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Zhu B, Cen Z, Chen Y, Shang K, Zhai J, Han M, Wang J, Chen Z, Wei T, Han Z. α-Pyrone mediates quorum sensing through the conservon system in Nocardiopsis sp. Microbiol Res 2024; 285:127767. [PMID: 38776619 DOI: 10.1016/j.micres.2024.127767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Actinobacteria produce a plethora of bioactive secondary metabolites that are often regulated by quorum-sensing signaling molecules via specific binding to their cognate TetR-type receptors. Here, we identified monocyclic α-pyrone as a new class of actinobacterial signaling molecules influencing quorum sensing process in Nocardiopsis sp. LDBS0036, primarily evidenced by a significant reduction in the production of phenazines in the pyrone-null mutant compared to the wild-type strain. Exogenous addition of the α-pyrone can partially restore the expression of some pathways to the wild strain level. Moreover, a unique multicomponent system referred to as a conservon, which is widespread in actinobacteria and generally contains four or five functionally conserved proteins, may play an important role in detecting and transmitting α-pyrone signals in LDBS0036. We found the biosynthetic gene clusters of α-pyrone and their associated conservon genes are highly conserved in Nocardiopsis, indicating the widespread prevalence and significant function of this regulate mechanism within Nocardiopsis genus. Furthermore, homologous α-pyrones from different actinobacterial species were also found to mediate interspecies communication. Our results thus provide insights into a novel quorum-sensing signaling system and imply that various modes of bacterial communication remain undiscovered.
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Affiliation(s)
- Boyu Zhu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziyun Cen
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiqiu Chen
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China; Hainan University, Haikou, Hainan 570100, China
| | - Kun Shang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - Ji'an Zhai
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meigui Han
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawei Wang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China; Hainan University, Haikou, Hainan 570100, China
| | - Zhiyong Chen
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - Taoshu Wei
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuang Han
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China.
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2
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Asmaey MA. Unravelling the Secrets of α-Pyrones from Aspergillus Fungi: A Comprehensive Review of Their Natural Sources, Biosynthesis, and Biological Activities. Chem Biodivers 2023; 20:e202301185. [PMID: 37823671 DOI: 10.1002/cbdv.202301185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
Aspergillus, one of the most product-rich and genetically robust genera, contains a diverse range of species with potential economic and ecological implications. Chemically, Aspergillus is one of the essential sources of polyketides, alkaloids, diphenyl ethers, diketopiperazines, and other miscellaneous compounds, displaying a variety of pharmacological activities. The α-pyrones are unsaturated six-membered lactones. Although α-pyrone has a small structure, it is responsible for the structural diversity of several natural and synthetic compounds and multiple biological activities. In this review, we have summarized approximately 178 α-pyrone containing metabolites derivatives identified/reported from terrestrial, marine, endophytic, and filamentous Aspergillus species, including their sources, biological properties, and biosynthetic pathways until mid-2023, for the first time. This review is the first to compile and analyze the available data on α-pyrone metabolites from Aspergillus, which could facilitate further research and innovation in this field. Additionally, it offers a valuable source of scaffolds for future bioactive drug development, as some of these metabolites have shown potent antimicrobial, anti-inflammatory, and anticancer effects. Therefore, this review has significant implications for the advancement of natural product chemistry, pharmacology, biotechnology, and medicine.
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Affiliation(s)
- Mostafa A Asmaey
- Department of Chemistry, Faculty of Science, Al-Azhar University, Assiut Branch, Assiut, 71524, Egypt
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3
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Zhan C, Lee N, Lan G, Dan Q, Cowan A, Wang Z, Baidoo EEK, Kakumanu R, Luckie B, Kuo RC, McCauley J, Liu Y, Valencia L, Haushalter RW, Keasling JD. Improved polyketide production in C. glutamicum by preventing propionate-induced growth inhibition. Nat Metab 2023; 5:1127-1140. [PMID: 37443355 DOI: 10.1038/s42255-023-00830-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/25/2023] [Indexed: 07/15/2023]
Abstract
Corynebacterium glutamicum is a promising host for production of valuable polyketides. Propionate addition, a strategy known to increase polyketide production by increasing intracellular methylmalonyl-CoA availability, causes growth inhibition in C. glutamicum. The mechanism of this inhibition was unclear before our work. Here we provide evidence that accumulation of propionyl-CoA and methylmalonyl-CoA induces growth inhibition in C. glutamicum. We then show that growth inhibition can be relieved by introducing methylmalonyl-CoA-dependent polyketide synthases. With germicidin as an example, we used adaptive laboratory evolution to leverage the fitness advantage of polyketide production in the presence of propionate to evolve improved germicidin production. Whole-genome sequencing revealed mutations in germicidin synthase, which improved germicidin titer, as well as mutations in citrate synthase, which effectively evolved the native glyoxylate pathway to a new methylcitrate pathway. Together, our results show that C. glutamicum is a capable host for polyketide production and we can take advantage of propionate growth inhibition to drive titers higher using laboratory evolution or to screen for production of polyketides.
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Affiliation(s)
- Chunjun Zhan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
| | - Namil Lee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
| | - Guangxu Lan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Qingyun Dan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Aidan Cowan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Zilong Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bridget Luckie
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rita C Kuo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joshua McCauley
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Luis Valencia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Robert W Haushalter
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA.
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark.
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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4
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Lacey HJ, Chen R, Vuong D, Lacey E, Rutledge PJ, Chooi YH, Piggott AM, Booth TJ. Resorculins: hybrid polyketide macrolides from Streptomyces sp. MST-91080. Org Biomol Chem 2023; 21:2531-2538. [PMID: 36876905 DOI: 10.1039/d2ob02332f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Fourteen-membered macrolides are a class of compounds with significant clinical value as antibacterial agents. As part of our ongoing investigation into the metabolites of Streptomyces sp. MST-91080, we report the discovery of resorculins A and B, unprecedented 3,5-dihydroxybenzoic acid (α-resorcylic acid)-containing 14-membered macrolides. We sequenced the genome of MST-91080 and identified the putative resorculin biosynthetic gene cluster (rsn BGC). The rsn BGC is hybrid of type I and type III polyketide synthases. Bioinformatic analysis revealed that the resorculins are relatives of known hybrid polyketides: kendomycin and venemycin. Resorculin A exhibited antibacterial activity against Bacillus subtilis (MIC 19.8 μg mL-1), while resorculin B showed cytotoxic activity against the NS-1 mouse myeloma cell line (IC50 3.6 μg mL-1).
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Affiliation(s)
- Heather J Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Rachel Chen
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- School of Natural Sciences, Macquarie University, NSW 2109, Australia
| | - Peter J Rutledge
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, NSW 2109, Australia
| | - Thomas J Booth
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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5
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Deflandre B, Stulanovic N, Planckaert S, Anderssen S, Bonometti B, Karim L, Coppieters W, Devreese B, Rigali S. The virulome of Streptomyces scabiei in response to cello-oligosaccharide elicitors. Microb Genom 2022; 8. [PMID: 35040428 PMCID: PMC8914351 DOI: 10.1099/mgen.0.000760] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The development of spots or lesions symptomatic of common scab on root and tuber crops is caused by few pathogenic Streptomyces with Streptomyces scabiei 87–22 as the model species. Thaxtomin phytotoxins are the primary virulence determinants, mainly acting by impairing cellulose synthesis, and their production in S. scabiei is in turn boosted by cello-oligosaccharides released from host plants. In this work we aimed to determine which molecules and which biosynthetic gene clusters (BGCs) of the specialized metabolism of S. scabiei 87–22 show a production and/or a transcriptional response to cello-oligosaccharides. Comparative metabolomic analyses revealed that molecules of the virulome of S. scabiei induced by cellobiose and cellotriose include (i) thaxtomin and concanamycin phytotoxins, (ii) desferrioxamines, scabichelin and turgichelin siderophores in order to acquire iron essential for housekeeping functions, (iii) ectoine for protection against osmotic shock once inside the host, and (iv) bottromycin and concanamycin antimicrobials possibly to prevent other microorganisms from colonizing the same niche. Importantly, both cello-oligosaccharides reduced the production of the spore germination inhibitors germicidins thereby giving the ‘green light’ to escape dormancy and trigger the onset of the pathogenic lifestyle. For most metabolites - either with induced or reduced production - cellotriose was revealed to be a slightly stronger elicitor compared to cellobiose, supporting an earlier hypothesis which suggested the trisaccharide was the real trigger for virulence released from the plant cell wall through the action of thaxtomins. Interestingly, except for thaxtomins, none of these BGCs’ expression seems to be under direct control of the cellulose utilization repressor CebR suggesting the existence of a yet unknown mechanism for switching on the virulome. Finally, a transcriptomic analysis revealed nine additional cryptic BGCs that have their expression awakened by cello-oligosaccharides, suggesting that other and yet to be discovered metabolites could be part of the virulome of S. scabiei.
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Affiliation(s)
- Benoit Deflandre
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Nudzejma Stulanovic
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Sören Planckaert
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Sinaeda Anderssen
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Beatrice Bonometti
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Latifa Karim
- Genomics Platform, GIGA, University of Liège, B-4000, Liège, Belgium
| | - Wouter Coppieters
- Genomics Platform, GIGA, University of Liège, B-4000, Liège, Belgium
| | - Bart Devreese
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Sébastien Rigali
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
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6
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Larsen JS, Pearson LA, Neilan BA. Genome Mining and Evolutionary Analysis Reveal Diverse Type III Polyketide Synthase Pathways in Cyanobacteria. Genome Biol Evol 2021; 13:6178795. [PMID: 33739400 PMCID: PMC8086630 DOI: 10.1093/gbe/evab056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2021] [Indexed: 11/30/2022] Open
Abstract
Cyanobacteria are prolific producers of natural products, including polyketides and hybrid compounds thereof. Type III polyketide synthases (PKSs) are of particular interest, due to their wide substrate specificity and simple reaction mechanism, compared with both type I and type II PKSs. Surprisingly, only two type III PKS products, hierridins, and (7.7)paracyclophanes, have been isolated from cyanobacteria. Here, we report the mining of 517 cyanobacterial genomes for type III PKS biosynthesis gene clusters. Approximately 17% of the genomes analyzed encoded one or more type III PKSs. Together with already characterized type III PKSs, the phylogeny of this group of enzymes was investigated. Our analysis showed that type III PKSs in cyanobacteria evolved into three major lineages, including enzymes associated with 1) (7.7)paracyclophane-like biosynthesis gene clusters, 2) hierridin-like biosynthesis gene clusters, and 3) cytochrome b5 genes. The evolutionary history of these enzymes is complex, with some sequences partitioning primarily according to speciation and others putatively according to their reaction type. Protein modeling showed that cyanobacterial type III PKSs generally have a smaller active site cavity (mean = 109.035 Å3) compared with enzymes from other organisms. The size of the active site did not correlate well with substrate size, however, the “Gatekeeper” amino acid residues within the active site were strongly correlated to enzyme phylogeny. Our study provides unprecedented insight into the distribution, diversity, and molecular evolution of cyanobacterial type III PKSs, which could facilitate the discovery, characterization, and exploitation of novel enzymes, biochemical pathways, and specialized metabolites from this biosynthetically talented clade of microorganisms.
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Affiliation(s)
- Joachim Steen Larsen
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, New South Wales, Australia
| | - Leanne Andrea Pearson
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, New South Wales, Australia
| | - Brett Anthony Neilan
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, New South Wales, Australia
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7
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Shi H, Li Y, Zhu J, Wang H, Shen Y. Discovery of Germicidin Glucuronides from Streptomyces sp. LZ35. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202101036] [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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8
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Sulheim S, Kumelj T, van Dissel D, Salehzadeh-Yazdi A, Du C, van Wezel GP, Nieselt K, Almaas E, Wentzel A, Kerkhoven EJ. Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. iScience 2020; 23:101525. [PMID: 32942174 PMCID: PMC7501462 DOI: 10.1016/j.isci.2020.101525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/19/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Many biosynthetic gene clusters (BGCs) require heterologous expression to realize their genetic potential, including silent and metagenomic BGCs. Although the engineered Streptomyces coelicolor M1152 is a widely used host for heterologous expression of BGCs, a systemic understanding of how its genetic modifications affect the metabolism is lacking and limiting further development. We performed a comparative analysis of M1152 and its ancestor M145, connecting information from proteomics, transcriptomics, and cultivation data into a comprehensive picture of the metabolic differences between these strains. Instrumental to this comparison was the application of an improved consensus genome-scale metabolic model (GEM) of S. coelicolor. Although many metabolic patterns are retained in M1152, we find that this strain suffers from oxidative stress, possibly caused by increased oxidative metabolism. Furthermore, precursor availability is likely not limiting polyketide production, implying that other strategies could be beneficial for further development of S. coelicolor for heterologous production of novel compounds.
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Affiliation(s)
- Snorre Sulheim
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7034 Trondheim, Norway
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Tjaša Kumelj
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Dino van Dissel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7034 Trondheim, Norway
| | - Ali Salehzadeh-Yazdi
- Department of Systems Biology and Bioinformatics, Faculty of Computer Science and Electrical Engineering, University of Rostock, 18057 Rostock, Germany
| | - Chao Du
- Microbial Biotechnology, Institute of Biology, Leiden University, 2300 Leiden, the Netherlands
| | - Gilles P. van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, 2300 Leiden, the Netherlands
| | - Kay Nieselt
- Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, 72070 Tübingen, Germany
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and General Practice, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7034 Trondheim, Norway
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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9
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Millan-Oropeza A, Henry C, Lejeune C, David M, Virolle MJ. Expression of genes of the Pho regulon is altered in Streptomyces coelicolor. Sci Rep 2020; 10:8492. [PMID: 32444655 PMCID: PMC7244524 DOI: 10.1038/s41598-020-65087-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/24/2020] [Indexed: 12/30/2022] Open
Abstract
Most currently used antibiotics originate from Streptomycetes and phosphate limitation is an important trigger of their biosynthesis. Understanding the molecular processes underpinning such regulation is of crucial importance to exploit the great metabolic diversity of these bacteria and get a better understanding of the role of these molecules in the physiology of the producing bacteria. To contribute to this field, a comparative proteomic analysis of two closely related model strains, Streptomyces lividans and Streptomyces coelicolor was carried out. These strains possess identical biosynthetic pathways directing the synthesis of three well-characterized antibiotics (CDA, RED and ACT) but only S. coelicolor expresses them at a high level. Previous studies established that the antibiotic producer, S. coelicolor, is characterized by an oxidative metabolism and a reduced triacylglycerol content compared to the none producer, S. lividans, characterized by a glycolytic metabolism. Our proteomic data support these findings and reveal that these drastically different metabolic features could, at least in part, due to the weaker abundance of proteins of the two component system PhoR/PhoP in S. coelicolor compared to S. lividans. In condition of phosphate limitation, PhoR/PhoP is known to control positively and negatively, respectively, phosphate and nitrogen assimilation and our study revealed that it might also control the expression of some genes of central carbon metabolism. The tuning down of the regulatory role of PhoR/PhoP in S. coelicolor is thus expected to be correlated with low and high phosphate and nitrogen availability, respectively and with changes in central carbon metabolic features. These changes are likely to be responsible for the observed differences between S. coelicolor and S. lividans concerning energetic metabolism, triacylglycerol biosynthesis and antibiotic production. Furthermore, a novel view of the contribution of the bio-active molecules produced in this context, to the regulation of the energetic metabolism of the producing bacteria, is proposed and discussed.
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Affiliation(s)
- Aaron Millan-Oropeza
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Céline Henry
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clara Lejeune
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Michelle David
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Marie-Joelle Virolle
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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10
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Nakamura T, Supratman U, Harneti D, Maharani R, Koseki T, Shiono Y. New compounds from Japanese oak wilt disease-associated fungus Raffaelea quercivora. Nat Prod Res 2020; 35:5304-5310. [PMID: 32290697 DOI: 10.1080/14786419.2020.1753054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Two new compounds, a new lactone, quercilactone A (1), and (17R)-hydroxynafuredin (5), as well as five known compounds, scytalone (2), 3S,4R-hydoxy-scytalone (3), nafuredin (4), (+)-(3R,5R)-3-hydroxy-5-decanolide (6) and 3-ethyl-4-hydroxy-6-methyl-2H-pyran-2-one (7), were isolated from Raffaelea quercivora, a fungus that causes Japanese oak wilt disease. The structures of these compounds were determined by 1D and 2D NMR spectroscopic analyses. The absolute configuration at C-17 of 5 was determined to be R by the modified Mosher's method. Compounds 1, 2, and 7 exhibited weak phytotoxic activity in lettuce seedlings at a concentration of 100 μg mL-1.
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Affiliation(s)
- Tomoki Nakamura
- Department of Food, Life, and Environmental Science, Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
| | - Unang Supratman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Desi Harneti
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Rani Maharani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Takuya Koseki
- Department of Food, Life, and Environmental Science, Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
| | - Yoshihito Shiono
- Department of Food, Life, and Environmental Science, Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
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11
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Stroe MC, Netzker T, Scherlach K, Krüger T, Hertweck C, Valiante V, Brakhage AA. Targeted induction of a silent fungal gene cluster encoding the bacteria-specific germination inhibitor fumigermin. eLife 2020; 9:52541. [PMID: 32083553 PMCID: PMC7034978 DOI: 10.7554/elife.52541] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/09/2020] [Indexed: 12/29/2022] Open
Abstract
Microorganisms produce numerous secondary metabolites (SMs) with various biological activities. Many of their encoding gene clusters are silent under standard laboratory conditions because for their activation they need the ecological context, such as the presence of other microorganisms. The true ecological function of most SMs remains obscure, but understanding of both the activation of silent gene clusters and the ecological function of the produced compounds is of importance to reveal functional interactions in microbiomes. Here, we report the identification of an as-yet uncharacterized silent gene cluster of the fungus Aspergillus fumigatus, which is activated by the bacterium Streptomyces rapamycinicus during the bacterial-fungal interaction. The resulting natural product is the novel fungal metabolite fumigermin, the biosynthesis of which requires the polyketide synthase FgnA. Fumigermin inhibits germination of spores of the inducing S. rapamycinicus, and thus helps the fungus to defend resources in the shared habitat against a bacterial competitor.
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Affiliation(s)
- Maria Cristina Stroe
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | | | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Christian Hertweck
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Department of Biomolecular Chemistry, HKI, Jena, Germany
| | - Vito Valiante
- Leibniz Research Group - Biobricks of Microbial Natural Product Syntheses, HKI, Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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12
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Transcriptional heterologous expression of two type III PKS from the lichen Cladonia uncialis. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01539-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Wiker F, Konnerth M, Helmle I, Kulik A, Kaysser L, Gross H, Gust B. Identification of Novel α-Pyrones from Conexibacter woesei Serving as Sulfate Shuttles. ACS Chem Biol 2019; 14:1972-1980. [PMID: 31419109 DOI: 10.1021/acschembio.9b00455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pyrones comprise a structurally diverse class of compounds. Although they are widespread in nature, their specific physiological functions remain unknown in most cases. We recently described that triketide pyrones mediate the sulfotransfer in caprazamycin biosynthesis. Herein, we report the identification of conexipyrones A-C, three previously unrecognized tetra-substituted α-pyrones, from the soil actinobacterium Conexibacter woesei. Insights into their biosynthesis via a type III polyketide synthase were obtained by feeding studies using isotope-enriched precursors. In vitro assays employing the genetically associated 3'-phosphoadenosine-5'-phosphosulfate (PAPS)-dependent sulfotransferase CwoeST revealed conexipyrones as the enzymes' genuine sulfate acceptor substrates. Furthermore, conexipyrones were determined to function as sulfate shuttles in a two-enzyme assay, because their sulfated derivatives were accepted as donor molecules by the PAPS-independent arylsulfate sulfotransferase (ASST) Cpz4 to yield sulfated caprazamycin intermediates.
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Affiliation(s)
- Franziska Wiker
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Martin Konnerth
- Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Irina Helmle
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andreas Kulik
- Institute of Microbiology and Infection Medicine, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Leonard Kaysser
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Bertolt Gust
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
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14
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Biosynthesis of Polyketides in Streptomyces. Microorganisms 2019; 7:microorganisms7050124. [PMID: 31064143 PMCID: PMC6560455 DOI: 10.3390/microorganisms7050124] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/24/2019] [Accepted: 04/27/2019] [Indexed: 12/12/2022] Open
Abstract
Polyketides are a large group of secondary metabolites that have notable variety in their structure and function. Polyketides exhibit a wide range of bioactivities such as antibacterial, antifungal, anticancer, antiviral, immune-suppressing, anti-cholesterol, and anti-inflammatory activity. Naturally, they are found in bacteria, fungi, plants, protists, insects, mollusks, and sponges. Streptomyces is a genus of Gram-positive bacteria that has a filamentous form like fungi. This genus is best known as one of the polyketides producers. Some examples of polyketides produced by Streptomyces are rapamycin, oleandomycin, actinorhodin, daunorubicin, and caprazamycin. Biosynthesis of polyketides involves a group of enzyme activities called polyketide synthases (PKSs). There are three types of PKSs (type I, type II, and type III) in Streptomyces responsible for producing polyketides. This paper focuses on the biosynthesis of polyketides in Streptomyces with three structurally-different types of PKSs.
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15
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Secondary Metabolites of Endophytic Actinomycetes: Isolation, Synthesis, Biosynthesis, and Biological Activities. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 108 2019; 108:207-296. [DOI: 10.1007/978-3-030-01099-7_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Genome mining reveals uncommon alkylpyrones as type III PKS products from myxobacteria. J Ind Microbiol Biotechnol 2018; 46:319-334. [PMID: 30506464 DOI: 10.1007/s10295-018-2105-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022]
Abstract
Type III polyketide synthases (PKSs) are comparatively small homodimeric enzymes affording natural products with diverse structures and functions. While type III PKS biosynthetic pathways have been studied thoroughly in plants, their counterparts from bacteria and fungi are to date scarcely characterized. This gap is exemplified by myxobacteria from which no type III PKS-derived small molecule has previously been isolated. In this study, we conducted a genomic survey of myxobacterial type III PKSs and report the identification of uncommon alkylpyrones as the products of type III PKS biosynthesis from the myxobacterial model strain Myxococcus xanthus DK1622 through a self-resistance-guided screening approach focusing on genes encoding pentapetide repeat proteins, proficient to confer resistance to topoisomerase inhibitors. Using promoter-induced gene expression in the native host as well as heterologous expression of biosynthetic type III PKS genes, sufficient amounts of material could be obtained for structural elucidation and bioactivity testing, revealing potent topoisomerase activity in vitro.
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17
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Lim Y, Jung ES, Lee JH, Kim EJ, Hong SJ, Lee YH, Lee CH. Non-targeted metabolomics unravels a media-dependent prodiginines production pathway in Streptomyces coelicolor A3(2). PLoS One 2018; 13:e0207541. [PMID: 30485320 PMCID: PMC6261592 DOI: 10.1371/journal.pone.0207541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/01/2018] [Indexed: 12/27/2022] Open
Abstract
The genus Streptomyces is the best-known source of therapeutic secondary metabolites, especially antibiotics with pharmaceutical applications. Here, we performed a comparative study based on the time-resolved metabolic disparity in S. coelicolor A3(2) subjected to fermentative cultivation in two different types of media (R2YE and RSM3) in order to investigate secondary metabolite production pathways. The relative abundance of secondary metabolites, such as prodiginines, indoles, germicidins, and selected diketopiperazines, was increased in S. coelicolor A3(2) cultivated in R2YE medium compared to that in RSM3 medium, variably at the late-log and stationary phases of fermentative growth. Correlation analysis indicated that “antibiotic prodiginines” contributed maximally to the absorption maxima (A530) of culture supernatants, indicating their optimal production at 96 hours in R2YE medium. A higher abundance of L-proline (48–72 hours) followed by prodiginines (96 hours) was evident, substantiating the intertwined links between precursor and activated prodiginines pathway. Similarly, the higher abundance of indoles was concurrent with tryptophan levels in the shikimate pathway, whereas diketopiperazines were synchronously abundant along with the levels of phenylalanine, leucine, and proline. Additionally, acetyl-CoA induced the acetate pathway, resulting in the production of germicidins. Thus, our results demonstrate that S. coelicolor A3(2) produces specific secondary metabolites by enhancing the dedicated metabolic pathway responsible for their production. In conclusion, our results from this study provide insight into the metabolic pathways of S. coelicolor A3(2), and can be applied to further optimize the production of prodiginines.
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Affiliation(s)
- Yonghwan Lim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | - Eun Sung Jung
- Department of Systems Biotechnology, Konkuk University, Seoul, Korea
| | | | | | | | | | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
- Department of Systems Biotechnology, Konkuk University, Seoul, Korea
- * E-mail:
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18
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Becerril A, Álvarez S, Braña AF, Rico S, Díaz M, Santamaría RI, Salas JA, Méndez C. Uncovering production of specialized metabolites by Streptomyces argillaceus: Activation of cryptic biosynthesis gene clusters using nutritional and genetic approaches. PLoS One 2018; 13:e0198145. [PMID: 29795673 PMCID: PMC5993118 DOI: 10.1371/journal.pone.0198145] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/14/2018] [Indexed: 11/22/2022] Open
Abstract
Sequencing of Streptomyces genomes has revealed they harbor a high number of biosynthesis gene cluster (BGC), which uncovered their enormous potentiality to encode specialized metabolites. However, these metabolites are not usually produced under standard laboratory conditions. In this manuscript we report the activation of BGCs for antimycins, carotenoids, germicidins and desferrioxamine compounds in Streptomyces argillaceus, and the identification of the encoded compounds. This was achieved by following different strategies, including changing the growth conditions, heterologous expression of the cluster and inactivating the adpAa or overexpressing the abrC3 global regulatory genes. In addition, three new carotenoid compounds have been identified.
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Affiliation(s)
- Adriana Becerril
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), Oviedo, Spain
| | - Susana Álvarez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
| | - Alfredo F. Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), Oviedo, Spain
| | - Sergio Rico
- Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain
| | - Margarita Díaz
- Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain
| | - Ramón I. Santamaría
- Departamento de Microbiología y Genética, Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain
| | - José A. Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), Oviedo, Spain
- * E-mail:
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19
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Parvez A, Giri S, Giri GR, Kumari M, Bisht R, Saxena P. Novel Type III Polyketide Synthases Biosynthesize Methylated Polyketides in Mycobacterium marinum. Sci Rep 2018; 8:6529. [PMID: 29695799 PMCID: PMC5916927 DOI: 10.1038/s41598-018-24980-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/12/2018] [Indexed: 01/09/2023] Open
Abstract
Mycobacterial pathogenesis is hallmarked by lipidic polyketides that decorate the cell envelope and mediate infection. However, factors mediating persistence remain largely unknown. Dynamic cell wall remodeling could facilitate the different pathogenic phases. Recent studies have implicated type III polyketide synthases (PKSs) in cell wall alterations in several bacteria. Comparative genome analysis revealed several type III pks gene clusters in mycobacteria. In this study, we report the functional characterization of two novel type III PKSs, MMAR_2470 and MMAR_2474, in Mycobacterium marinum. These type III pkss belong to a unique pks genomic cluster conserved exclusively in pathogenic mycobacteria. Cell-free reconstitution assays and high-resolution mass spectrometric analyses revealed methylated polyketide products in independent reactions of both proteins. MMAR_2474 protein exceptionally biosynthesized methylated alkyl-resorcinol and methylated acyl-phloroglucinol products from the same catalytic core. Structure-based homology modeling, product docking, and mutational studies identified residues that could facilitate the distinctive catalysis of these proteins. Functional investigations in heterologous mycobacterial strain implicated MMAR_2474 protein to be vital for mycobacterial survival in stationary biofilms. Our investigations provide new insights into type III PKSs conserved in pathogenic mycobacterial species.
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Affiliation(s)
- Amreesh Parvez
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - Samir Giri
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India.,Department of Ecology, School of Biology, University of Osnabrück, Osnabrück, 49076, Germany
| | - Gorkha Raj Giri
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - Monika Kumari
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India.,Department of Biochemistry, University College of Medical Sciences, Delhi, 110095, India
| | - Renu Bisht
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - Priti Saxena
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India.
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20
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Lee WC, Jeong MC, Lee Y, Kwak C, Lee JY, Kim Y. Structure and substrate specificity of β-ketoacyl-acyl carrier protein synthase III from Acinetobacter baumannii. Mol Microbiol 2018. [PMID: 29528170 DOI: 10.1111/mmi.13950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Originally annotated as the initiator of fatty acid synthesis (FAS), β-ketoacyl-acyl carrier protein synthase III (KAS III) is a unique component of the bacterial FAS system. Novel variants of KAS III have been identified that promote the de novo use of additional extracellular fatty acids by FAS. These KAS III variants prefer longer acyl-groups, notably octanoyl-CoA. Acinetobacter baumannii, a clinically important nosocomial pathogen, contains such a multifunctional KAS III (AbKAS III). To characterize the structural basis of its substrate specificity, we determined the crystal structures of AbKAS III in the presence of different substrates. The acyl-group binding cavity of AbKAS III and co-crystal structure of AbKAS III and octanoyl-CoA confirmed that the cavity can accommodate acyl groups with longer alkyl chains. Interestingly, Cys264 formed a disulfide bond with residual CoA used in the crystallization, which distorted helices at the putative interface with acyl-carrier proteins. The crystal structure of KAS III in the alternate conformation can also be utilized for designing novel antibiotics.
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Affiliation(s)
- Woo Cheol Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Min-Cheol Jeong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Yeongjoon Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Chulhee Kwak
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jee-Young Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
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21
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Čihák M, Kameník Z, Šmídová K, Bergman N, Benada O, Kofroňová O, Petříčková K, Bobek J. Secondary Metabolites Produced during the Germination of Streptomyces coelicolor. Front Microbiol 2017; 8:2495. [PMID: 29326665 PMCID: PMC5733532 DOI: 10.3389/fmicb.2017.02495] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/30/2017] [Indexed: 11/16/2022] Open
Abstract
Spore awakening is a series of actions that starts with purely physical processes and continues via the launching of gene expression and metabolic activities, eventually achieving a vegetative phase of growth. In spore-forming microorganisms, the germination process is controlled by intra- and inter-species communication. However, in the Streptomyces clade, which is capable of developing a plethora of valuable compounds, the chemical signals produced during germination have not been systematically studied before. Our previously published data revealed that several secondary metabolite biosynthetic genes are expressed during germination. Therefore, we focus here on the secondary metabolite production during this developmental stage. Using high-performance liquid chromatography-mass spectrometry, we found that the sesquiterpenoid antibiotic albaflavenone, the polyketide germicidin A, and chalcone are produced during germination of the model streptomycete, S. coelicolor. Interestingly, the last two compounds revealed an inhibitory effect on the germination process. The secondary metabolites originating from the early stage of microbial growth may coordinate the development of the producer (quorum sensing) and/or play a role in competitive microflora repression (quorum quenching) in their nature environments.
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Affiliation(s)
- Matouš Čihák
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia
| | - Zdeněk Kameník
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Klára Šmídová
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia.,Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Natalie Bergman
- Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
| | - Oldřich Benada
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia.,Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
| | - Olga Kofroňová
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Kateřina Petříčková
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia
| | - Jan Bobek
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia.,Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia.,Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
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22
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Zhao Y, Liu D, Proksch P, Yu S, Lin W. Angupyrones A - E, α-Pyrone Analogues with ARE-Activation from a Sponge-Associated Fungus Truncatella angustata. Chem Biodivers 2017; 14. [PMID: 28599098 DOI: 10.1002/cbdv.201700236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/06/2017] [Indexed: 11/07/2022]
Abstract
TLC-DPPH guided fractionation of a sponge-associated fungus Truncatella angustata with a solid culture resulted in the isolation of five new α-pyrone-based analogues namely angupyrones A - E (1 - 5), and 3-ethyl-4-hydroxy-6-methyl-2-pyrone. Their structures were determined on the basis of extensive spectroscopic analyses, including the modified Mosher's method, bulkiness rule, and specific rotation for the configurational assignments. Angupyrones A - E exhibited moderate antioxidant response element activation in HepG2C8 cells, while the preliminary structure-activity relationship was discussed.
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Affiliation(s)
- Yang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, P. R. China
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, P. R. China
| | - Peter Proksch
- Institute für Pharmazeutische Biologie und Biotechnologie, Heinrich-Heine-Universität Düsseldorf, DE-40225, Düsseldorf
| | - Siwang Yu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, P. R. China
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191, P. R. China
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23
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Bhat ZS, Rather MA, Maqbool M, Lah HU, Yousuf SK, Ahmad Z. α-pyrones: Small molecules with versatile structural diversity reflected in multiple pharmacological activities-an update. Biomed Pharmacother 2017; 91:265-277. [PMID: 28460229 DOI: 10.1016/j.biopha.2017.04.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/18/2017] [Accepted: 04/10/2017] [Indexed: 12/15/2022] Open
Abstract
The investigations in the chemistry and biology of α-pyrone (2-pyrone) are of vital importance as they constitute an essential pharmacophore in many naturally occurring and biologically active synthetic agents. They are a promising class of biorenewable platform chemicals that provide access to an array of chemical products and intermediates. Literature survey reveals that a simple change in the substitution pattern on the 2-pyrone ring system often leads to diverse biological activities. In this review, we present a brief overview of 2-pyrone pharmacophore followed by highlighting their pharmacological properties and potential applicability till date. Particular attention is focused on the distinctive chemotherapeutic activities of 2-pyrones as anti-HIV, anti-TB and anti-cancer agents followed by their potential role against neurodegeneration, hypercholesterolemia, microbial infections, chronic obstructive lung disease, inflammation, antinociception and immunomodulation. Since 2005, when 2-pyrones came in limelight, their detailed pharmacological activities have been well documented. This review has mainly been prepared on the basis of original reports published in recent two decades with an aim to attract the attention of researchers towards this versatile scaffold for future endeavors that may lead to the development of potential drug candidates against above diseases.
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Affiliation(s)
- Zubair Shanib Bhat
- Clinical Microbiology and PK/PD Division, Council of scientific and industrial research (CSIR) -Indian Institute of Integrative Medicine (IIIM), Sanatnagar, Srinagar, 190005, India; Academy of Scientific and Innovative Research (AcSIR), Indian Institute of Integrative Medicine (CSIR), Sanatnagar Srinagar, Jammu and Kashmir 190005, India
| | - Muzafar Ahmad Rather
- Clinical Microbiology and PK/PD Division, Council of scientific and industrial research (CSIR) -Indian Institute of Integrative Medicine (IIIM), Sanatnagar, Srinagar, 190005, India
| | - Mubashir Maqbool
- Clinical Microbiology and PK/PD Division, Council of scientific and industrial research (CSIR) -Indian Institute of Integrative Medicine (IIIM), Sanatnagar, Srinagar, 190005, India
| | - Hafiz Ul Lah
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Sanatnagar, Srinagar, 190005, India
| | - Syed Khalid Yousuf
- Academy of Scientific and Innovative Research (AcSIR), Indian Institute of Integrative Medicine (CSIR), Sanatnagar Srinagar, Jammu and Kashmir 190005, India; Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Sanatnagar, Srinagar, 190005, India
| | - Zahoor Ahmad
- Clinical Microbiology and PK/PD Division, Council of scientific and industrial research (CSIR) -Indian Institute of Integrative Medicine (IIIM), Sanatnagar, Srinagar, 190005, India; Academy of Scientific and Innovative Research (AcSIR), Indian Institute of Integrative Medicine (CSIR), Sanatnagar Srinagar, Jammu and Kashmir 190005, India.
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24
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Ma M, Rateb ME, Yang D, Rudolf JD, Zhu X, Huang Y, Zhao LX, Jiang Y, Duan Y, Shen B. Germicidins H–J from Streptomyces sp. CB00361. J Antibiot (Tokyo) 2016; 70:200-203. [DOI: 10.1038/ja.2016.100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/23/2016] [Accepted: 07/11/2016] [Indexed: 12/19/2022]
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Huang H, Hou L, Li H, Qiu Y, Ju J, Li W. Activation of a plasmid-situated type III PKS gene cluster by deletion of a wbl gene in deepsea-derived Streptomyces somaliensis SCSIO ZH66. Microb Cell Fact 2016; 15:116. [PMID: 27350607 PMCID: PMC4924298 DOI: 10.1186/s12934-016-0515-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/17/2016] [Indexed: 11/16/2022] Open
Abstract
Background Actinomycete genome sequencing has disclosed a large number of cryptic secondary metabolite biosynthetic gene clusters. However, their unavailable or limited expression severely hampered the discovery of bioactive compounds. The whiB-like (wbl) regulatory genes play important roles in morphological differentiation as well as secondary metabolism; and hence the wblAso gene was probed and set as the target to activate cryptic gene clusters in deepsea-derived Streptomyces somaliensis SCSIO ZH66. Results wblAso from deepsea-derived S. somaliensis SCSIO ZH66 was inactivated, leading to significant changes of secondary metabolites production in the ΔwblAso mutant, from which α-pyrone compound violapyrone B (VLP B) was isolated. Subsequently, the VLP biosynthetic gene cluster was identified and characterized, which consists of a type III polyketide synthase (PKS) gene vioA and a regulatory gene vioB; delightedly, inactivation of vioB led to isolation of another four VLPs analogues, among which one was new and two exhibited improved anti-MRSA (methicillin-resistant Staphylococcus aureus, MRSA) activity than VLP B. Moreover, transcriptional analysis revealed that the expression levels of whi genes (whiD, whiG, whiH and whiI) and wbl genes (wblC, wblE, wblH, wblI and wblK) were repressed by different degrees, suggesting an intertwined regulation mechanism of wblAso in morphological differentiation and secondary metabolism of S. somaliensis SCSIO ZH66. Conclusions wblA orthologues would be effective targets for activation of cryptic gene clusters in marine-derived Streptomyces strains, notwithstanding the regulation mechanisms might be varied in different strains. Moreover, the availability of the vio gene cluster has enriched the diversity of type III PKSs, providing new opportunities to expand the chemical space of polyketides through biosynthetic engineering. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0515-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huiming Huang
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Lukuan Hou
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Yanhong Qiu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jianhua Ju
- CAS Key Laboratory of Marine Bio-resources Sustainable Utilization, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
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Exploiting the Biosynthetic Potential of Type III Polyketide Synthases. Molecules 2016; 21:molecules21060806. [PMID: 27338328 PMCID: PMC6274091 DOI: 10.3390/molecules21060806] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/15/2016] [Accepted: 06/17/2016] [Indexed: 11/17/2022] Open
Abstract
Polyketides are structurally and functionally diverse secondary metabolites that are biosynthesized by polyketide synthases (PKSs) using acyl-CoA precursors. Recent studies in the engineering and structural characterization of PKSs have facilitated the use of target enzymes as biocatalysts to produce novel functionally optimized polyketides. These compounds may serve as potential drug leads. This review summarizes the insights gained from research on type III PKSs, from the discovery of chalcone synthase in plants to novel PKSs in bacteria and fungi. To date, at least 15 families of type III PKSs have been characterized, highlighting the utility of PKSs in the development of natural product libraries for therapeutic development.
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Niu G, Chater KF, Tian Y, Zhang J, Tan H. Specialised metabolites regulating antibiotic biosynthesis in Streptomyces spp. FEMS Microbiol Rev 2016; 40:554-73. [PMID: 27288284 DOI: 10.1093/femsre/fuw012] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2016] [Indexed: 12/11/2022] Open
Abstract
Streptomyces bacteria are the major source of antibiotics and other secondary metabolites. Various environmental and physiological conditions affect the onset and level of production of each antibiotic by influencing concentrations of the ligands for conserved global regulatory proteins. In addition, as reviewed here, well-known autoregulators such as γ-butyrolactones, themselves products of secondary metabolism, accumulate late in growth to concentrations allowing their effective interaction with cognate binding proteins, in a necessary prelude to antibiotic biosynthesis. Most autoregulator binding proteins target the conserved global regulatory gene adpA, and/or regulatory genes for 'cluster-situated regulators' (CSRs) linked to antibiotic biosynthetic gene clusters. It now appears that some CSRs bind intermediates and end products of antibiotic biosynthesis, with regulatory effects interwoven with those of autoregulators. These ligands can exert cross-pathway effects within producers of more than one antibiotic, and when excreted into the extracellular environment may have population-wide effects on production, and mediate interactions with neighbouring microorganisms in natural communities, influencing speciation. Greater understanding of these autoregulatory and cross-regulatory activities may aid the discovery of new signalling molecules and their use in activating cryptic antibiotic biosynthetic pathways.
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Affiliation(s)
- Guoqing Niu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Keith F Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Yuqing Tian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Brameyer S, Heermann R. Quorum Sensing and LuxR Solos in Photorhabdus. Curr Top Microbiol Immunol 2016; 402:103-119. [PMID: 27848037 DOI: 10.1007/82_2016_28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacterial communication via small diffusible molecules to mediate group-coordinated behaviour is commonly referred to as 'quorum sensing'. The prototypical quorum sensing system of Gram-negative bacteria consists of a LuxI-type autoinducer synthase that produces acyl-homoserine lactones (AHLs) as signals and a LuxR-type receptor that detects the AHLs to control expression of specific genes. However, many bacteria possess LuxR homologs but lack a cognate LuxI-type AHL-synthase. Those LuxR-type receptors are designated as 'LuxR orphans' or 'solos'. Entomopathogenic bacteria of the genus Photorhabdus all harbour a large number of LuxR solos, more than any other bacteria examined so far. Two novel quorum sensing systems were found to regulate cell clumping in Photorhabdus and therefore affect pathogenicity. In Photorhabdus luminescens and Photorhabdus temperata the LuxR solo PluR senses α-pyrones named 'photopyrones' instead of AHLs, which are produced by the pyrone synthase PpyS. In contrast, Photorhabdus asymbiotica, a closely related insect and human pathogen, has the PluR homolog PauR, which senses dialkylresorcinols produced by the DarABC pathway to regulate pathogenicity. All three Photorhabdus species harbour at least one LuxR solo with an intact AHL-binding motif, which might also allow sensing of exogenous AHLs. However, the majority of the LuxR solos in all Photorhabdus species have a PAS4 signal-binding domain. These receptors are assumed to detect eukaryotic compounds and are proposed to be involved in host sensing. Overall, because of the large number of LuxR solos they encode, bacteria of the genus Photorhabdus are ideal candidates to study and to identify novel bacterial communication networks.
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Affiliation(s)
- Sophie Brameyer
- Biozentrum, Bereich Mikrobiologie, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Martinsried/München, Germany
| | - Ralf Heermann
- Biozentrum, Bereich Mikrobiologie, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Martinsried/München, Germany.
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Kresovic D, Schempp F, Cheikh-Ali Z, Bode HB. A novel and widespread class of ketosynthase is responsible for the head-to-head condensation of two acyl moieties in bacterial pyrone biosynthesis. Beilstein J Org Chem 2015; 11:1412-7. [PMID: 26425196 PMCID: PMC4578411 DOI: 10.3762/bjoc.11.152] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/22/2015] [Indexed: 01/22/2023] Open
Abstract
The biosynthesis of photopyrones, novel quorum sensing signals in Photorhabdus, has been studied by heterologous expression of the photopyrone synthase PpyS catalyzing the head-to-head condensation of two acyl moieties. The biochemical mechanism of pyrone formation has been investigated by amino acid exchange and bioinformatic analysis. Additionally, the evolutionary origin of PpyS has been studied by phylogenetic analyses also revealing homologous enzymes in Pseudomonas sp. GM30 responsible for the biosynthesis of pseudopyronines including a novel derivative. Moreover this novel class of ketosynthases is only distantly related to other pyrone-forming enzymes identified in the biosynthesis of the potent antibiotics myxopyronin and corallopyronin.
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Affiliation(s)
- Darko Kresovic
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany
| | - Florence Schempp
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany
| | - Zakaria Cheikh-Ali
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany ; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany
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Nakamura H, Wang JX, Balskus EP. Assembly line termination in cylindrocyclophane biosynthesis: discovery of an editing type II thioesterase domain in a type I polyketide synthase. Chem Sci 2015; 6:3816-3822. [PMID: 29218151 PMCID: PMC5707447 DOI: 10.1039/c4sc03132f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 04/11/2015] [Indexed: 01/18/2023] Open
Abstract
Investigation of cylindrocyclophane biosynthesis reveals a C-terminal thioesterase domain involved in PKS assembly line editing, not termination.
The termination step is an important source of structural diversity in polyketide biosynthesis. Most type I polyketide synthase (PKS) assembly lines are terminated by a thioesterase (TE) domain located at the C-terminus of the final module, while other PKS assembly lines lack a terminal TE domain and are instead terminated by a separate enzyme in trans. In cylindrocyclophane biosynthesis, the type I modular PKS assembly line is terminated by a freestanding type III PKS (CylI). Unexpectedly, the final module of the type I PKS (CylH) also possesses a C-terminal TE domain. Unlike typical type I PKSs, the CylH TE domain does not influence assembly line termination by CylI in vitro. Instead, this domain phylogenetically resembles a type II TE and possesses activity consistent with an editing function. This finding may shed light on the evolution of unusual PKS termination logic. In addition, the presence of related type II TE domains in many cryptic type I PKS and nonribosomal peptide synthetase (NRPS) assembly lines has implications for pathway annotation, product prediction, and engineering.
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Affiliation(s)
- H Nakamura
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , USA .
| | - J X Wang
- Small Molecule Mass Spectrometry Facility , FAS Division of Science , Cambridge , Massachusetts 02138 , USA
| | - E P Balskus
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , USA .
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31
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Abstract
This review covers a breakthrough in the structural biology of the gigantic modular polyketide synthases (PKS): the structural characterization of intact modules by single-particle cryo-electron microscopy and small-angle X-ray scattering.
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Affiliation(s)
- Kira J. Weissman
- Molecular and Structural Enzymology Group
- Université de Lorraine
- IMoPA
- UMR 7365
- Vandœuvre-lès-Nancy
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32
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Montebello AN, Brecht RM, Turner RD, Ghali M, Pu X, Nagarajan R. Acyl-ACP substrate recognition in Burkholderia mallei BmaI1 acyl-homoserine lactone synthase. Biochemistry 2014; 53:6231-42. [PMID: 25215658 PMCID: PMC4188261 DOI: 10.1021/bi5009529] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The acyl-homoserine lactone (AHL) autoinducer mediated quorum sensing regulates virulence in several pathogenic bacteria. The hallmark of an efficient quorum sensing system relies on the tight specificity in the signal generated by each bacterium. Since AHL signal specificity is derived from the acyl-chain of the acyl-ACP (ACP = acyl carrier protein) substrate, AHL synthase enzymes must recognize and react with the native acyl-ACP with high catalytic efficiency while keeping reaction rates with non-native acyl-ACPs low. The mechanism of acyl-ACP substrate recognition in these enzymes, however, remains elusive. In this study, we investigated differences in catalytic efficiencies for shorter and longer chain acyl-ACP substrates reacting with an octanoyl-homoserine lactone synthase Burkholderia mallei BmaI1. With the exception of two-carbon shorter hexanoyl-ACP, the catalytic efficiencies of butyryl-ACP, decanoyl-ACP, and octanoyl-CoA reacting with BmaI1 decreased by greater than 20-fold compared to the native octanoyl-ACP substrate. Furthermore, we also noticed kinetic cooperativity when BmaI1 reacted with non-native acyl-donor substrates. Our kinetic data suggest that non-native acyl-ACP substrates are unable to form a stable and productive BmaI1·acyl-ACP·SAM ternary complex and are thus effectively discriminated by the enzyme. These results offer insights into the molecular basis of substrate recognition for the BmaI1 enzyme.
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Affiliation(s)
- Aubrey N Montebello
- Department of Chemistry and Biochemistry, Boise State University , 1910 University Drive, Boise, Idaho 83725, United States
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Abstract
Polyketide natural products constitute a broad class of compounds with diverse structural features and biological activities. Their biosynthetic machinery, represented by type I polyketide synthases (PKSs), has an architecture in which successive modules catalyse two-carbon linear extensions and keto-group processing reactions on intermediates covalently tethered to carrier domains. Here we used electron cryo-microscopy to determine sub-nanometre-resolution three-dimensional reconstructions of a full-length PKS module from the bacterium Streptomyces venezuelae that revealed an unexpectedly different architecture compared to the homologous dimeric mammalian fatty acid synthase. A single reaction chamber provides access to all catalytic sites for the intramodule carrier domain. In contrast, the carrier from the preceding module uses a separate entrance outside the reaction chamber to deliver the upstream polyketide intermediate for subsequent extension and modification. This study reveals for the first time, to our knowledge, the structural basis for both intramodule and intermodule substrate transfer in polyketide synthases, and establishes a new model for molecular dissection of these multifunctional enzyme systems.
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Challis GL. Exploitation of the Streptomyces coelicolor A3(2) genome sequence for discovery of new natural products and biosynthetic pathways. J Ind Microbiol Biotechnol 2013; 41:219-32. [PMID: 24322202 DOI: 10.1007/s10295-013-1383-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 11/15/2013] [Indexed: 11/28/2022]
Abstract
Streptomyces, and related genera of Actinobacteria, are renowned for their ability to produce antibiotics and other bioactive natural products with a wide range of applications in medicine and agriculture. Streptomyces coelicolor A3(2) is a model organism that has been used for more than five decades to study the genetic and biochemical basis for the production of bioactive metabolites. In 2002, the complete genome sequence of S. coelicolor was published. This greatly accelerated progress in understanding the biosynthesis of metabolites known or suspected to be produced by S. coelicolor and revealed that streptomycetes have far greater potential to produce bioactive natural products than suggested by classical bioassay-guided isolation studies. In this article, efforts to exploit the S. coelicolor genome sequence for the discovery of novel natural products and biosynthetic pathways are summarized.
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Affiliation(s)
- Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK,
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36
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Pyrones as bacterial signaling molecules. Nat Chem Biol 2013; 9:573-8. [PMID: 23851573 DOI: 10.1038/nchembio.1295] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 06/12/2013] [Indexed: 01/26/2023]
Abstract
Bacteria communicate via small diffusible molecules and thereby mediate group-coordinated behavior, a process referred to as quorum sensing. The prototypical quorum sensing system found in Gram-negative bacteria consists of a LuxI-type autoinducer synthase that produces N-acyl homoserine lactones (AHLs) as signals and a LuxR-type receptor that detects the AHLs to control expression of specific genes. However, many proteobacteria have proteins with homology to LuxR receptors yet lack any cognate LuxI-like AHL synthase. Here we show that in the insect pathogen Photorhabdus luminescens the orphan LuxR-type receptor PluR detects endogenously produced α-pyrones that serve as signaling molecules at low nanomolar concentrations. Additionally, the ketosynthase PpyS was identified as pyrone synthase. Reconstitution of the entire system containing PluR, the PluR-target operon we termed pcf and PpyS in Escherichia coli demonstrated that the cell-cell communication circuit is portable. Our research thus deorphanizes a signaling system and suggests that additional modes of bacterial communication may await discovery.
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Nakamura H, Balskus EP. Using Chemical Knowledge to Uncover New Biological Function: Discovery of the Cylindrocyclophane Biosynthetic Pathway. Synlett 2013; 24:1464-1470. [PMID: 31723311 PMCID: PMC6853628 DOI: 10.1055/s-0033-1338879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
An understanding of organic chemistry can play a central role in uncovering enzymes with new biochemical functions. We have recently identified the enzymes involved in the biosynthesis of the cylindrocyclophanes, a structurally unique family of natural products, and found that this pathway employs a remarkable macrocyclization event that requires functionalization of an unactivated carbon atom. This work illustrates the potential of using chemically guided approaches for enzyme discovery.
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Affiliation(s)
- Hitomi Nakamura
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P Balskus
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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Raju R, Piggott AM, Quezada M, Capon RJ. Nocardiopsins C and D and nocardiopyrone A: new polyketides from an Australian marine-derived Nocardiopsis sp. Tetrahedron 2013. [DOI: 10.1016/j.tet.2012.10.104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Nakamura H, Hamer HA, Sirasani G, Balskus EP. Cylindrocyclophane biosynthesis involves functionalization of an unactivated carbon center. J Am Chem Soc 2012; 134:18518-21. [PMID: 23106426 DOI: 10.1021/ja308318p] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cylindrocyclophanes are a family of natural products that share a remarkable paracyclophane carbon scaffold. Using genome sequencing and bioinformatic analyses, we have discovered a biosynthetic gene cluster involved in the assembly of cylindrocyclophane F. Through a combination of in vitro enzyme characterization and feeding studies, we confirm the connection between this gene cluster and cylindrocyclophane production, elucidate the chemical events involved in initiating and terminating an unusual type I polyketide synthase assembly line, and discover that macrocycle assembly involves functionalization of an unactivated carbon center.
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Affiliation(s)
- Hitomi Nakamura
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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