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Sharma H, Ganguly S, Sahana MH, Goswami RK. Stereoselective synthesis of thailandamide A methyl ester. Org Biomol Chem 2024; 22:1409-1419. [PMID: 38285182 DOI: 10.1039/d3ob02107f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
A convergent strategy for the stereoselective synthesis of the methyl ester of the structurally challenging and highly labile antibacterial polyene polyketide natural product thailandamide A has been developed. The key steps include the Zincke aldehyde reaction, Stille cross coupling, Negishi reaction, Julia-Kocienski olefination, cross metathesis, and the less explored Pd(I)-based Heck coupling to access different unsaturation bonds. Additionally, Urpi acetal aldol, Evans methylation, and Crimmins acetate aldol reactions were employed to construct four out of six asymmetric centers of the molecule.
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Affiliation(s)
- Himangshu Sharma
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India.
| | - Swapnamoy Ganguly
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India.
| | - Moinul Haque Sahana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India.
| | - Rajib Kumar Goswami
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India.
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2
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Hennrich O, Weinmann L, Kulik A, Harms K, Klahn P, Youn JW, Surup F, Mast Y. Biotransformation-coupled mutasynthesis for the generation of novel pristinamycin derivatives by engineering the phenylglycine residue. RSC Chem Biol 2023; 4:1050-1063. [PMID: 38033732 PMCID: PMC10685826 DOI: 10.1039/d3cb00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/06/2023] [Indexed: 12/02/2023] Open
Abstract
Streptogramins are the last line of defense antimicrobials with pristinamycin as a representative substance used as therapeutics against highly resistant pathogenic bacteria. However, the emergence of (multi)drug-resistant pathogens renders these valuable antibiotics useless; making it necessary to derivatize compounds for new compound characteristics, which is often difficult by chemical de novo synthesis due to the complex nature of the molecules. An alternative to substance derivatization is mutasynthesis. Herein, we report about a mutasynthesis approach, targeting the phenylglycine (Phg) residue for substance derivatization, a pivotal component of streptogramin antibiotics. Mutasynthesis with halogenated Phg(-like) derivatives altogether led to the production of two new derivatized natural compounds, as there are 6-chloropristinamycin I and 6-fluoropristinamycin I based on LC-MS/MS analysis. 6-Chloropristinamycin I and 6-fluoropristinamycin I were isolated by preparative HPLC, structurally confirmed using NMR spectroscopy and tested for antimicrobial bioactivity. In a whole-cell biotransformation approach using an engineered E. coli BL21(DE3) pET28-hmo/pACYC-bcd-gdh strain, Phg derivatives were generated fermentatively. Supplementation with the E. coli biotransformation fermentation broth containing 4-fluorophenylglycine to the pristinamycin mutasynthesis strain resulted in the production of 6-fluoropristinamycin I, demonstrating an advanced level of mutasynthesis.
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Affiliation(s)
- Oliver Hennrich
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Leoni Weinmann
- Institute of Microbiology, University Stuttgart, Allmandring 31 D-70569 Stuttgart Germany
| | - Andreas Kulik
- Department Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Auf der Morgenstelle 28 D-72076 Tübingen Germany
| | - Karen Harms
- Microbial Drugs Department, Helmholtz-Centre for Infection Research 38124 Braunschweig Germany
| | - Philipp Klahn
- Division of Organic and Medicinal Chemistry, Department of Chemistry and Molecular Biology, University of Gothenburg, Kemigården 4 412 96 Göteborg Sweden
- Centre of Antimicrobial Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Jung-Won Youn
- Institute of Microbiology, University Stuttgart, Allmandring 31 D-70569 Stuttgart Germany
| | - Frank Surup
- Microbial Drugs Department, Helmholtz-Centre for Infection Research 38124 Braunschweig Germany
| | - Yvonne Mast
- Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B 38124 Braunschweig Germany
- Technische Universität Braunschweig, Institut für Mikrobiologie, Rebenring 56 38106 Braunschweig Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen Tübingen Germany
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3
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Lindig A, Schwarz J, Hubmann G, Rosenthal K, Lütz S. Bivariate One Strain Many Compounds Designs Expand the Secondary Metabolite Production Space in Corallococcus coralloides. Microorganisms 2023; 11:2592. [PMID: 37894250 PMCID: PMC10609524 DOI: 10.3390/microorganisms11102592] [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: 09/21/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The scarcely investigated myxobacterium Corallococcus coralloides holds a large genome containing many uncharacterized biosynthetic gene clusters (BGCs) that potentially encode the synthesis of entirely new natural products. Despite its promising genomic potential, suitable cultivation conditions have not yet been found to activate the synthesis of new secondary metabolites (SMs). Finding the right cultivation conditions to activate BGCs in the genome remains a major bottleneck, and its full biosynthetic potential has so far not been determined. We therefore applied a bivariate "one strain many compounds" (OSMAC) approach, using a combination of two elicitor changes at once, for the activation of BGCs and concomitant SM production by C. coralloides. The screening was carried out in Duetz-System 24-well plates, applying univariate and bivariate OSMAC conditions. We combined biotic additives and organic solvents with a complex growth medium for univariate conditions and with minimal medium for bivariate conditions. The success in the activation of BGCs was evaluated by determining the number of new mass features detected in the respective extracts. We found synergistic effects in the bivariate OSMAC designs, evidenced by the detection of completely new mass features in the bivariate OSMAC experiments, which were not detected in the univariate OSMAC designs with only one elicitor. Overall, the bivariate OSMAC screening led to 55 new mass features, which were not detected in the univariate OSMAC design. Molecular networks revealed that these new mass features embody potential novel natural compounds and chemical derivatives like the N-acyl fatty amine N-pentyloctadecanamide and possibly sulfur-containing natural products. Hence, the presence of multiple elicitors in the bivariate OSMAC designs successfully activated the biosynthetic potential in C. coralloides. We propose bivariate OSMAC designs with a complex combination of elicitors as a straightforward strategy to robustly expand the SM space of microorganisms with large genomes.
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Affiliation(s)
- Anton Lindig
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - Jenny Schwarz
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - Georg Hubmann
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - Katrin Rosenthal
- School of Science, Constructor University, 28759 Bremen, Germany;
| | - Stephan Lütz
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Straße 66, 44227 Dortmund, Germany
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4
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Askar AG, Yüksel E, Bozbuğa R, Öcal A, Kütük H, Dinçer D, Canhilal R, Dababat AA, İmren M. Evaluation of Entomopathogenic Nematodes against Common Wireworm Species in Potato Cultivation. Pathogens 2023; 12:pathogens12020288. [PMID: 36839560 PMCID: PMC9961910 DOI: 10.3390/pathogens12020288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/12/2023] Open
Abstract
Wireworms (Coleoptera: Elateridae) are common insect pests that attack a wide range of economically important crops including potatoes. The control of wireworms is of prime importance in potato production due to the potential damage of the larvae to tuber quantity and quality. Chemical insecticides, the main control strategy against wireworms, generally fail to provide satisfactory control due to the lack of available chemicals and the soil-dwelling habits of the larvae. In the last decades, new eco-friendly concepts have emerged in the sustainable control of wireworms, one of which is entomopathogenic nematodes (EPNs). EPNs are soil-inhabitant organisms and represent an ecological approach to controlling a great variety of soil-dwelling insect pests. In this study, the susceptibility of Agriotes sputator Linnaeus and A. rufipalpis Brullé larvae, the most common wireworm species in potato cultivation in Türkiye, to native EPN strains [Steinernema carpocapsae (Sc_BL22), S. feltiae (Sf_BL24 and Sf_KAY4), and Heterorhabditis bacteriophora (Hb_KAY10 and Hb_AF12)] were evaluated at two temperatures (25 and 30 °C) in pot experiments. Heterorhabditis bacteriophora Hb_AF12 was the most effective strain at 30 °C six days post-inoculation and caused 37.5% mortality to A. rufipalpis larvae. Agriotes sputator larvae were more susceptible to tested EPNs at the same exposure time, and 50% mortality was achieved by two EPNs species, Hb_AF12 and Sc_BL22. All EPN species/strains induced mortality over 70% to both wireworm species at both temperatures at 100 IJs/cm2, 18 days post-treatment. The results suggest that tested EPN species/strains have great potential in the control of A. sputator and A. rufipalpis larvae.
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Affiliation(s)
- Arife Gümüş Askar
- Istanbul Directorate of Agricultural Quarantine, Bakırköy, 34149 Istanbul, Türkiye
- Correspondence: (A.G.A.); (E.Y.)
| | - Ebubekir Yüksel
- Department of Plant Protection, Faculty of Agriculture, Kayseri Erciyes University, Melikgazi, 38030 Kayseri, Türkiye
- Correspondence: (A.G.A.); (E.Y.)
| | - Refik Bozbuğa
- Department of Plant Protection, Faculty of Agriculture, Eskişehir Osmangazi University, Odunpazarı, 26160 Eskişehir, Türkiye
| | - Atilla Öcal
- Atatürk Horticultural Central Research Institute, Merkez, 77100 Yalova, Türkiye
| | - Halil Kütük
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Gölköy, 14030 Bolu, Türkiye
| | - Dilek Dinçer
- Biological Control Research Institute, Yüreğir, 01321 Adana, Türkiye
| | - Ramazan Canhilal
- Department of Plant Protection, Faculty of Agriculture, Kayseri Erciyes University, Melikgazi, 38030 Kayseri, Türkiye
| | - Abdelfattah A. Dababat
- International Maize and Wheat Improvement Centre (CIMMYT) 39, Emek, 06511 Ankara, Türkiye
| | - Mustafa İmren
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Gölköy, 14030 Bolu, Türkiye
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Su X, Yu H, Wang X, Zhang C, Wang H, Kong X, Qu Y, Luan Y, Meng Y, Guan J, Song G, Wang L, Song W, Zhao Y. Cyanidin chloride protects mice from methicillin-resistant Staphylococcus aureus-induced pneumonia by targeting Sortase A. Virulence 2022; 13:1434-1445. [PMID: 35983964 PMCID: PMC9397467 DOI: 10.1080/21505594.2022.2112831] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has been developing rapidly in recent years. It poses a severe peril to global health care, and the new strategies to against the MRSA is urgently needed. Sortase A (SrtA) regulates the anchoring of many surface proteins. Compounds repress Staphylococcus aureus (S. aureus) cysteine transpeptidase SrtA are considered adequate potent virulence inhibitors. Then, we describe the identification of an effective SrtA inhibitor, cyanidin chloride, a bioflavonoid compound isolated from various plants. It has a reversible inhibitory effect on SrtA activity at an IC50 of 21.91 μg/mL. As a SrtA inhibitor, cyanidin chloride antagonizes SrtA-related virulence phenotypes due to its breadth and specificity, including fibrinogen adhesion, A549 cell invasion, biofilm formation, and surface protein (SpA) anchoring. Subsequently, molecular docking and fluorescence quenching revealed that SrtA and cyanidin chloride had robust mutual affinity. Further mechanistic studies revealed that Arg-197, Gly-167, and Sep-116 were the key-binding sites mediating the interaction between SrtA and cyanidin chloride. Notably, a significant therapeutic effect of cyanidin chloride in vivo was also observed on the mouse pneumonia model induced by MRSA. In conclusion, our study indicates that cyanidin chloride potentially represents a new candidate SrtA inhibitor for S. aureus and potentially be developed as a new antivirulence agent.
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Affiliation(s)
- Xin Su
- College of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Hangqian Yu
- Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Xingye Wang
- College of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Chi Zhang
- College of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Heming Wang
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Xiangri Kong
- College of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China,College of Animal Science, Jilin University, Changchun, China
| | - Yishen Qu
- Endocrinology Department, Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, China
| | - Yanhe Luan
- College of Animal Science, Jilin University, Changchun, China
| | - Ying Meng
- College of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jiyu Guan
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Guangqi Song
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Li Wang
- College of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China,CONTACT Li Wang
| | - Wu Song
- College of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China,Wu Song
| | - Yicheng Zhao
- College of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, China,Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China,Yicheng Zhao
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6
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Gümüşsoy A, Yüksel E, Özer G, İmren M, Canhilal R, Amer M, Dababat AA. Identification and Biocontrol Potential of Entomopathogenic Nematodes and Their Endosymbiotic Bacteria in Apple Orchards against the Codling Moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae). INSECTS 2022; 13:1085. [PMID: 36554995 PMCID: PMC9786672 DOI: 10.3390/insects13121085] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), is one of the major pests in pome fruit production worldwide. Heavy treatment of the larvae of C. pomonella with insecticides triggered the development of resistance to many groups of insecticides. In addition, the increasing concern about the adverse effects of synthetic insecticides on human health and the environment has led to the development of sustainable and eco-friendly control practices for C. pomonella. The entomopathogenic nematodes (EPNs) (Steinernema and Heterorhabditis spp.) and their endosymbionts (Xenorhabdus and Photorhabdus spp.) represent a newly emerging approach to controlling a wide range of insect pests. In the present study, field surveys were conducted in apple orchards to isolate and identify EPNs and their endosymbionts and evaluate their insecticidal efficacy on the larvae of C. pomonella. EPNs were isolated from 12 of 100 soil samples (12%). Seven samples were identified as Steinernema feltiae (Filipjev, 1934) (Rhabditida: Steinernematidae), whereas five samples were assigned to Heterorhabditis bacteriophora (Poinar, 1976) (Rhabditida: Heterorhabditidae). The pathogenicity of the EPN species/isolates was screened on the last instar larvae of G. mellonella. The two most pathogenic isolates from each EPN species were tested against fifth instar larvae of C. pomonella under controlled conditions. The maximum mortality (100%) was achieved by all EPN species/isolates at a concentration of 100 IJs/larva 96 h after treatment. The endosymbionts of selected H. bacteriophora and S. feltiae species were identified as Photorhabdus luminescens subsp. kayaii and Xenorhabdus bovienii, respectively. The mortality rates ranged between 25 and 62% when the fifth larval instar larvae of C. pomonella were exposed to the treatment of cell-free supernatants of symbiotic bacteria. In essence, the present survey indicated that EPNs and their symbiotic bacteria have good potential for biological control of C. pomonella.
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Affiliation(s)
- Asım Gümüşsoy
- Department of Plant Protection, Faculty of Agriculture, Erciyes University, Melikgazi, 38030 Kayseri, Türkiye
| | - Ebubekir Yüksel
- Department of Plant Protection, Faculty of Agriculture, Erciyes University, Melikgazi, 38030 Kayseri, Türkiye
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Abant Izzet Baysal University, 14030 Bolu, Türkiye
| | - Mustafa İmren
- Department of Plant Protection, Faculty of Agriculture, Abant Izzet Baysal University, 14030 Bolu, Türkiye
| | - Ramazan Canhilal
- Department of Plant Protection, Faculty of Agriculture, Erciyes University, Melikgazi, 38030 Kayseri, Türkiye
| | - Mohammed Amer
- Department of Mechanical Engineering, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
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Hooper AR, Oštrek A, Milian‐Lopez A, Sarlah D. Bioinspired Total Synthesis of Pyritide A2 through Pyridine Ring Synthesis. Angew Chem Int Ed Engl 2022; 61:e202212299. [PMID: 36123301 PMCID: PMC9827874 DOI: 10.1002/anie.202212299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Indexed: 01/12/2023]
Abstract
Pyritides belong to the ribosomally synthesized and post-translationally modified peptide class of natural products that were recently genome-predicted and are structurally defined by unique pyridine-containing macrocycles. Inspired by their biosynthesis, proceeding through peptide modification and cycloaddition to form the heterocyclic core, we report the chemical synthesis of pyritide A2 involving pyridine ring synthesis from an amino acid precursor through aza-Diels-Alder reaction. This strategy permitted the preparation of the decorated pyridine core with an appended amino acid residue in two steps from a commercially available arginine derivative and secured pyritide A2 in ten steps. Moreover, the synthetic logic enables efficient preparation of different pyridine subunits associated with pyritides, allowing rapid and convergent access to this new class of natural products and analogues thereof.
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Affiliation(s)
- Annie R. Hooper
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA
| | - Andraž Oštrek
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA,Department of ChemistryUniversity of PaviaViale Taramelli 1227100PaviaItaly
| | - Ana Milian‐Lopez
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA
| | - David Sarlah
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA,Department of ChemistryUniversity of PaviaViale Taramelli 1227100PaviaItaly
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8
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Natural products from Photorhabdus and Xenorhabdus: mechanisms and impacts. Appl Microbiol Biotechnol 2022; 106:4387-4399. [PMID: 35723692 DOI: 10.1007/s00253-022-12023-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/21/2022]
Abstract
Insects and fungal pathogens pose constant problems to public health and agriculture, especially in resource-limited parts of the world; and the use of chemical pesticides continues to be the main methods for the control of these organisms. Photorhabdus spp. and Xenorhabdus spp., (Fam; Morganellaceae), enteric symbionts of Steinernema, and Heterorhabditis nematodes are naturally found in soil on all continents, except Antarctic, and on many islands throughout the world. These bacteria produce diverse secondary metabolites that have important biological and ecological functions. Secondary metabolites include non-ribosomal peptides, polyketides, and/or hybrid natural products that are synthesized using polyketide synthetase (PRS), non-ribosomal peptide synthetase (NRPS), or similar enzymes and are sources of new pesticide/drug compounds and/or can serve as lead molecules for the design and synthesize of new alternatives that could replace current ones. This review addresses the effects of these bacterial symbionts on insect pests, fungal phytopathogens, and animal pathogens and discusses the substances, mechanisms, and impacts on agriculture and public health. KEY POINTS: • Insects and fungi are a constant menace to agricultural and public health. • Chemical-based control results in resistance development. • Photorhabdus and Xenorhabdus are compelling sources of biopesticides.
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Bach E, Passaglia LMP, Jiao J, Gross H. Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites. Crit Rev Microbiol 2021; 48:121-160. [PMID: 34346791 DOI: 10.1080/1040841x.2021.1946009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.
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Affiliation(s)
- Evelise Bach
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Junjing Jiao
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Harald Gross
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
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Ghosh S, Sarangi AN, Mukherjee M, Singh D, Madhavi M, Tripathy S. Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India. Bioinform Biol Insights 2021; 15:11779322211025332. [PMID: 34220198 PMCID: PMC8221699 DOI: 10.1177/11779322211025332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/24/2021] [Indexed: 12/03/2022] Open
Abstract
Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.
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Affiliation(s)
- Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Mayuri Mukherjee
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Madduluri Madhavi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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11
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Danelius E, Halaby S, van der Donk WA, Gonen T. MicroED in natural product and small molecule research. Nat Prod Rep 2021; 38:423-431. [PMID: 32939523 PMCID: PMC7965795 DOI: 10.1039/d0np00035c] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Covering: 2013 to 2020The electron cryo-microscopy (cryo-EM) method Microcrystal Electron Diffraction (MicroED) allows the collection of high-resolution structural data from vanishingly small crystals that appear like amorphous powders or very fine needles. Since its debut in 2013, data collection and analysis schemes have been fine-tuned, and there are currently close to 100 structures determined by MicroED. Although originally developed to study proteins, MicroED is also very powerful for smaller systems, with some recent and very promising examples from the field of natural products. Herein, we review what has been achieved so far and provide examples of natural product structures, as well as demonstrate the expected future impact of MicroED to the field of natural product and small molecule research.
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Affiliation(s)
- Emma Danelius
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA 90095, USA.
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Qiao Y, Zhang Q, Chen D, Liu M, Liu W. Application of CRISPR/Cas9 Gene Editing System in Obtaining Natural Products in Actinomycetes. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202105035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Mou SB, Xiao W, Wang HQ, Chen KY, Xiang Z. Syntheses of the Carotane-type Terpenoids (+)-Schisanwilsonene A and (+)-Tormesol via a Two-Stage Approach. Org Lett 2020; 23:400-404. [DOI: 10.1021/acs.orglett.0c03894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Shu-Bin Mou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wen Xiao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Hua-Qi Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Kai-Yue Chen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Zheng Xiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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Mode of entry of secondary metabolites of the bacteria Xenorhabdus szentirmaii and X. nematophila into Tetranychus urticae, and their toxicity to the predatory mites Phytoseiulus persimilis and Neoseiulus californicus. J Invertebr Pathol 2020; 174:107418. [PMID: 32525025 DOI: 10.1016/j.jip.2020.107418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022]
Abstract
The bacterial metabolites in supernatants of Xenorhabdus species have acaricidal activity, but this mode of entry into mites has not yet been elucidated. Herein, we report on the possible mode of entry of Xenorhabdus szentirmaii and Xenorhabdus nematophila supernatants into Tetranychus urticae (Acari: Tetranychidae) adult females. We also assessed the toxicity of the supernatants against the developmental stages of the predatory mites, Phytoseiulus persimilis and Neoseiulus californicus (Acari: Phytoseiidae). Experiments were conducted at 25 ± 1 °C, 70 ± 5% relative humidity, and 16:8h light:dark conditions. Our data showed that the bioactive acaricidal compound is most effective (86.5 to 89% mortality) when the entire integument of T. urticae comes in contact with it compared to contact of the ventral side only (26.5-34%). Against P. persimilis and N. californicus at 6 days post-application (dpa), the eggs were not affected by the X. szentirmaii or X. nematophila supernatant, whereas mortality of the mobile stages (larva, protonymph, deutonymph, adult) was 18.5% to 39.2%. Overall, the predatory mites were less affected by the bacterial metabolites than T. urticae. We hypothesize that the differences in morphology such as longer legs and thicker cuticle, as well as the diet of the predatory mites, reduce the contact of the body parts to the supernatant-treated surfaces. We need to isolate, identify, and characterize the X. szentirmaii and X. nematophila metabolite(s) and demonstrate efficacy to pestiferous mites and safety to plants, non-target organisms and the environment before it can be used as an acaricide.
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Umstätter F, Domhan C, Hertlein T, Ohlsen K, Mühlberg E, Kleist C, Zimmermann S, Beijer B, Klika KD, Haberkorn U, Mier W, Uhl P. Vancomycin Resistance Is Overcome by Conjugation of Polycationic Peptides. Angew Chem Int Ed Engl 2020; 59:8823-8827. [PMID: 32190958 PMCID: PMC7323874 DOI: 10.1002/anie.202002727] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Indexed: 01/09/2023]
Abstract
Multidrug-resistant bacteria represent one of the biggest challenges facing modern medicine. The increasing prevalence of glycopeptide resistance compromises the efficacy of vancomycin, for a long time considered as the last resort for the treatment of resistant bacteria. To reestablish its activity, polycationic peptides were conjugated to vancomycin. By site-specific conjugation, derivatives that bear the peptide moiety at four different sites of the antibiotic were synthesized. The most potent compounds exhibited an approximately 1000-fold increased antimicrobial activity and were able to overcome the most important types of vancomycin resistance. Additional blocking experiments using d-Ala-d-Ala revealed a mode of action beyond inhibition of cell-wall formation. The antimicrobial potential of the lead candidate FU002 for bacterial infection treatments could be demonstrated in an in vivo study. Molecular imaging and biodistribution studies revealed that conjugation engenders superior pharmacokinetics.
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Affiliation(s)
- Florian Umstätter
- Department of Nuclear MedicineHeidelberg University HospitalIm Neuenheimer Feld 40069120HeidelbergGermany
| | - Cornelius Domhan
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityGermany
| | - Tobias Hertlein
- Institute for Molecular Infection Biology (IMIB)University of WürzburgGermany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology (IMIB)University of WürzburgGermany
| | - Eric Mühlberg
- Department of Nuclear MedicineHeidelberg University HospitalIm Neuenheimer Feld 40069120HeidelbergGermany
| | - Christian Kleist
- Department of Nuclear MedicineHeidelberg University HospitalIm Neuenheimer Feld 40069120HeidelbergGermany
| | - Stefan Zimmermann
- Medical Microbiology and HygieneHeidelberg University HospitalGermany
| | - Barbro Beijer
- Department of Nuclear MedicineHeidelberg University HospitalIm Neuenheimer Feld 40069120HeidelbergGermany
| | - Karel D. Klika
- German Cancer Research Center (DKFZ)NMR Spectroscopy Analysis UnitGermany
| | - Uwe Haberkorn
- Department of Nuclear MedicineHeidelberg University HospitalGermany
- Clinical Cooperation Unit Nuclear MedicineGerman Cancer Research Center (DKFZ)Germany
- Translational Lung Research Center Heidelberg (TLRC)German Center for Lung Research (DZL)Germany
| | - Walter Mier
- Department of Nuclear MedicineHeidelberg University HospitalIm Neuenheimer Feld 40069120HeidelbergGermany
| | - Philipp Uhl
- Department of Nuclear MedicineHeidelberg University HospitalIm Neuenheimer Feld 40069120HeidelbergGermany
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Umstätter F, Domhan C, Hertlein T, Ohlsen K, Mühlberg E, Kleist C, Zimmermann S, Beijer B, Klika KD, Haberkorn U, Mier W, Uhl P. Überwindung von Vancomycinresistenzen durch Modifikation mit polykationischen Peptiden. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Florian Umstätter
- Abteilung Nuklearmedizin Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg Deutschland
| | - Cornelius Domhan
- Institut für Pharmazie und Molekulare Biotechnologie Universität Heidelberg Deutschland
| | - Tobias Hertlein
- Institut für Molekulare Infektionsbiologie Universität Würzburg Deutschland
| | - Knut Ohlsen
- Institut für Molekulare Infektionsbiologie Universität Würzburg Deutschland
| | - Eric Mühlberg
- Abteilung Nuklearmedizin Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg Deutschland
| | - Christian Kleist
- Abteilung Nuklearmedizin Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg Deutschland
| | - Stefan Zimmermann
- Zentrum für Infektiologie Universitätsklinikum Heidelberg Deutschland
| | - Barbro Beijer
- Abteilung Nuklearmedizin Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg Deutschland
| | - Karel D. Klika
- Deutsches Krebsforschungszentrum (DKFZ) NMR-Analytik Deutschland
| | - Uwe Haberkorn
- Abteilung Nuklearmedizin Universitätsklinikum Heidelberg Deutschland
- Klinische Kooperationseinheit Nuklearmedizin Deutsches Krebsforschungszentrum Deutschland
- Translational Lung Research Center Heidelberg (TLRC) Deutsches Zentrum für Lungenforschung (DZL) Deutschland
| | - Walter Mier
- Abteilung Nuklearmedizin Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg Deutschland
| | - Philipp Uhl
- Abteilung Nuklearmedizin Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg Deutschland
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Heterogeneity in Bacterial Specialized Metabolism. J Mol Biol 2019; 431:4589-4598. [DOI: 10.1016/j.jmb.2019.04.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 11/17/2022]
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Affiliation(s)
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign and Howard Hughes Medical Institute
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Lei X, Fan Q, Huang T, Liu H, Zhao G, Ding X. Efficient circular gene knockout system for Burkholderiales strain DSM 7029 and Mycobacterium smegmatis mc2 155. Acta Biochim Biophys Sin (Shanghai) 2019; 51:697-706. [PMID: 31187113 DOI: 10.1093/abbs/gmz054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Indexed: 11/14/2022] Open
Abstract
Multiple gene knockouts are often employed in studies of microbial physiology and genetics. However, the selective markers that confer antibiotic resistance are generally limited, so it is necessary to remove these resistance genes before the next round of using, which is time consuming and labor intensive. Here, we created a universal circular gene knockout system for both the gram-negative bacterial Burkholderiales strain DSM 7029 and the gram-positive bacterial Mycobacterium smegmatis mc2 155, by combining the homologous recombination with multiple serine integrase-meditated site-specific recombination systems. In this system, a resistance gene and an integrase gene were constructed within the two attachment sites corresponding to a second, different integrase to form a cassette for gene disruption, which could be easily removed by the second integrase during the subsequent round of gene knockout. The sacB gene was also employed for negative selection. As the integrase-mediated deletion of the resistance/integrase gene cassette was highly efficient and concurrent with the following knockout round, the cyclic use of three cassettes could achieve multiple gene knockout in a sequential manner. Following the modularity concept in synthetic biology, common components of the knockout plasmids were retained as BioBricks, accelerating the knockout plasmids construction process. The circular gene knockout system can also be used for multiple gene insertions and applied to other microorganisms.
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Affiliation(s)
- Xiaolai Lei
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiuxia Fan
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Tian Huang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Haiyun Liu
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Guoping Zhao
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center, Shanghai, China
| | - Xiaoming Ding
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
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Yang YJ, Singh RP, Lan X, Zhang CS, Li YZ, Li YQ, Sheng DH. Genome Editing in Model Strain Myxococcus xanthus DK1622 by a Site-Specific Cre/loxP Recombination System. Biomolecules 2018; 8:biom8040137. [PMID: 30404219 PMCID: PMC6316027 DOI: 10.3390/biom8040137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 11/17/2022] Open
Abstract
Myxococcus xanthus DK1622 is a rich source of novel secondary metabolites, and it is often used as an expression host of exogenous biosynthetic gene clusters. However, the frequency of obtaining large genome-deletion variants by using traditional strategies is low, and progenies generated by homologous recombination contain irregular deletions. The present study aims to develop an efficient genome-engineering system for this bacterium based on the Cre/loxP system. We first verified the functionality of the native cre system that was integrated into the chromosome with an inducible promoter PcuoA. Then we assayed the deletion frequency of 8-bp-spacer-sequence mutants in loxP by Cre recombinase which was expressed by suicide vector pBJ113 or self-replicative vector pZJY41. It was found that higher guanine content in a spacer sequence had higher deletion frequency, and the self-replicative vector was more suitable for the Cre/loxP system, probably due to the leaky expression of inducible promoter PcuoA. We also inspected the effects of different antibiotics and the native or synthetic cre gene. Polymerase chain reaction (PCR) and sequencing of new genome joints confirmed that the Cre/loxP system was able to delete a 466 kb fragment in M. xanthus. This Cre/loxP-mediated recombination could serve as an alternative genetic manipulation method.
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Affiliation(s)
- Ying-Jie Yang
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Qingdao 266237, China.
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Raghvendra Pratap Singh
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Qingdao 266237, China.
- Research and Development Department, Biotechnology, Uttaranchal University, Dehradun 248007, India.
| | - Xin Lan
- Department of Bio-Chemistry, Qingdao Technical College, Qingdao 266555, China.
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Qingdao 266237, China.
| | - Yi-Qiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Duo-Hong Sheng
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Qingdao 266237, China.
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Abstract
Gibson one-step, isothermal assembly method (Gibson assembly) can be used to efficiently assemble large DNA molecules by in vitro recombination involving a 5'-exonuclease, a DNA polymerase and a DNA ligase. In the past few years, this robust DNA assembly method has been widely applied to seamlessly construct genes, genetic pathways and even entire genomes. Here, we expand this method to clone large DNA fragments with high GC contents, such as antibiotic biosynthetic gene clusters from Streptomyces . Due to the low isothermal condition (50 °C) in the Gibson reaction system, the complementary overlaps with high GC contents are proposed to easily form mismatched linker pairings, which leads to low assembly efficiencies mainly due to vector self-ligation. So, we modified this classic method by the following two steps. First, a pair of universal terminal single-stranded DNA overhangs with high AT contents are added to the ends of the BAC vector. Second, two restriction enzyme sites are introduced into the respective sides of the designed overlaps to achieve the hierarchical assembly of large DNA molecules. The optimized Gibson assembly method facilitates fast acquisition of large DNA fragments with high GC contents from Streptomyces.
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Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
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Affiliation(s)
- Joachim J Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Maja Remškar
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
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Tobias NJ, Linck A, Bode HB. Natural Product Diversification Mediated by Alternative Transcriptional Starting. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713199] [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)
- Nicholas J. Tobias
- Fachbereich Biowissenschaften; Merck Stiftungsprofessur für Molekulare Biotechnologie; Goethe-Universität Frankfurt; Frankfurt am Main Germany
| | - Annabell Linck
- Fachbereich Biowissenschaften; Merck Stiftungsprofessur für Molekulare Biotechnologie; Goethe-Universität Frankfurt; Frankfurt am Main Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften; Merck Stiftungsprofessur für Molekulare Biotechnologie; Goethe-Universität Frankfurt; Frankfurt am Main Germany
- Buchmann Institute for Molecular Life Sciences; Goethe-Universität Frankfurt; Frankfurt am Main Germany
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Discovery of recombinases enables genome mining of cryptic biosynthetic gene clusters in Burkholderiales species. Proc Natl Acad Sci U S A 2018; 115:E4255-E4263. [PMID: 29666226 PMCID: PMC5939090 DOI: 10.1073/pnas.1720941115] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Natural products biosynthesized by cryptic gene clusters represent a largely untapped source for drug discovery. However, mining of these products by promoter engineering is restricted by the lack of streamlined genetic tools, especially in nonmodel biosynthetic gene cluster (BGC)-rich bacteria. Here, we describe the discovery of a pair of bacteriophage recombinases and application of recombinase-assisted promoter engineering to rapidly identify and activate several cryptic biosynthetic gene clusters in two Burkholderiales strains that currently lack effective genetic tools. Construction of an efficient genome engineering platform in a natural product producer expedites mining of cryptic BGCs in their native backgrounds, and host melioration for yield or structure optimization. This strategy enables potentially scalable discovery of novel metabolites with intriguing bioactivities from many other bacteria. Bacterial genomes encode numerous cryptic biosynthetic gene clusters (BGCs) that represent a largely untapped source of drugs or pesticides. Mining of the cryptic products is limited by the unavailability of streamlined genetic tools in native producers. Precise genome engineering using bacteriophage recombinases is particularly useful for genome mining. However, recombinases are usually host-specific. The genome-guided discovery of novel recombinases and their transient expression could boost cryptic BGC mining. Herein, we reported a genetic system employing Red recombinases from Burkholderiales strain DSM 7029 for efficient genome engineering in several Burkholderiales species that currently lack effective genetic tools. Using specialized recombinases-assisted in situ insertion of functional promoters, we successfully mined five cryptic nonribosomal peptide synthetase/polyketide synthase BGCs, two of which were silent. Two classes of lipopeptides, glidopeptins and rhizomides, were identified through extensive spectroscopic characterization. This recombinase expression strategy offers utility within other bacteria species, allowing bioprospecting for potentially scalable discovery of novel metabolites with attractive bioactivities.
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Tobias NJ, Linck A, Bode HB. Natural Product Diversification Mediated by Alternative Transcriptional Starting. Angew Chem Int Ed Engl 2018; 57:5699-5702. [PMID: 29508935 DOI: 10.1002/anie.201713199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Indexed: 11/08/2022]
Abstract
Photorhabdus luminescens dedicates a significant proportion of its genome to the production of natural products. These products and the structural variation in their derivatives may occur by a number of well-described mechanisms, such as module skipping or precursor promiscuity. Cappable-seq was used to identify transcriptional start sites of many of the gene clusters present in P. luminescens TTO1. We discovered that variations associated with the non-ribosomal peptide synthetase Kol, which is responsible for kolossin A production, possessed a number of internal transcripts that lead to synthesis of the smaller kolossin derivatives kolossin B and C. The data here support a new mechanism of natural product biosynthetic variation whereby mRNA may code for shorter NRPS enzymes in addition to full-length proteins, resulting in the production of smaller peptide derivatives.
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Affiliation(s)
- Nicholas J Tobias
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Annabell Linck
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
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Ishikawa F, Tanabe G, Kakeya H. Activity-Based Protein Profiling of Non-ribosomal Peptide Synthetases. Curr Top Microbiol Immunol 2018; 420:321-349. [PMID: 30178264 DOI: 10.1007/82_2018_133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-ribosomal peptide (NRP) natural products are one of the most promising resources for drug discovery and development because of their wide-ranging of therapeutic potential, and their behavior as virulence factors and signaling molecules. The NRPs are biosynthesized independently of the ribosome by enzyme assembly lines known as the non-ribosomal peptide synthetase (NRPS) machinery. Genetic, biochemical, and bioinformatics analyses have provided a detailed understanding of the mechanism of NRPS catalysis. However, proteomic techniques for natural product biosynthesis remain a developing field. New strategies are needed to investigate the proteomes of diverse producer organisms and directly analyze the endogenous NRPS machinery. Advanced platforms should verify protein expression, protein folding, and activities and also enable the profiling of the NRPS machinery in biological samples from wild-type, heterologous, and engineered bacterial systems. Here, we focus on activity-based protein profiling strategies that have been recently developed for studies aimed at visualizing and monitoring the NRPS machinery and also for rapid labeling, identification, and biochemical analysis of NRPS enzyme family members as required for proteomic chemistry in natural product sciences.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan.
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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Tobias NJ, Wolff H, Djahanschiri B, Grundmann F, Kronenwerth M, Shi YM, Simonyi S, Grün P, Shapiro-Ilan D, Pidot SJ, Stinear TP, Ebersberger I, Bode HB. Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus. Nat Microbiol 2017; 2:1676-1685. [PMID: 28993611 DOI: 10.1038/s41564-017-0039-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 09/08/2017] [Indexed: 12/25/2022]
Abstract
Xenorhabdus and Photorhabdus species dedicate a large amount of resources to the production of specialized metabolites derived from non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS). Both bacteria undergo symbiosis with nematodes, which is followed by an insect pathogenic phase. So far, the molecular basis of this tripartite relationship and the exact roles that individual metabolites and metabolic pathways play have not been well understood. To close this gap, we have significantly expanded the database for comparative genomics studies in these bacteria. Clustering the genes encoded in the individual genomes into hierarchical orthologous groups reveals a high-resolution picture of functional evolution in this clade. It identifies groups of genes-many of which are involved in secondary metabolite production-that may account for the niche specificity of these bacteria. Photorhabdus and Xenorhabdus appear very similar at the DNA sequence level, which indicates their close evolutionary relationship. Yet, high-resolution mass spectrometry analyses reveal a huge chemical diversity in the two taxa. Molecular network reconstruction identified a large number of previously unidentified metabolite classes, including the xefoampeptides and tilivalline. Here, we apply genomic and metabolomic methods in a complementary manner to identify and elucidate additional classes of natural products. We also highlight the ability to rapidly and simultaneously identify potentially interesting bioactive products from NRPSs and PKSs, thereby augmenting the contribution of molecular biology techniques to the acceleration of natural product discovery.
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Affiliation(s)
- Nicholas J Tobias
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Hendrik Wolff
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Bardya Djahanschiri
- Department of Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Florian Grundmann
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Max Kronenwerth
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Yi-Ming Shi
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Svenja Simonyi
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Peter Grün
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - David Shapiro-Ilan
- USDA-ARS, SEA, SE Fruit and Tree Nut Research Unit, 21 Dunbar Road, Byron, GA, 31008, USA
| | - Sacha J Pidot
- Department of Microbiology and Immunology, University of Melbourne, at the Doherty Institute for Infection and Immunity, Parkville, Victoria, 3010, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, at the Doherty Institute for Infection and Immunity, Parkville, Victoria, 3010, Australia
| | - Ingo Ebersberger
- Department of Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany.,Senckenberg Climate and Research Centre (BIK-F), Frankfurt am Main, 60325, Germany
| | - Helge B Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany. .,Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany.
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28
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Yang YJ, Wang Y, Li ZF, Gong Y, Zhang P, Hu WC, Sheng DH, Li YZ. Increasing on-target cleavage efficiency for CRISPR/Cas9-induced large fragment deletion in Myxococcus xanthus. Microb Cell Fact 2017; 16:142. [PMID: 28814300 PMCID: PMC5559782 DOI: 10.1186/s12934-017-0758-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The CRISPR/Cas9 system is a powerful tool for genome editing, in which the sgRNA binds and guides the Cas9 protein for the sequence-specific cleavage. The protocol is employable in different organisms, but is often limited by cell damage due to the endonuclease activity of the introduced Cas9 and the potential off-target DNA cleavage from incorrect guide by the 20 nt spacer. RESULTS In this study, after resolving some critical limits, we have established an efficient CRISPR/Cas9 system for the deletion of large genome fragments related to the biosynthesis of secondary metabolites in Myxococcus xanthus cells. We revealed that the high expression of a codon-optimized cas9 gene in M. xanthus was cytotoxic, and developed a temporally high expression strategy to reduce the cell damage from high expressions of Cas9. We optimized the deletion protocol by using the tRNA-sgRNA-tRNA chimeric structure to ensure correct sgRNA sequence. We found that, in addition to the position-dependent nucleotide preference, the free energy of a 20 nt spacer was a key factor for the deletion efficiency. CONCLUSIONS By using the developed protocol, we achieved the CRISPR/Cas9-induced deletion of large biosynthetic gene clusters for secondary metabolites in M. xanthus DK1622 and its epothilone-producing mutant. The findings and the proposals described in this paper were suggested to be workable in other organisms, for example, other Gram negative bacteria with high GC content.
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Affiliation(s)
- Ying-jie Yang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Ye Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Zhi-feng Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Ya Gong
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Wen-chao Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Duo-hong Sheng
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
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29
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Bian X, Tang B, Yu Y, Tu Q, Gross F, Wang H, Li A, Fu J, Shen Y, Li YZ, Stewart AF, Zhao G, Ding X, Müller R, Zhang Y. Heterologous Production and Yield Improvement of Epothilones in Burkholderiales Strain DSM 7029. ACS Chem Biol 2017; 12:1805-1812. [PMID: 28467833 DOI: 10.1021/acschembio.7b00097] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cloning of microbial natural product biosynthetic gene clusters and their heterologous expression in a suitable host have proven to be a feasible approach to improve the yield of valuable natural products and to begin mining cryptic natural products in microorganisms. Myxobacteria are a prolific source of novel bioactive natural products with only limited choices of heterologous hosts that have been exploited. Here, we describe the use of Burkholderiales strain DSM 7029 as a potential heterologous host for the functional expression of myxobacterial secondary metabolites. Using a newly established electroporation procedure, the 56 kb epothilone biosynthetic gene cluster from the myxobacterium Sorangium cellulosum was introduced into the chromosome of strain DSM 7029 by transposition. Production of epothilones A, B, C, and D was detected despite their yields being low. Optimization of the medium, introduction of the exogenous methylmalonyl-CoA biosynthetic pathway, and overexpression of rare tRNA genes resulted in an approximately 75-fold increase in the total yields of epothilones to 307 μg L-1. These results show that strain DSM 7029 has the potential to produce epothilones with reasonable titers and might be a broadly applicable host for the heterologous expression of other myxobacterial polyketide synthases and nonribosomal peptide synthetases, expediting the process of genome mining.
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Affiliation(s)
- Xiaoying Bian
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany
| | - Biao Tang
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
| | - Yucong Yu
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
| | - Qiang Tu
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany
| | - Frank Gross
- Genomics,
Biotechnology Center, Technische Universität Dresden, Dresden 01062, Germany
| | - Hailong Wang
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - Aiying Li
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - Jun Fu
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
- Genomics,
Biotechnology Center, Technische Universität Dresden, Dresden 01062, Germany
| | - Yuemao Shen
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - Yue-zhong Li
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - A. Francis Stewart
- Genomics,
Biotechnology Center, Technische Universität Dresden, Dresden 01062, Germany
| | - Guoping Zhao
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
- CAS
Key Laboratory of Synthetic Biology, Institute of Plant Physiology
and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaoming Ding
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
| | - Rolf Müller
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany
| | - Youming Zhang
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
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Abstract
Covering: 2010 up to 2017Life on Earth is characterized by a remarkable abundance of symbiotic and highly refined relationships among life forms. Defined as any kind of close, long-term association between two organisms, symbioses can be mutualistic, commensalistic or parasitic. Historically speaking, selective pressures have shaped symbioses in which one organism (typically a bacterium or fungus) generates bioactive small molecules that impact the host (and possibly other symbionts); the symbiosis is driven fundamentally by the genetic machineries available to the small molecule producer. The human microbiome is now integral to the most recent chapter in animal-microbe symbiosis studies and plant-microbe symbioses have significantly advanced our understanding of natural products biosynthesis; this also is the case for studies of fungal-microbe symbioses. However, much less is known about microbe-microbe systems involving interspecies interactions. Microbe-derived small molecules (i.e. antibiotics and quorum sensing molecules, etc.) have been shown to regulate transcription in microbes within the same environmental niche, suggesting interspecies interactions whereas, intraspecies interactions, such as those that exploit autoinducing small molecules, also modulate gene expression based on environmental cues. We, and others, contend that symbioses provide almost unlimited opportunities for the discovery of new bioactive compounds whose activities and applications have been evolutionarily optimized. Particularly intriguing is the possibility that environmental effectors can guide laboratory expression of secondary metabolites from "orphan", or silent, biosynthetic gene clusters (BGCs). Notably, many of the studies summarized here result from advances in "omics" technologies and highlight how symbioses have given rise to new anti-bacterial and antifungal natural products now being discovered.
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Affiliation(s)
- Navid Adnani
- University of Wisconsin Madison, School of Pharmacy, Div. of Pharmaceutical Sciences, 777 Highland Ave., Madison, WI 53705-2222, USA.
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31
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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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32
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Haack FS, Poehlein A, Kröger C, Voigt CA, Piepenbring M, Bode HB, Daniel R, Schäfer W, Streit WR. Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearum. Front Microbiol 2016; 7:1668. [PMID: 27833590 PMCID: PMC5080296 DOI: 10.3389/fmicb.2016.01668] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/05/2016] [Indexed: 11/18/2022] Open
Abstract
Janthinobacterium and Duganella are well-known for their antifungal effects. Surprisingly, almost nothing is known on molecular aspects involved in the close bacterium-fungus interaction. To better understand this interaction, we established the genomes of 11 Janthinobacterium and Duganella isolates in combination with phylogenetic and functional analyses of all publicly available genomes. Thereby, we identified a core and pan genome of 1058 and 23,628 genes. All strains encoded secondary metabolite gene clusters and chitinases, both possibly involved in fungal growth suppression. All but one strain carried a single gene cluster involved in the biosynthesis of alpha-hydroxyketone-like autoinducer molecules, designated JAI-1. Genome-wide RNA-seq studies employing the background of two isolates and the corresponding JAI-1 deficient strains identified a set of 45 QS-regulated genes in both isolates. Most regulated genes are characterized by a conserved sequence motif within the promoter region. Among the most strongly regulated genes were secondary metabolite and type VI secretion system gene clusters. Most intriguing, co-incubation studies of J. sp. HH102 or its corresponding JAI-1 synthase deletion mutant with the plant pathogen Fusarium graminearum provided first evidence of a QS-dependent interaction with this pathogen.
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Affiliation(s)
- Frederike S Haack
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Goettingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany
| | - Cathrin Kröger
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Christian A Voigt
- Department of Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Meike Piepenbring
- Department of Mycology, Goethe University Frankfurt Frankfurt am Main, Germany
| | - Helge B Bode
- Merck-Stiftungsprofessur für Molekulare Biotechnologie Fachbereich Biowissenschaften and Buchmann Institute for Molecular Life Sciences, Goethe Universität Frankfurt Frankfurt am Main, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Goettingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany
| | - Wilhelm Schäfer
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
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33
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Kasai S, Konno S, Ishikawa F, Kakeya H. Functional profiling of adenylation domains in nonribosomal peptide synthetases by competitive activity-based protein profiling. Chem Commun (Camb) 2016; 51:15764-7. [PMID: 26365322 DOI: 10.1039/c5cc04953a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe competitive activity-based protein profiling (ABPP) to accelerate the functional prediction and assessment of adenylation (A) domains in nonribosomal peptide synthetases (NRPSs) in proteomic environments. Using a library of sulfamoyloxy-linked aminoacyl-AMP analogs, the competitive ABPP technique offers a simple and rapid assay system for adenylating enzymes and provides insight into enzyme substrate candidates and enzyme active-site architecture.
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Affiliation(s)
- Shota Kasai
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - Sho Konno
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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34
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Jensen PR. Natural Products and the Gene Cluster Revolution. Trends Microbiol 2016; 24:968-977. [PMID: 27491886 DOI: 10.1016/j.tim.2016.07.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/29/2016] [Accepted: 07/19/2016] [Indexed: 11/24/2022]
Abstract
Genome sequencing has created unprecedented opportunities for natural-product discovery and new insight into the diversity and distributions of natural-product biosynthetic gene clusters (BGCs). These gene collectives are highly evolved for horizontal exchange, thus providing immediate opportunities to test the effects of small molecules on fitness. The marine actinomycete genus Salinispora maintains extraordinary levels of BGC diversity and has become a useful model for studies of secondary metabolism. Most Salinispora BGCs are observed infrequently, resulting in high population-level diversity while conforming to constraints associated with maximum genome size. Comparative genomics is providing a mechanism to assess secondary metabolism in the context of evolution and evidence that some products represent ecotype-defining traits while others appear selectively neutral.
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Affiliation(s)
- Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Center for Microbiome Innovation, Scripps Institution of Oceanography, University of California San Diego, San Diego, California, USA.
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35
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Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol 2016. [PMID: 27084023 DOI: 10.1128/aem.01055-01016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
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Affiliation(s)
- Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Matthew B Crook
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Evangelia D Kouri
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | | | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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36
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Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol 2016; 82:3698-3710. [PMID: 27084023 PMCID: PMC4907175 DOI: 10.1128/aem.01055-16] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
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Affiliation(s)
- Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Matthew B Crook
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Evangelia D Kouri
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | | | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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37
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38
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Klapper M, Götze S, Barnett R, Willing K, Stallforth P. Bacterial Alkaloids Prevent Amoebal Predation. Angew Chem Int Ed Engl 2016; 55:8944-7. [PMID: 27294402 DOI: 10.1002/anie.201603312] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 01/20/2023]
Abstract
Bacterial defense mechanisms have evolved to protect bacteria against predation by nematodes, predatory bacteria, or amoebae. We identified novel bacterial alkaloids (pyreudiones A-D) that protect the producer, Pseudomonas fluorescens HKI0770, against amoebal predation. Isolation, structure elucidation, total synthesis, and a proposed biosynthetic pathway for these structures are presented. The generation of P. fluorescens gene-deletion mutants unable to produce pyreudiones rendered the bacterium edible to a variety of soil-dwelling amoebae.
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Affiliation(s)
- Martin Klapper
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Junior Research Group Chemistry of Microbial Communication, Jena, Germany
| | - Sebastian Götze
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Junior Research Group Chemistry of Microbial Communication, Jena, Germany
| | - Robert Barnett
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Junior Research Group Chemistry of Microbial Communication, Jena, Germany
| | - Karsten Willing
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Bio Pilot Plant, Jena, Germany
| | - Pierre Stallforth
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany. .,Junior Research Group Chemistry of Microbial Communication, Jena, Germany.
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Krauser S, Weyler C, Blaß LK, Heinzle E. Directed multistep biocatalysis using tailored permeabilized cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 137:185-234. [PMID: 23989897 DOI: 10.1007/10_2013_240] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
: Recent developments in the field of biocatalysis using permeabilized cells are reviewed here, with a special emphasis on the newly emerging area of multistep biocatalysis using permeabilized cells. New methods of metabolic engineering using in silico network design and new methods of genetic engineering provide the opportunity to design more complex biocatalysts for the synthesis of complex biomolecules. Methods for the permeabilization of cells are thoroughly reviewed. We provide an extended review of useful available databases and bioinformatics tools, particularly for setting up genome-scale reconstructed networks. Examples described include phosphorylated carbohydrates, sugar nucleotides, and polyketides.
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Affiliation(s)
- Steffen Krauser
- Biochemical Engineering Institute, Saarland University, 66123, Saarbrücken, Germany
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Korp J, Vela Gurovic MS, Nett M. Antibiotics from predatory bacteria. Beilstein J Org Chem 2016; 12:594-607. [PMID: 27340451 PMCID: PMC4902038 DOI: 10.3762/bjoc.12.58] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/11/2016] [Indexed: 11/23/2022] Open
Abstract
Bacteria, which prey on other microorganisms, are commonly found in the environment. While some of these organisms act as solitary hunters, others band together in large consortia before they attack their prey. Anecdotal reports suggest that bacteria practicing such a wolfpack strategy utilize antibiotics as predatory weapons. Consistent with this hypothesis, genome sequencing revealed that these micropredators possess impressive capacities for natural product biosynthesis. Here, we will present the results from recent chemical investigations of this bacterial group, compare the biosynthetic potential with that of non-predatory bacteria and discuss the link between predation and secondary metabolism.
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Affiliation(s)
- Juliane Korp
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - María S Vela Gurovic
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) -CONICET- Carrindanga Km 11, Bahía Blanca 8000, Argentina
| | - Markus Nett
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Beutenbergstr. 11, 07745 Jena, Germany
- Department of Biochemical and Chemical Engineering, Technical Biology, Technical University Dortmund, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
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41
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Karwehl S, Jansen R, Huch V, Stadler M. Sorazolons, Carbazole Alkaloids from Sorangium cellulosum Strain Soce375. JOURNAL OF NATURAL PRODUCTS 2016; 79:369-375. [PMID: 26866461 DOI: 10.1021/acs.jnatprod.5b00997] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Sorazolons A (1) to E2 (9) were isolated from Sorangium cellulosum strain Soce375. Their molecular structures were elucidated using extensive HRESIMS and NMR analysis. The absolute configuration of sorazolon A (1) was determined by comparison of the experimental CD spectrum with quantum chemical calculated spectra for both enantiomers. Sorazolons D2 (7), E (8), and E2 (9) exhibit a moderate cytotoxic activity against mouse fibroblast cell line L929 with IC50 values between 5.0 μM and 0.09 mM.
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Affiliation(s)
- Sabrina Karwehl
- Department of Microbial Drugs, Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , Braunschweig, Germany
| | - Rolf Jansen
- Department of Microbial Drugs, Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , Braunschweig, Germany
| | - Volker Huch
- Department of Inorganic Chemistry, Saarland University , Building C 4.1, 66123 Saarbrücken, Germany
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig , Braunschweig, Germany
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42
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Zhao X, van der Donk WA. Structural Characterization and Bioactivity Analysis of the Two-Component Lantibiotic Flv System from a Ruminant Bacterium. Cell Chem Biol 2016; 23:246-256. [PMID: 27028884 PMCID: PMC4814930 DOI: 10.1016/j.chembiol.2015.11.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/10/2015] [Accepted: 11/20/2015] [Indexed: 12/17/2022]
Abstract
The discovery of new ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) has greatly benefitted from the influx of genomic information. The lanthipeptides are a subset of this class of compounds. Adopting the genome-mining approach revealed a novel lanthipeptide gene cluster encoded in the genome of Ruminococcus flavefaciens FD-1, an anaerobic bacterium that is an important member of the rumen microbiota of livestock. The post-translationally modified peptides were produced via heterologous expression in Escherichia coli. Subsequent structural characterization and assessment of their bioactivity revealed features reminiscent of and distinct from previously reported lanthipeptides. The lanthipeptides of R. flavefaciens FD-1 represent a unique example within two-component lanthipeptides, consisting of a highly conserved α-peptide and a diverse set of eight β-peptides.
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Affiliation(s)
- Xiling Zhao
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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Identification of the Sfp-Type PPTase EppA from the Lichenized Fungus Evernia prunastri. PLoS One 2016; 11:e0145624. [PMID: 26784935 PMCID: PMC4718654 DOI: 10.1371/journal.pone.0145624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/07/2015] [Indexed: 01/12/2023] Open
Abstract
In the last decades, natural products from lichens have gained more interest for pharmaceutical application due to the broad range of their biological activity. However, isolation of the compounds of interest directly from the lichen is neither feasible nor sustainable due to slow growth of many lichens. In order to develop a pipeline for heterologous expression of lichen biosynthesis gene clusters and thus the sustainable production of their bioactive compounds we have identified and characterized the phosphopantheteinyl transferase (PPTase) EppA from the lichen Evernia prunastri. The Sfp-type PPTase EppA was functionally characterized through heterologous expression in E. coli using the production of the blue pigment indigoidine as readout and by complementation of a lys5 deletion in S. cerevisiae.
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Simonetti SO, Larghi EL, Kaufman TS. The 3,4-dioxygenated 5-hydroxy-4-aryl-quinolin-2(1H)-one alkaloids. Results of 20 years of research, uncovering a new family of natural products. Nat Prod Rep 2016; 33:1425-1446. [DOI: 10.1039/c6np00064a] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The title alkaloids are discussed. Emphasis is placed on their isolation, source microorganisms and structure, as well as relevant biological activities and synthetic progress.
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Affiliation(s)
- Sebastian O. Simonetti
- Instituto de Química Rosario (IQUIR, CONICET-UNR)
- Facultad de Ciencias Bioquímicas y Farmacéuticas – Universidad Nacional de Rosario
- (2000) Rosario
- Argentina
| | - Enrique L. Larghi
- Instituto de Química Rosario (IQUIR, CONICET-UNR)
- Facultad de Ciencias Bioquímicas y Farmacéuticas – Universidad Nacional de Rosario
- (2000) Rosario
- Argentina
| | - Teodoro S. Kaufman
- Instituto de Química Rosario (IQUIR, CONICET-UNR)
- Facultad de Ciencias Bioquímicas y Farmacéuticas – Universidad Nacional de Rosario
- (2000) Rosario
- Argentina
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45
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Bozhüyük KAJ, Zhou Q, Engel Y, Heinrich A, Pérez A, Bode HB. Natural Products from Photorhabdus and Other Entomopathogenic Bacteria. Curr Top Microbiol Immunol 2016; 402:55-79. [PMID: 28091935 DOI: 10.1007/82_2016_24] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although the first natural products (NP) from Photorhabdus and Xenorhabdus bacteria have been known now for almost 30 years, a huge variety of new compounds have been identified in the last 5-10 years, mainly due to the application of modern mass spectrometry. Additionally, application of molecular methods that allow the activation of NP production in several different strains as well as efficient heterologous expression methods have led to the production and validation of many new compounds. In this chapter we discuss the benefit of using Photorhabdus as a model system for microbial chemical ecology. We also examine non-ribosomal peptide synthetases as the most important pathway for NP production. Finally, we discuss the origin and function of all currently known NPs and the development of the molecular and chemical tools used to identify these NPs faster.
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Affiliation(s)
- Kenan A J Bozhüyük
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Qiuqin Zhou
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Yvonne Engel
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Antje Heinrich
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Alexander Pérez
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Endowed Chair for Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
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46
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Tao W, Yurkovich ME, Wen S, Lebe KE, Samborskyy M, Liu Y, Yang A, Liu Y, Ju Y, Deng Z, Tosin M, Sun Y, Leadlay PF. A genomics-led approach to deciphering the mechanism of thiotetronate antibiotic biosynthesis. Chem Sci 2016; 7:376-385. [PMID: 28791099 PMCID: PMC5518548 DOI: 10.1039/c5sc03059e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/06/2015] [Indexed: 12/31/2022] Open
Abstract
Thiolactomycin (TLM) is a thiotetronate antibiotic that selectively targets bacterial fatty acid biosynthesis through inhibition of the β-ketoacyl-acyl carrier protein synthases (KASI/II) that catalyse chain elongation on the type II (dissociated) fatty acid synthase. It has proved effective in in vivo infection models of Mycobacterium tuberculosis and continues to attract interest as a template for drug discovery. We have used a comparative genomics approach to uncover the (hitherto elusive) biosynthetic pathway to TLM and related thiotetronates. Analysis of the whole-genome sequence of Streptomyces olivaceus Tü 3010 producing the more ramified thiotetronate Tü 3010 provided initial evidence that such thiotetronates are assembled by a novel iterative polyketide synthase-nonribosomal peptide synthetase, and revealed the identity of other pathway enzymes, encoded by adjacent genes. Subsequent genome sequencing of three other thiotetronate-producing actinomycetes, including the Lentzea sp. ATCC 31319 that produces TLM, confirmed that near-identical clusters were also present in these genomes. In-frame gene deletion within the cluster for Tü 3010 from Streptomyces thiolactonus NRRL 15439, or within the TLM cluster, led to loss of production of the respective thiotetronate, confirming their identity. Each cluster houses at least one gene encoding a KASI/II enzyme, suggesting plausible mechanisms for self-resistance. A separate genetic locus encodes a cysteine desulfurase and a (thiouridylase-like) sulfur transferase to supply the sulfur atom for thiotetronate ring formation. Transfer of the main Tü 3010 gene cluster (stu gene cluster) into Streptomyces avermitilis led to heterologous production of this thiotetronate, showing that an equivalent sulfur donor can be supplied by this host strain. Mutational analysis of the Tü 3010 and TLM clusters has revealed the unexpected role of a cytochrome P450 enzyme in thiotetronate ring formation. These insights have allowed us to propose a mechanism for sulfur insertion, and have opened the way to engineering of the biosynthesis of TLM and other thiotetronates to produce novel analogues.
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Affiliation(s)
- W Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - M E Yurkovich
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
| | - S Wen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - K E Lebe
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
| | - M Samborskyy
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
| | - Y Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - A Yang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - Y Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - Y Ju
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - Z Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - M Tosin
- Department of Chemistry , University of Warwick , Library Road , Coventry CV4 7AL , UK
| | - Y Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - P F Leadlay
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
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Abstract
UNLABELLED The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system, an RNA-guided nuclease for specific genome editing in vivo, has been adopted in a wide variety of organisms. In contrast, the in vitro application of the CRISPR/Cas9 system has rarely been reported. We present here a highly efficient in vitro CRISPR/Cas9-mediated editing (ICE) system that allows specific refactoring of biosynthetic gene clusters in Streptomyces bacteria and other large DNA fragments. Cleavage by Cas9 of circular pUC18 DNA was investigated here as a simple model, revealing that the 3'→5' exonuclease activity of Cas9 generates errors with 5 to 14 nucleotides (nt) randomly missing at the editing joint. T4 DNA polymerase was then used to repair the Cas9-generated sticky ends, giving substantial improvement in editing accuracy. Plasmid pYH285 and cosmid 10A3, harboring a complete biosynthetic gene cluster for the antibiotics RK-682 and holomycin, respectively, were subjected to the ICE system to delete the rkD and homE genes in frame. Specific insertion of the ampicillin resistance gene (bla) into pYH285 was also successfully performed. These results reveal the ICE system to be a rapid, seamless, and highly efficient way to edit DNA fragments, and a powerful new tool for investigating and engineering biosynthetic gene clusters. IMPORTANCE Recent improvements in cloning strategies for biosynthetic gene clusters promise rapid advances in understanding and exploiting natural products in the environment. For manipulation of such biosynthetic gene clusters to generate valuable bioactive compounds, efficient and specific gene editing of these large DNA fragments is required. In this study, a highly efficient in vitro DNA editing system has been established. When combined with end repair using T4 DNA polymerase, Cas9 precisely and seamlessly catalyzes targeted editing, including in-frame deletion or insertion of the gene(s) of interest. This in vitro CRISPR editing (ICE) system promises a step forward in our ability to engineer biosynthetic pathways.
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Ishikawa F, Suzuki T, Dohmae N, Kakeya H. A Multiple-Labeling Strategy for Nonribosomal Peptide Synthetases Using Active-Site-Directed Proteomic Probes for Adenylation Domains. Chembiochem 2015; 16:2590-4. [PMID: 26467472 DOI: 10.1002/cbic.201500481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/07/2022]
Abstract
Genetic approaches have greatly contributed to our understanding of nonribosomal peptide biosynthetic machinery; however, proteomic investigations are limited. Here, we developed a highly sensitive detection strategy for multidomain nonribosomal peptide synthetases (NRPSs) by using a multiple-labeling technique with active-site-directed probes for adenylation domains. When applied to gramicidin S-producing and -nonproducing strains of Aneurinibacillus migulanus (DSM 5759 and DSM 2895, respectively), the multiple technique sensitively detected an active multidomain NRPS (GrsB) in lysates obtained from the organisms. This functional proteomics method revealed an unknown inactive precursor (or other inactive form) of GrsB in the nonproducing strain. This method provides a new option for the direct detection, functional analysis, and high-resolution identification of low-abundance active NRPS enzymes in native proteomic environments.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes. Proc Natl Acad Sci U S A 2015; 112:12175-80. [PMID: 26324907 DOI: 10.1073/pnas.1500873112] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although natural products have been a particularly rich source of human medicines, activity-based screening results in a very high rate of rediscovery of known molecules. Based on the large number of natural product biosynthetic genes in microbial genomes, many have proposed "genome mining" as an alternative approach for discovery efforts; however, this idea has yet to be performed experimentally on a large scale. Here, we demonstrate the feasibility of large-scale, high-throughput genome mining by screening a collection of over 10,000 actinomycetes for the genetic potential to make phosphonic acids, a class of natural products with diverse and useful bioactivities. Genome sequencing identified a diverse collection of phosphonate biosynthetic gene clusters within 278 strains. These clusters were classified into 64 distinct groups, of which 55 are likely to direct the synthesis of unknown compounds. Characterization of strains within five of these groups resulted in the discovery of a new archetypical pathway for phosphonate biosynthesis, the first (to our knowledge) dedicated pathway for H-phosphinates, and 11 previously undescribed phosphonic acid natural products. Among these compounds are argolaphos, a broad-spectrum antibacterial phosphonopeptide composed of aminomethylphosphonate in peptide linkage to a rare amino acid N(5)-hydroxyarginine; valinophos, an N-acetyl l-Val ester of 2,3-dihydroxypropylphosphonate; and phosphonocystoximate, an unusual thiohydroximate-containing molecule representing a new chemotype of sulfur-containing phosphonate natural products. Analysis of the genome sequences from the remaining strains suggests that the majority of the phosphonate biosynthetic repertoire of Actinobacteria has been captured at the gene level. This dereplicated strain collection now provides a reservoir of numerous, as yet undiscovered, phosphonate natural products.
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Identification of benzo[a]pyrene-metabolizing bacteria in forest soils by using DNA-based stable-isotope probing. Appl Environ Microbiol 2015; 81:7368-76. [PMID: 26253666 DOI: 10.1128/aem.01983-15] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/02/2015] [Indexed: 01/21/2023] Open
Abstract
DNA-based stable-isotope probing (DNA-SIP) was used in this study to investigate the uncultivated bacteria with benzo[a]pyrene (BaP) metabolism capacities in two Chinese forest soils (Mt. Maoer in Heilongjiang Province and Mt. Baicaowa in Hubei Province). We characterized three different phylotypes with responsibility for BaP degradation, none of which were previously reported as BaP-degrading microorganisms by SIP. In Mt. Maoer soil microcosms, the putative BaP degraders were classified as belonging to the genus Terrimonas (family Chitinophagaceae, order Sphingobacteriales), whereas Burkholderia spp. were the key BaP degraders in Mt. Baicaowa soils. The addition of metabolic salicylate significantly increased BaP degradation efficiency in Mt. Maoer soils, and the BaP-metabolizing bacteria shifted to the microorganisms in the family Oxalobacteraceae (genus unclassified). Meanwhile, salicylate addition did not change either BaP degradation or putative BaP degraders in Mt. Baicaowa. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD) genes were amplified, sequenced, and quantified in the DNA-SIP (13)C heavy fraction to further confirm the BaP metabolism. By illuminating the microbial diversity and salicylate additive effects on BaP degradation across different soils, the results increased our understanding of BaP natural attenuation and provided a possible approach to enhance the bioremediation of BaP-contaminated soils.
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