrone baumin. Molecular networking quantified similarities between tandem mass spectrometry (MS/MS) spectra among these fungi, enabling three groups of natural products to be identified that are unique to anaerobic fungi. Overall, these results support the finding that anaerobic gut fungi synthesize natural products, which could be harnessed as a source of antimicrobials, therapeutics, and other bioactive compounds.
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17
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Neuwirth T, Letzel A, Tank C, Ishida K, Cyrulies M, Schmölz L, Lorkowski S, Hertweck C. Induced Production, Synthesis, and Immunomodulatory Action of Clostrisulfone, a Diarylsulfone from Clostridium acetobutylicum. Chemistry 2020; 26:15855-15858. [PMID: 32996646 PMCID: PMC7756337 DOI: 10.1002/chem.202003500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/29/2020] [Indexed: 01/25/2023]
Abstract
The anaerobe Clostridium acetobutylicum belongs to the most important industrially used bacteria. Whereas genome mining points to a high potential for secondary metabolism in C. acetobutylicum, the functions of most biosynthetic gene clusters are cryptic. We report that the addition of supra-physiological concentrations of cysteine triggered the formation of a novel natural product, clostrisulfone (1). Its structure was fully elucidated by NMR, MS and the chemical synthesis of a reference compound. Clostrisulfone is the first reported natural product with a diphenylsulfone scaffold. A biomimetic synthesis suggests that pentamethylchromanol-derived radicals capture sulfur dioxide to form 1. In a cell-based assay using murine macrophages a biphasic and dose-dependent regulation of the LPS-induced release of nitric oxide was observed in the presence of 1.
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Affiliation(s)
- Toni Neuwirth
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Anne‐Catrin Letzel
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Cedric Tank
- BioPilotPlantLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Keishi Ishida
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Michael Cyrulies
- BioPilotPlantLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Lisa Schmölz
- Institute of Nutritional SciencesFriedrich Schiller University JenaDornburger Straße 2507743JenaGermany
| | - Stefan Lorkowski
- Institute of Nutritional SciencesFriedrich Schiller University JenaDornburger Straße 2507743JenaGermany
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
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18
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Li JS, Du Y, Gu D, Cai W, Green A, Ng S, Leung A, Del Rio Flores A, Zhang W. Discovery and Biosynthesis of Clostyrylpyrones from the Obligate Anaerobe Clostridium roseum. Org Lett 2020; 22:8204-8209. [PMID: 33052676 DOI: 10.1021/acs.orglett.0c02656] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anaerobic bacteria are a promising new source for natural product discovery. Examination of extracts from the obligate anaerobe Clostridium roseum led to the discovery of a new family of natural products, the clostyrylpyrones. The polyketide synthase-based biosynthetic mechanism of clostyrylpyrones is further proposed on the basis of bioinformatic, gene knockout, biochemical analysis, and heterologous expression studies.
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Affiliation(s)
- Jeffrey S Li
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Di Gu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Allison Green
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Samuel Ng
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Alexander Leung
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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19
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Krespach MKC, García-Altares M, Flak M, Hanno Schoeler, Scherlach K, Netzker T, Schmalzl A, Mattern DJ, Schroeckh V, Komor A, Mittag M, Hertweck C, Brakhage AA. Lichen-like association of Chlamydomonas reinhardtii and Aspergillus nidulans protects algal cells from bacteria. THE ISME JOURNAL 2020; 14:2794-2805. [PMID: 32753730 PMCID: PMC7784976 DOI: 10.1038/s41396-020-0731-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 11/09/2022]
Abstract
Organismal interactions within microbial consortia and their responses to harmful intruders remain largely understudied. An important step toward the goal of understanding functional ecological interactions and their evolutionary selection is the study of increasingly complex microbial interaction systems. Here, we discovered a tripartite biosystem consisting of the fungus Aspergillus nidulans, the unicellular green alga Chlamydomonas reinhardtii, and the algicidal bacterium Streptomyces iranensis. Genetic analyses and MALDI-IMS demonstrate that the bacterium secretes the algicidal compound azalomycin F upon contact with C. reinhardtii. In co-culture, A. nidulans attracts the motile alga C. reinhardtii, which becomes embedded and surrounded by fungal mycelium and is shielded from the algicide. The filamentous fungus Sordaria macrospora was susceptible to azalomycin F and failed to protect C. reinhardtii despite chemotactically attracting the alga. Because S. macrospora was susceptible to azalomycin F, this data imply that for protection the fungus needs to be resistant. Formation of the lichen-like association between C. reinhardtii and A. nidulans increased algal growth. The protection depends on the increased amounts of membrane lipids provided by resistant fungi, thereby generating a protective shelter against the bacterial toxin. Our findings reveal a strategy whereby algae survive lethal environmental algicides through cooperation with fungi.
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Affiliation(s)
- Mario K C Krespach
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - María García-Altares
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain
| | - Michal Flak
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hanno Schoeler
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Biologie des Bactéries Intracellulaires, Institut Pasteur, 28 rue du Dr. Roux, 75015, Paris, France
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Anica Schmalzl
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Derek J Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Anna Komor
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics, and Molecular Botany, Friedrich Schiller University Jena, Jena, Germany
| | - Christian Hertweck
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany.
- Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany.
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20
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Ishida K, Shabuer G, Schieferdecker S, Pidot SJ, Stinear TP, Knuepfer U, Cyrulies M, Hertweck C. Oak-Associated Negativicute Equipped with Ancestral Aromatic Polyketide Synthase Produces Antimycobacterial Dendrubins. Chemistry 2020; 26:13147-13151. [PMID: 32597507 PMCID: PMC7693217 DOI: 10.1002/chem.202001939] [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: 04/21/2020] [Revised: 06/26/2020] [Indexed: 11/07/2022]
Abstract
Anaerobic bacteria have only recently been recognized as a source of antibiotics; yet, the metabolic potential of Negativicutes (Gram-negative staining Firmicutes) such as the oak-associated Dendrosporobacter quercicolus has remained unknown. Genome mining of D. quercicolus and phylogenetic analyses revealed a gene cluster for a type II polyketide synthase (PKS) complex that belongs to the most ancestral enzyme systems of this type. Metabolic profiling, NMR analyses, and stable-isotope labeling led to the discovery of a new family of anthraquinone-type polyphenols, the dendrubins, which are diversified by acylation, methylation, and dimerization. Dendrubin A and B were identified as strong antibiotics against a range of clinically relevant, human-pathogenic mycobacteria.
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Affiliation(s)
- Keishi Ishida
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Gulimila Shabuer
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sebastian Schieferdecker
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, University of Melbourne, 792 Elizabeth Street, 3000, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, 792 Elizabeth Street, 3000, Melbourne, Australia
| | - Uwe Knuepfer
- Biopilot Plant, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Michael Cyrulies
- Biopilot Plant, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany.,Institute for Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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21
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Luo SL, Hu LJ, Huang XJ, Su JC, Shao XH, Wang L, Xu HH, Li CC, Wang Y, Ye WC. Discovery and Biomimetic Synthesis of a Phloroglucinol-Terpene Adduct Collection from Baeckea frutescens and Its Biogenetic Origin Insight. Chemistry 2020; 26:11104-11108. [PMID: 32315480 DOI: 10.1002/chem.202001111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Indexed: 01/20/2023]
Abstract
A phloroglucinol-terpene adduct (PTA) collection consisting of twenty-four molecules featuring three skeletons was discovered from Baeckea frutescens. Inspired by its biosynthetic hypothesis, we synthesized this PTA collection by reductive activation of stable phloroglucinol precursors into highly reactive ortho-quinone methide (o-QM) intermediates and subsequently Diels-Alder cycloaddition. We also demonstrated, for the first time, the generation process of the active o-QM by performing dynamic NMR and HPLC-MS monitoring experiments. Moreover, the PTA collection showed significant antifeedant effect toward the Plutella xylostella larvae.
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Affiliation(s)
- Shi-Lin Luo
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of, TCM and New Drugs Research, Jinan University, Guangzhou, 510632, P. R. China
| | - Li-Jun Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of, TCM and New Drugs Research, Jinan University, Guangzhou, 510632, P. R. China
| | - Xiao-Jun Huang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of, TCM and New Drugs Research, Jinan University, Guangzhou, 510632, P. R. China
| | - Jun-Cheng Su
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of, TCM and New Drugs Research, Jinan University, Guangzhou, 510632, P. R. China
| | - Xue-Hua Shao
- Institute of Fruit Tree Research, Guangdong Academy of, Agricultural Sciences, Guangzhou, 510640, P. R. China
| | - Lei Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of, TCM and New Drugs Research, Jinan University, Guangzhou, 510632, P. R. China
| | - Han-Hong Xu
- State Key Laboratory for Conservation and Utilization of, Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, P. R. China
| | - Chuang-Chuang Li
- Department of Chemistry, South University of Science and Technology of China, Shenzhen, 518055, P. R. China
| | - Ying Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of, TCM and New Drugs Research, Jinan University, Guangzhou, 510632, P. R. China
| | - Wen-Cai Ye
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, P. R. China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of, TCM and New Drugs Research, Jinan University, Guangzhou, 510632, P. R. China
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22
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Herisse M, Ishida K, Porter JL, Howden B, Hertweck C, Stinear TP, Pidot SJ. Identification and Mobilization of a Cryptic Antibiotic Biosynthesis Gene Locus from a Human-Pathogenic Nocardia Isolate. ACS Chem Biol 2020; 15:1161-1168. [PMID: 31697466 DOI: 10.1021/acschembio.9b00763] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genus Nocardia contains >50 human pathogenic species that cause a range of illnesses from skin and soft tissue infections to lung and brain infections. However, despite their membership in the most prominent family of secondary metabolite producers (the Actinomycetes), the ability of Nocardia species, especially those that cause human infections, to produce secondary metabolites has not been as well studied. Using genome mining, we have investigated cryptic secondary metabolite biosynthesis gene clusters from Nocardia species and identified a conserved locus within human pathogenic strains of Nocardia brasiliensis and Nocardia vulneris. Direct capture and heterologous expression in a Streptomyces host activated the biosynthetic locus, revealing it to be the source of the brasiliquinones, benz[a]anthraquinone antibiotics whose biosynthetic pathway has remained hidden for over two decades, until now. Our findings highlight these hitherto neglected human pathogenic Nocardia as a source of diverse and important natural products.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Jessica L. Porter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Ben Howden
- Microbiological Diagnostic Unit, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
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23
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Investigation of secondary metabolism in the industrial butanol hyper-producer Clostridium saccharoperbutylacetonicum N1-4. J Ind Microbiol Biotechnol 2020; 47:319-328. [PMID: 32103460 DOI: 10.1007/s10295-020-02266-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/12/2020] [Indexed: 12/15/2022]
Abstract
Clostridium saccharoperbutylacetonicum N1-4 (Csa) is a historically significant anaerobic bacterium which can perform saccharolytic fermentations to produce acetone, butanol, and ethanol (ABE). Recent genomic analyses have highlighted this organism's potential to produce polyketide and nonribosomal peptide secondary metabolites, but little is known regarding the identity and function of these metabolites. This study provides a detailed bioinformatic analysis of seven biosynthetic gene clusters (BGCs) present in the Csa genome that are predicted to produce polyketides/nonribosomal peptides. An RNA-seq-based untargeted transcriptomic approach revealed that five of seven BGCs were expressed during ABE fermentation. Additional characterization of a highly expressed nonribosomal peptide synthetase gene led to the discovery of its associated metabolite and its biosynthetic pathway. Transcriptomic analysis suggested an association of this nonribosomal peptide synthetase gene with butanol tolerance, which was supported by butanol challenge assays.
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24
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Schieferdecker S, Shabuer G, Knuepfer U, Hertweck C. Clostrindolin is an antimycobacterial pyrone alkaloid from Clostridium beijerinckii. Org Biomol Chem 2020; 17:6119-6121. [PMID: 31168541 DOI: 10.1039/c9ob00968j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anaerobic bacteria represent an underexplored source of bioactive natural products with unusual structural features. Here we report the isolation and structure elucidation of an antimycobacterial natural product, clostroindolin, produced by Clostridium beijerinckii. Furthermore, we provide first insights into structure activity relationships, which might guide the development of novel antibiotics against mycobacteria.
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Affiliation(s)
- Sebastian Schieferdecker
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11, 07745 Jena, Germany.
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25
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da Silva WL, Yang KT, Pettis GS, Soares NR, Giorno R, Clark CA. Flooding-Associated Soft Rot of Sweetpotato Storage Roots Caused by Distinct Clostridium Isolates. PLANT DISEASE 2019; 103:3050-3056. [PMID: 31642734 DOI: 10.1094/pdis-03-19-0548-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Flooding of sweetpotatoes in the field leads to development of soft rot on the storage roots while they remain submerged or on subsequent harvest and storage. Incidences of flooding after periods of intense rainy weather are on the rise in the southeastern United States, which is home to the majority of sweetpotato production in the nation. In an effort to characterize the causative agent(s) of this devastating disease, here we describe two distinct bacterial strains isolated from soft-rotted sweetpotato storage roots retrieved from an intentionally flooded field. Both of these anaerobic spore-forming isolates were identified as members of the genus Clostridium based on sequence similarity of multiple housekeeping genes, and both were confirmed to cause soft rot disease on sweetpotato and other vegetable crops. Despite these common features, the isolates were distinguishable by several phenotypic and biochemical properties, and phylogenetic analysis placed them in separate well-supported clades within the genus. Overall, our results demonstrate that multiple plant-pathogenic Clostridium species can cause soft rot disease on sweetpotato and suggest that a variety of other plant hosts may also be susceptible.
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Affiliation(s)
- Washington L da Silva
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, New Haven, CT 06511
| | - Kuei-Ting Yang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Gregg S Pettis
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Natasha R Soares
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Rebecca Giorno
- School of Biological Sciences, Louisiana Tech University, Ruston, LA 71272
| | - Christopher A Clark
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
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26
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Sugimoto Y, Camacho FR, Wang S, Chankhamjon P, Odabas A, Biswas A, Jeffrey PD, Donia MS. A metagenomic strategy for harnessing the chemical repertoire of the human microbiome. Science 2019; 366:science.aax9176. [DOI: 10.1126/science.aax9176] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022]
Abstract
Extensive progress has been made in determining the effects of the microbiome on human physiology and disease, but the underlying molecules and mechanisms governing these effects remain largely unexplored. Here, we combine a new computational algorithm with synthetic biology to access biologically active small molecules encoded directly in human microbiome–derived metagenomic sequencing data. We discover that members of a clinically used class of molecules are widely encoded in the human microbiome and that they exert potent antibacterial activities against neighboring microbes, implying a possible role in niche competition and host defense. Our approach paves the way toward a systematic unveiling of the chemical repertoire encoded by the human microbiome and provides a generalizable platform for discovering molecular mediators of microbiome-host and microbiome-microbiome interactions.
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Affiliation(s)
- Yuki Sugimoto
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Francine R. Camacho
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Shuo Wang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | | | - Arman Odabas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Abhishek Biswas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Research Computing, Office of Information Technology, Princeton University, Princeton, NJ 08544, USA
| | - Philip D. Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Mohamed S. Donia
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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27
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Schieferdecker S, Shabuer G, Letzel AC, Urbansky B, Ishida-Ito M, Ishida K, Cyrulies M, Dahse HM, Pidot S, Hertweck C. Biosynthesis of Diverse Antimicrobial and Antiproliferative Acyloins in Anaerobic Bacteria. ACS Chem Biol 2019; 14:1490-1497. [PMID: 31243958 DOI: 10.1021/acschembio.9b00228] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Metabolic profiling and genome mining revealed that anaerobic bacteria have the potential to produce acyloin natural products. In addition to sattazolin A and B, three new sattazolin congeners and a novel acyloin named clostrocyloin were isolated from three strains of Clostridium beijerinckii, a bacterium used for industrial solvent production. Bioactivity profiling showed that the sattazolin derivatives possess antimicrobial activities against mycobacteria and pseudomonads with only low cytotoxicity. Clostrocyloin was found to be mainly active against fungi. The thiamine diphosphate (ThDP)-dependent sattazolin-producing synthase was identified in silico and characterized both in vivo and in in vitro enzyme assays. A related acyloin synthase from the clostrocyloin producer was shown to be responsible for the production of the acyloin core of clostrocyloin. The biotransformation experiments provided first insights into the substrate scope of the clostrocyloin synthase and revealed biosynthetic intermediates.
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Affiliation(s)
- Sebastian Schieferdecker
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gulimila Shabuer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Anne-Catrin Letzel
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Barbara Urbansky
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Michael Cyrulies
- BioPilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Sacha Pidot
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth Street, Victoria 3010, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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Thynne E, Mead OL, Chooi YH, McDonald MC, Solomon PS. Acquisition and Loss of Secondary Metabolites Shaped the Evolutionary Path of Three Emerging Phytopathogens of Wheat. Genome Biol Evol 2019; 11:890-905. [PMID: 30793159 PMCID: PMC6431248 DOI: 10.1093/gbe/evz037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
White grain disorder is a recently emerged wheat disease in Australia, caused by Eutiarosporella darliae, E. pseudodarliae, and E. tritici-australis. The disease cycle of these pathogens and the molecular basis of their interaction with wheat are poorly understood. To address this knowledge gap, we undertook a comparative genomics analysis focused on the secondary metabolite gene repertoire among these three species. This analysis revealed a diverse array of secondary metabolite gene clusters in these pathogens, including modular polyketide synthase genes. These genes have only been previously associated with bacteria and this is the first report of such genes in fungi. Subsequent phylogenetic analyses provided strong evidence that the modular PKS genes were horizontally acquired from a bacterial or a protist species. We also uncovered a secondary metabolite gene cluster with three polyketide/nonribosomal peptide synthase genes (Hybrid-1, -2, and -3) in E. darliae and E. pseudodarliae. In contrast, only remnant and partial genes homologous to this cluster were identified in E. tritici-australis, suggesting loss of this cluster. Homologues of Hybrid-2 in other fungi have been proposed to facilitate disease in woody plants, suggesting a possible alternative host range for E. darliae and E. pseudodarliae. Subsequent assays confirmed that E. darliae and E. pseudodarliae were both pathogenic on woody plants, but E. tritici-australis was not, implicating woody plants as potential host reservoirs for the fungi. Combined, these data have advanced our understanding of the lifestyle and potential host-range of these recently emerged wheat pathogens and shed new light on fungal secondary metabolism.
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Affiliation(s)
- Elisha Thynne
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Oliver L Mead
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, Faculty of Science, The University of Western Australia, Perth, Australia
| | - Megan C McDonald
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Peter S Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
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Type E Botulinum Neurotoxin-Producing Clostridium butyricum Strains Are Aerotolerant during Vegetative Growth. mSystems 2019; 4:mSystems00299-18. [PMID: 31058231 PMCID: PMC6495232 DOI: 10.1128/msystems.00299-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/10/2019] [Indexed: 11/21/2022] Open
Abstract
Botulinum neurotoxins, the causative agents of the potentially fatal disease of botulism, are produced by certain Clostridium strains during vegetative growth, usually in anaerobic environments. Our findings indicate that, contrary to current understanding, the growth of neurotoxigenic C. butyricum strains and botulinum neurotoxin type E production can continue upon transfer from anaerobic to aerated conditions and that adaptation of strains to oxygenated environments requires global changes in proteomic and metabolic profiles. We hypothesize that aerotolerance might constitute an unappreciated factor conferring physiological advantages on some botulinum toxin-producing clostridial strains, allowing them to adapt to otherwise restrictive environments. Clostridium butyricum, the type species of the genus Clostridium, is considered an obligate anaerobe, yet it has been shown to grow in the presence of oxygen. C. butyricum strains atypically producing the botulinum neurotoxin type E are the leading cause of type E human botulism in Italy. Here, we show that type E botulinum neurotoxin-producing C. butyricum strains growing exponentially were able to keep growing and producing toxin in vitro upon exposure to air, although less efficiently than under ideal oxygen-depleted conditions. Bacterial growth in air was maintained when the initial cell density was higher than 103 cells/ml. No spores were detected in the cultures aerated for 5 h. To understand the biological mechanisms allowing the adaptation of vegetative cells of C. butyricum type E to oxygen, we compared the proteome and metabolome profiles of the clostridial cultures grown for 5 h under either aerated or anaerobic conditions. The results indicated that bacterial cells responded to oxygen stress by slowing growth and modulating the expression of proteins involved in carbohydrate uptake and metabolism, redox homeostasis, DNA damage response, and bacterial motility. Moreover, the ratio of acetate to butyrate was significantly higher under aeration. This study demonstrates for the first time that a botulinum neurotoxin-producing Clostridium can withstand oxygen during vegetative growth. IMPORTANCE Botulinum neurotoxins, the causative agents of the potentially fatal disease of botulism, are produced by certain Clostridium strains during vegetative growth, usually in anaerobic environments. Our findings indicate that, contrary to current understanding, the growth of neurotoxigenic C. butyricum strains and botulinum neurotoxin type E production can continue upon transfer from anaerobic to aerated conditions and that adaptation of strains to oxygenated environments requires global changes in proteomic and metabolic profiles. We hypothesize that aerotolerance might constitute an unappreciated factor conferring physiological advantages on some botulinum toxin-producing clostridial strains, allowing them to adapt to otherwise restrictive environments.
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Adamek M, Alanjary M, Ziemert N. Applied evolution: phylogeny-based approaches in natural products research. Nat Prod Rep 2019; 36:1295-1312. [DOI: 10.1039/c9np00027e] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we highlight how phylogenetic analyses can be used to facilitate natural product discovery and structure elucidation.
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Affiliation(s)
- Martina Adamek
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
| | | | - Nadine Ziemert
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
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31
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Dunbar KL, Büttner H, Molloy EM, Dell M, Kumpfmüller J, Hertweck C. Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kyle L. Dunbar
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Evelyn M. Molloy
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
- Natural Product Chemistry; Friedrich Schiller University; 07743 Jena Germany
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32
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Dunbar KL, Büttner H, Molloy EM, Dell M, Kumpfmüller J, Hertweck C. Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria. Angew Chem Int Ed Engl 2018; 57:14080-14084. [PMID: 30193003 DOI: 10.1002/anie.201807970] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/23/2018] [Indexed: 12/18/2022]
Abstract
Closthioamide (CTA) is a unique symmetric nonribosomal peptide with six thioamide moieties that is produced by the Gram-positive obligate anaerobe Ruminiclostridium cellulolyticum. CTA displays potent inhibitory activity against important clinical pathogens, making it a promising drug candidate. Yet, the biosynthesis of this DNA gyrase-targeting antibiotic has remained enigmatic. Using a combination of genome mining, genome editing (targeted group II intron, CRISPR/Cas9), and heterologous expression, we show that CTA biosynthesis involves specialized enzymes for starter unit biosynthesis, amide bond formation, thionation, and dimerization. Surprisingly, CTA biosynthesis involves a novel thiotemplated peptide assembly line that markedly differs from known nonribosomal peptide synthetases. These findings provide the first insights into the biosynthesis of thioamide-containing nonribosomal peptides and offer a starting point for the discovery of related natural products.
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Affiliation(s)
- Kyle L Dunbar
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Evelyn M Molloy
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Natural Product Chemistry, Friedrich Schiller University, 07743, Jena, Germany
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33
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Li JS, Barber CC, Zhang W. Natural products from anaerobes. J Ind Microbiol Biotechnol 2018; 46:375-383. [PMID: 30284140 DOI: 10.1007/s10295-018-2086-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/25/2018] [Indexed: 12/27/2022]
Abstract
Natural product discovery in the microbial world has historically been biased toward aerobes. Recent in silico analysis demonstrates that genomes of anaerobes encode unexpected biosynthetic potential for natural products, however, chemical data on natural products from the anaerobic world are extremely limited. Here, we review the current body of work on natural products isolated from strictly anaerobic microbes, including recent genome mining efforts to discover polyketides and non-ribosomal peptides from anaerobes. These known natural products of anaerobes have demonstrated interesting molecular scaffolds, biosynthetic logic, and/or biological activities, making anaerobes a promising reservoir for future natural product discovery.
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Affiliation(s)
- Jeffrey S Li
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Colin Charles Barber
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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34
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Rischer M, Raguž L, Guo H, Keiff F, Diekert G, Goris T, Beemelmanns C. Biosynthesis, Synthesis, and Activities of Barnesin A, a NRPS-PKS Hybrid Produced by an Anaerobic Epsilonproteobacterium. ACS Chem Biol 2018; 13:1990-1995. [PMID: 29901979 DOI: 10.1021/acschembio.8b00445] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the wealth of physiological knowledge and plentiful genomes available, only few natural products of anaerobic bacteria have been identified until today and even less have been linked to their biosynthetic gene cluster. Here, we analyzed a unique NRPS-PKS hybrid gene cluster from an anaerobic Epsilonproteobacterium ( Sulfurospirillum barnesii). Phylogenetic analysis of key biosynthetic genes, gene expression studies, and comparative metabolomics resulted in the identification of the first anoxically biosynthesized NRPS-PKS hybrid metabolite: a lipo-dipeptide with a vinylogous side chain, called barnesin A. The absolute structure was verified by a modular total synthesis, and barnesin and derivatives were found to have antimicrobial activity, as well as selective and nanomolar inhibitory activity, against pharmacological important cysteine proteases, such as cathepsin B.
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Affiliation(s)
- Maja Rischer
- Leibniz Institute for Natural Product Research and Infection Biology−Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Luka Raguž
- Leibniz Institute for Natural Product Research and Infection Biology−Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology−Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Francois Keiff
- Leibniz Institute for Natural Product Research and Infection Biology−Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology−Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
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Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. MICROBIOME 2018; 6:58. [PMID: 29587885 PMCID: PMC5870681 DOI: 10.1186/s40168-018-0445-0] [Citation(s) in RCA: 501] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.
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Affiliation(s)
- M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Paloma Durán
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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36
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Molloy EM, Hertweck C. Antimicrobial discovery inspired by ecological interactions. Curr Opin Microbiol 2017; 39:121-127. [PMID: 29169087 DOI: 10.1016/j.mib.2017.09.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/06/2017] [Indexed: 01/08/2023]
Abstract
Bacteria represent an unparalleled source of antibiotics used to treat infectious diseases. Yet, genome analyses have revealed that their full biosynthetic potential is much larger than expected. Valuable strategies to unearth hidden antibiotics are genome mining, pathway engineering and triggering, as well as co-cultivation approaches. Nevertheless, there is growing understanding that it is often essential to consider the ecological context and that there is a great potential for antimicrobial discovery from bacteria engaged in well-defined interactions with other organisms. Various ecological scenarios involving antimicrobial agents are outlined in this review: predator-prey and pathogenic interactions, the protection of insect assets such as offspring and cultivars, as well as host protection in symbiotic relationships with plants, invertebrates and animals/humans. The illustrative examples given reinforce the idea that examination of interactions between organisms can yield new antimicrobial compounds, and ultimately further our understanding of the function of these molecules in the environment.
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Affiliation(s)
- Evelyn M Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany; Natural Product Chemistry, Friedrich Schiller University, 07743 Jena, Germany.
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37
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The industrial anaerobe Clostridium acetobutylicum uses polyketides to regulate cellular differentiation. Nat Commun 2017; 8:1514. [PMID: 29138399 PMCID: PMC5686105 DOI: 10.1038/s41467-017-01809-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/17/2017] [Indexed: 11/24/2022] Open
Abstract
Polyketides are an important class of bioactive small molecules valued not only for their diverse therapeutic applications, but also for their role in controlling interesting biological phenotypes in their producing organisms. While numerous polyketides are known to be derived from aerobic organisms, only a single family of polyketides has been identified from anaerobic organisms. Here we uncover a family of polyketides native to the anaerobic bacterium Clostridium acetobutylicum, an organism well-known for its historical use as an industrial producer of the organic solvents acetone, butanol, and ethanol. Through mutational analysis and chemical complementation assays, we demonstrate that these polyketides act as chemical triggers of sporulation and granulose accumulation in this strain. This study represents a significant addition to the body of work demonstrating the existence and importance of polyketides in anaerobes, and showcases a strategy of manipulating the secondary metabolism of an organism to improve traits relevant for industrial applications. Polyketides are secondary metabolites mainly found in aerobic organisms with wide applications in medicine and agriculture. Here, the authors uncover new polyketides native to the anaerobic bacterium Clostridium acetobutylicum and show their role in triggering sporulation and granulose accumulation.
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Abstract
Bacterial aromatic polyketides, exemplified by anthracyclines, angucyclines, tetracyclines, and pentangular polyphenols, are a large family of natural products with diverse structures and biological activities and are usually biosynthesized by type II polyketide synthases (PKSs). Since the starting point of biosynthesis and combinatorial biosynthesis in 1984–1985, there has been a continuous effort to investigate the biosynthetic logic of aromatic polyketides owing to the urgent need of developing promising therapeutic candidates from these compounds. Recently, significant advances in the structural and mechanistic identification of enzymes involved in aromatic polyketide biosynthesis have been made on the basis of novel genetic, biochemical, and chemical technologies. This review highlights the progress in bacterial type II PKSs in the past three years (2013–2016). Moreover, novel compounds discovered or created by genome mining and biosynthetic engineering are also included.
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Affiliation(s)
- Zhuan Zhang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Hai-Xue Pan
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
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39
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Kumar M, Brader G, Sessitsch A, Mäki A, van Elsas JD, Nissinen R. Plants Assemble Species Specific Bacterial Communities from Common Core Taxa in Three Arcto-Alpine Climate Zones. Front Microbiol 2017; 8:12. [PMID: 28174556 PMCID: PMC5258723 DOI: 10.3389/fmicb.2017.00012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 01/03/2017] [Indexed: 02/01/2023] Open
Abstract
Evidence for the pivotal role of plant-associated bacteria to plant health and productivity has accumulated rapidly in the last years. However, key questions related to what drives plant bacteriomes remain unanswered, among which is the impact of climate zones on plant-associated microbiota. This is particularly true for wild plants in arcto-alpine biomes. Here, we hypothesized that the bacterial communities associated with pioneer plants in these regions have major roles in plant health support, and this is reflected in the formation of climate and host plant specific endophytic communities. We thus compared the bacteriomes associated with the native perennial plants Oxyria digyna and Saxifraga oppositifolia in three arcto-alpine regions (alpine, low Arctic and high Arctic) with those in the corresponding bulk soils. As expected, the bulk soil bacterial communities in the three regions were significantly different. The relative abundances of Proteobacteria decreased progressively from the alpine to the high-arctic soils, whereas those of Actinobacteria increased. The candidate division AD3 and Acidobacteria abounded in the low Arctic soils. Furthermore, plant species and geographic region were the major determinants of the structures of the endophere communities. The plants in the alpine region had higher relative abundances of Proteobacteria, while plants from the low- and high-arctic regions were dominated by Firmicutes. A highly-conserved shared set of ubiquitous bacterial taxa (core bacteriome) was found to occur in the two plant species. Burkholderiales, Actinomycetales and Rhizobiales were the main taxa in this core, and they were also the main contributors to the differences in the endosphere bacterial community structures across compartments as well as regions. We postulate that the composition of this core is driven by selection by the two plants.
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Affiliation(s)
- Manoj Kumar
- Department of Microbial Ecology, University of GroningenGroningen, Netherlands
- Department of Biological and Environmental Science, University of JyväskyläJyväskylä, Finland
| | - Günter Brader
- Health and Environment Department, AIT Austrian Institute of TechnologyTulln, Austria
| | - Angela Sessitsch
- Health and Environment Department, AIT Austrian Institute of TechnologyTulln, Austria
| | - Anita Mäki
- Department of Biological and Environmental Science, University of JyväskyläJyväskylä, Finland
| | - Jan D. van Elsas
- Department of Microbial Ecology, University of GroningenGroningen, Netherlands
| | - Riitta Nissinen
- Department of Biological and Environmental Science, University of JyväskyläJyväskylä, Finland
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40
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Covington BC, McLean JA, Bachmann BO. Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites. Nat Prod Rep 2017; 34:6-24. [PMID: 27604382 PMCID: PMC5214543 DOI: 10.1039/c6np00048g] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
| | - John A McLean
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA. and Center for Innovative Technology, Vanderbilt University, 5401 Stevenson Center, Nashville, TN 37235, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
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Wohlleben W, Mast Y, Stegmann E, Ziemert N. Antibiotic drug discovery. Microb Biotechnol 2016; 9:541-8. [PMID: 27470984 PMCID: PMC4993170 DOI: 10.1111/1751-7915.12388] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 07/08/2016] [Indexed: 01/25/2023] Open
Abstract
Due to the threat posed by the increase of highly resistant pathogenic bacteria, there is an urgent need for new antibiotics; all the more so since in the last 20 years, the approval for new antibacterial agents had decreased. The field of natural product discovery has undergone a tremendous development over the past few years. This has been the consequence of several new and revolutionizing drug discovery and development techniques, which is initiating a ‘New Age of Antibiotic Discovery’. In this review, we concentrate on the most significant discovery approaches during the last and present years and comment on the challenges facing the community in the coming years.
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Affiliation(s)
- Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Germany
| | - Yvonne Mast
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Germany
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Hofer U. Bacterial physiology: Cropping up in an aerobic niche. Nat Rev Microbiol 2015; 14:2. [PMID: 26639782 DOI: 10.1038/nrmicro.2015.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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