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Deng RX, Li HL, Sheng CL, Wang W, Hu HB, Zhang XH. Characterization of Lomofungin Gene Cluster Enables the Biosynthesis of Related Phenazine Derivatives. ACS Synth Biol 2024. [PMID: 39250825 DOI: 10.1021/acssynbio.4c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Phenazine-based small molecules are nitrogen-containing heterocyclic compounds with diverse bioactivities and electron transfer properties that exhibit promising applications in pharmaceutical and electrochemical industries. However, the biosynthetic mechanism of highly substituted natural phenazines remains poorly understood. In this study, we report the direct cloning and heterologous expression of the lomofungin biosynthetic gene cluster (BGC) from Streptomyces lomondensis S015. Reconstruction and overexpression of the BGCs in Streptomyces coelicolor M1152 resulted in eight phenazine derivatives including two novel hybrid phenazine metabolites, and the biosynthetic pathway of lomofungin was proposed. Furthermore, gene deletion suggested that NAD(P)H-dependent oxidoreductase gene lomo14 is a nonessential gene in the biosynthesis of lomofungin. Cytotoxicity evaluation of the isolated phenazines and lomofungin was performed. Specifically, lomofungin shows substantial inhibition against two human cancer cells, HCT116 and 5637. These results provide insights into the biosynthetic mechanism of lomofungin, which will be useful for the directed biosynthesis of natural phenazine derivatives.
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Affiliation(s)
- Ru-Xiang Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hui-Ling Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao-Lan Sheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong-Bo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Hong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Shende VV, Bauman KD, Moore BS. The shikimate pathway: gateway to metabolic diversity. Nat Prod Rep 2024; 41:604-648. [PMID: 38170905 PMCID: PMC11043010 DOI: 10.1039/d3np00037k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.
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Affiliation(s)
- Vikram V Shende
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Katherine D Bauman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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Zhukrovska K, Binda E, Fedorenko V, Marinelli F, Yushchuk O. The Impact of Heterologous Regulatory Genes from Lipodepsipeptide Biosynthetic Gene Clusters on the Production of Teicoplanin and A40926. Antibiotics (Basel) 2024; 13:115. [PMID: 38391501 PMCID: PMC10886168 DOI: 10.3390/antibiotics13020115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
StrR-like pathway-specific transcriptional regulators (PSRs) function as activators in the biosynthesis of various antibiotics, including glycopeptides (GPAs), aminoglycosides, aminocoumarins, and ramoplanin-like lipodepsipeptides (LDPs). In particular, the roles of StrR-like PSRs have been previously investigated in the biosynthesis of streptomycin, novobiocin, GPAs like balhimycin, teicoplanin, and A40926, as well as LDP enduracidin. In the current study, we focused on StrR-like PSRs from the ramoplanin biosynthetic gene cluster (BGC) in Actinoplanes ramoplaninifer ATCC 33076 (Ramo5) and the chersinamycin BGC in Micromonospora chersina DSM 44151 (Chers28). Through the analysis of the amino acid sequences of Ramo5 and Chers28, we discovered that these proteins are phylogenetically distant from other experimentally investigated StrR PSRs, although all StrR-like PSRs found in BGCs for different antibiotics share a conserved secondary structure. To investigate whether Ramo5 and Chers28, given their phylogenetic positions, might influence the biosynthesis of other antibiotic pathways governed by StrR-like PSRs, the corresponding genes (ramo5 and chers28) were heterologously expressed in Actinoplanes teichomyceticus NRRL B-16726 and Nonomuraea gerenzanensis ATCC 39727, which produce the clinically-relevant GPAs teicoplanin and A40926, respectively. Recombinant strains of NRRL B-16726 and ATCC 39727 expressing chers28 exhibited improved antibiotic production, although the expression of ramo5 did not yield the same effect. These results demonstrate that some StrR-like PSRs can "cross-talk" between distant biosynthetic pathways and might be utilized as tools for the activation of silent BGCs regulated by StrR-like PSRs.
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Affiliation(s)
- Kseniia Zhukrovska
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Oleksandr Yushchuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
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Chanama M, Prombutara P, Chanama S. Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria. Sci Rep 2023; 13:8794. [PMID: 37258607 DOI: 10.1038/s41598-023-36039-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/28/2023] [Indexed: 06/02/2023] Open
Abstract
Actinobacteria are well known as a rich source of diversity of bioactive secondary metabolites. Kutzneria, a rare actinobacteria belonging to the family Pseudonocardiaceae has abundance of secondary metabolite biosynthetic gene clusters (BGCs) and is one of important source of natural products and worthy of priority investigation. Currently, Kutzneria chonburiensis SMC256T has been the latest type-strain of the genus and its genome sequence has not been reported yet. Therefore, we present the first report of new complete genome sequence of SMC256T (genome size of 10.4 Mbp) with genome annotation and feature comparison between SMC256T and other publicly available Kutzneria species. The results from comparative and functional genomic analyses regarding the phylogenomic and the clusters of orthologous groups of proteins (COGs) analyses indicated that SMC256T is most closely related to Kutzneria sp. 744, Kutzneria kofuensis, Kutzneria sp. CA-103260 and Kutzneria buriramensis. Furthermore, a total of 322 BGCs were also detected and showed diversity among the Kutzneria genomes. Out of which, 38 clusters showing the best hit to the most known BGCs were predicted in the SMC256Tgenome. We observed that six clusters responsible for biosynthesis of antimicrobials/antitumor metabolites were strain-specific in Kutzneria chonburiensis. These putative metabolites include virginiamycin S1, lysolipin I, esmeraldin, rakicidin, aclacinomycin and streptoseomycin. Based on these findings, the genome of Kutzneria chonburiensis contains distinct and unidentified BGCs different from other members of the genus, and the use of integrative genomic-based approach would be a useful alternative effort to target, isolate and identify putative and undiscovered secondary metabolites suspected to have new and/or specific bioactivity in the Kutzneria.
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Affiliation(s)
- Manee Chanama
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, 10400, Thailand.
| | - Pinidphon Prombutara
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Suchart Chanama
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
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Yang Y, Kessler MGC, Marchán-Rivadeneira MR, Han Y. Combating Antimicrobial Resistance in the Post-Genomic Era: Rapid Antibiotic Discovery. Molecules 2023; 28:molecules28104183. [PMID: 37241928 DOI: 10.3390/molecules28104183] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Constantly evolving drug-resistant "superbugs" have caused an urgent demand for novel antimicrobial agents. Natural products and their analogs have been a prolific source of antimicrobial agents, even though a high rediscovery rate and less targeted research has made the field challenging in the pre-genomic era. With recent advancements in technology, natural product research is gaining new life. Genome mining has allowed for more targeted excavation of biosynthetic potential from natural sources that was previously overlooked. Researchers use bioinformatic algorithms to rapidly identify and predict antimicrobial candidates by studying the genome before even entering the lab. In addition, synthetic biology and advanced analytical instruments enable the accelerated identification of novel antibiotics with distinct structures. Here, we reviewed the literature for noteworthy examples of novel antimicrobial agents discovered through various methodologies, highlighting the candidates with potent effectiveness against antimicrobial-resistant pathogens.
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Affiliation(s)
- Yuehan Yang
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
| | - Mara Grace C Kessler
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Honors Tutorial College, Ohio University, Athens, OH 45701, USA
| | - Maria Raquel Marchán-Rivadeneira
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
- Center for Research on Health in Latinamerica (CISeAL)-Biological Science Department, Pontificia Universidad Católica del Ecuador (PUCE), Quito 170143, Ecuador
| | - Yong Han
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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Makwana P, Hungund SP, Pradeep ANR. Dipteran endoparasitoid Exorista bombycis utilizes antihemocyte components against host defense of silkworm Bombyx mori. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 112:e21976. [PMID: 36205611 DOI: 10.1002/arch.21976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/07/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Dipteran endoparasitoids avoid host immune response; however, antidefense components from the Dipterans are unknown. Infestation of commercial silkworm Bombyx mori Linnaeus (Lepidoptera: Bombycidae) by endoparasitoid Exorista bombycis Louis (Diptera: Tachinidae) induced immune reactions, cytotoxicity, granulation, degranulation, and augmented release of cytotoxic marker enzyme lactate dehydrogenase (LDH), and degranulation-mediator enzyme β-hexosaminidase in hemocytes. In this study, by reverse phase high-performance liquid chromatography, fractions of E. bombycis larval tissue protein with antihemocytic activity are separated. From the fraction, peptides of hemocyte aggregation inhibitor protein (HAIP) and pyridoxamine phosphate oxidase (PNPO) are identified by mass spectrometry. Interacting partners of HAIP and PNPO are retrieved that further enhance the virulence of the parasitoid. PNPO and HAIP genes showed a four- to seven fold increase in expression in the integument of the parasitoid larva. Together, the dipteran endoparasitoid E. bombycis exploit antihemocyte activity to inhibit host defense reactions in addition to defense evasion contemplated.
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Affiliation(s)
- Pooja Makwana
- Seribiotech Research Laboratory, CSB-Kodathi Campus, Bangalore, Karnataka, India
- Biotechnology Division, Central Sericultural Research & Training Institute, Berhampore, West Bengal, India
| | - Shambhavi P Hungund
- Seribiotech Research Laboratory, CSB-Kodathi Campus, Bangalore, Karnataka, India
| | - Appukuttan Nair R Pradeep
- Seribiotech Research Laboratory, CSB-Kodathi Campus, Bangalore, Karnataka, India
- Biotechnology Division, Central Sericultural Research & Training Institute, Berhampore, West Bengal, India
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George SE, Devereux R, James J, Wan Y, Diamond GL, Bradham KD, Thomas DJ. Dietary lead modulates the mouse intestinal microbiome: Subacute exposure to lead acetate and lead contaminated soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114430. [PMID: 37192935 PMCID: PMC10181873 DOI: 10.1016/j.ecoenv.2022.114430] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The effect of dietary lead on the intestinal microbiome has not been fully elucidated. To determine if there was an association between microflora modulation, predicted functional genes, and Pb exposure, mice were provided diets amended with increasing concentrations of a single lead compound, lead acetate, or a well characterized complex reference soil containing lead, i.e. 6.25-25 mg/kg Pb acetate (PbOAc) or 7.5-30 mg/kg Pb in reference soil SRM 2710a having 0.552 % Pb among other heavy metals such as Cd. Feces and ceca were collected following 9 days of treatment and the microbiome analyzed by 16 S rRNA gene sequencing. Treatment effects on the microbiome were observed in both feces and ceca of mice. Changes in the cecal microbiomes of mice fed Pb as Pb acetate or as a constituent in SRM 2710a were statistically different except for a few exceptions regardless of dietary source. This was accompanied by increased average abundance of functional genes associated with metal resistance, including those related to siderophore synthesis and arsenic and/or mercury detoxification. Akkermansia, a common gut bacterium, was the highest ranked species in control microbiomes whereas Lactobacillus ranked highest in treated mice. Firmicutes/Bacteroidetes ratios in the ceca of SRM 2710a treated mice increased more than with PbOAc, suggestive of changes in gut microbiome metabolism that promotes obesity. Predicted functional gene average abundance related to carbohydrate, lipid, and/or fatty acid biosynthesis and degradation were greater in the cecal microbiome of SRM 2710a treated mice. Bacilli/Clostridia increased in the ceca of PbOAc treated mice and may be indicative of increased risk of host sepsis. Family Deferribacteraceae also was modulated by PbOAc or SRM 2710a possibly impacting inflammatory response. Understanding the relationship between microbiome composition, predicted functional genes, and Pb concentration, especially in soil, may provide new insights into the utility of various remediation methodologies that minimize dysbiosis and modulate health effects, thus assisting in the selection of an optimal treatment for contaminated sites.
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Affiliation(s)
- S. Elizabeth George
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, Gulf Breeze, FL 32561, United States
| | - Richard Devereux
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, Gulf Breeze, FL 32561, United States
| | - Joseph James
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, Gulf Breeze, FL 32561, United States
| | - Yongshan Wan
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, Gulf Breeze, FL 32561, United States
| | | | - Karen D. Bradham
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Environmental Measurement & Modeling, Research Triangle Park, NC 27711, United States
| | - David J. Thomas
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure, Chemical Characterization & Exposure Division, Research Triangle Park, NC 27711, United States
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Dong J, He B, Wang R, Zuo X, Zhan R, Hu L, Li Y, He J. Characterization of the diastaphenazine/izumiphenazine C biosynthetic gene cluster from plant endophyte Streptomyces diastaticus W2. Microb Biotechnol 2022; 15:1168-1177. [PMID: 34487423 PMCID: PMC8966011 DOI: 10.1111/1751-7915.13909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/23/2021] [Indexed: 11/29/2022] Open
Abstract
Two phenazine compounds, diastaphenazine and izumiphenazine C, with complex structures and promising antitumour activity have been isolated from the plant endophytic actinomycete Streptomyces diastaticus W2. Their putative biosynthetic gene cluster (dap) was identified by heterologous expression and gene knockout. There are twenty genes in the dap cluster. dap14-19 related to shikimic pathway were potentially involved in the precursor chorismic acid biosynthesis, and dapBCDEFG were confirmed to be responsible for the biosynthesis of the dibenzopyrazine ring, the nuclear structure of phenazines. Two transcriptional regulatory genes dapR and dap4 played the positive regulatory roles on the phenazine biosynthetic pathway. Most notably, the dimerization of the dibenzopyrazine ring in diastaphenazine and the loading of the complex side chain in izumiphenazine C could be catalysed by the cyclase homologous gene dap5, suggesting an unusual modification strategy tailoring complex phenazine biosynthesis. Moreover, metabolite analysis of the gene deletion mutant strain S. albus::23C5Δdap2 and substrate assay of the methyltransferase Dap2 clearly revealed the biosynthetic route of the complex side chain in izumiphenazine C.
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Affiliation(s)
- Junli Dong
- State Key Laboratory of Agricultural MicrobiologyCollege of Life Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Beibei He
- State Key Laboratory of Agricultural MicrobiologyCollege of Life Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Ruinan Wang
- State Key Laboratory of Agricultural MicrobiologyCollege of Life Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Xiuli Zuo
- State Key Laboratory of Agricultural MicrobiologyCollege of Life Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Rui Zhan
- State Key Laboratory of Agricultural MicrobiologyCollege of Life Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Linfang Hu
- Key Laboratory of Microbial Diversity in Southwest ChinaMinistry of EducationCollege of Life ScienceYunnan UniversityKunming650091China
| | - Yiqing Li
- Key Laboratory of Microbial Diversity in Southwest ChinaMinistry of EducationCollege of Life ScienceYunnan UniversityKunming650091China
| | - Jing He
- State Key Laboratory of Agricultural MicrobiologyCollege of Life Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
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Wan Y, Liu H, Xian M, Huang W. Biosynthetic Pathway Construction and Production Enhancement of 1-Hydroxyphenazine Derivatives in Pseudomonas chlororaphis H18. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1223-1231. [PMID: 35057615 DOI: 10.1021/acs.jafc.1c07760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
1-Hydroxyphenazine derivatives are phenazine family chemicals with broad-spectrum antibacterial and potential biological activities. However, the lack of variety and low titer hinder their applications. In this research, three enzymes PhzS (monooxygenase), NaphzNO1 (N-monooxygenase), and LaphzM (methyltransferase) were heterologously expressed in a phenazine-1-carboxylic acid generating strain Pseudomonas chlororaphis H18. Four phenazines, 1-hydroxyphenazine, 1-methoxyphenazine, 1-hydroxyphenazine N' 10-oxide, and a novel phenazine derivative 1-methoxyphenazine N' 10-oxide, were isolated, characterized in the genetically modified strains, and exhibited excellent antimicrobial activities. Next, we verified the hydroxyl methylation activity of LaphzM and elucidated the biosynthetic pathway of 1-methoxyphenazine N' 10-oxide in vitro. Moreover, the titer of 1-hydroxyphenazine derivatives was engineered. The three compounds 1-methoxyphenazine, 1-hydroxyphenazine N' 10-oxide, and 1-methoxyphenazine N' 10-oxide all reach the highest titer reported to date. This work provides a promising platform for phenazine derivatives' combinatorial biosynthesis and engineering.
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Affiliation(s)
- Yupeng Wan
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongchen Liu
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Wei Huang
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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Ke J, Zhao Z, Coates CR, Hadjithomas M, Kuftin A, Louie K, Weller D, Thomashow L, Mouncey NJ, Northen TR, Yoshikuni Y. Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE. Metab Eng 2021; 69:188-197. [PMID: 34890798 DOI: 10.1016/j.ymben.2021.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 02/08/2023]
Abstract
Phenazines (Phzs), a family of chemicals with a phenazine backbone, are secondary metabolites with diverse properties such as antibacterial, anti-fungal, or anticancer activity. The core derivatives of phenazine, phenazine-1-carboxylic acid (PCA) and phenazine-1,6-dicarboxylic acid (PDC), are themselves precursors for various other derivatives. Recent advances in genome mining tools have enabled researchers to identify many biosynthetic gene clusters (BGCs) that might produce novel Phzs. To characterize the function of these BGCs efficiently, we performed modular construct assembly and subsequent multi-chassis heterologous expression using chassis-independent recombinase-assisted genome engineering (CRAGE). CRAGE allowed rapid integration of a PCA BGC into 23 diverse γ-proteobacteria species and allowed us to identify top PCA producers. We then used the top five chassis hosts to express four partially refactored PDC BGCs. A few of these platforms produced high levels of PDC. Specifically, Xenorhabdus doucetiae and Pseudomonas simiae produced PDC at a titer of 293 mg/L and 373 mg/L, respectively, in minimal media. These titers are significantly higher than those previously reported. Furthermore, selectivity toward PDC production over PCA production was improved by up to 9-fold. The results show that these strains are promising chassis for production of PCA, PDC, and their derivatives, as well as for function characterization of Phz BGCs identified via bioinformatics mining.
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Affiliation(s)
- Jing Ke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhiying Zhao
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cameron R Coates
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michalis Hadjithomas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrea Kuftin
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine Louie
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Linda Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Nigel J Mouncey
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Global Center for Food, Land, and Water Resources, Hokkaido University, Hokkaido, 060-8589, Japan.
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11
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Functional Analysis of Phenazine Biosynthesis Genes in Burkholderia spp. Appl Environ Microbiol 2021; 87:AEM.02348-20. [PMID: 33741619 DOI: 10.1128/aem.02348-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/09/2021] [Indexed: 01/15/2023] Open
Abstract
Burkholderia encompasses a group of ubiquitous Gram-negative bacteria that includes numerous saprophytes as well as species that cause infections in animals, immunocompromised patients, and plants. Some species of Burkholderia produce colored, redox-active secondary metabolites called phenazines. Phenazines contribute to competitiveness, biofilm formation, and virulence in the opportunistic pathogen Pseudomonas aeruginosa, but knowledge of their diversity, biosynthesis, and biological functions in Burkholderia is lacking. In this study, we screened publicly accessible genome sequence databases and identified phenazine biosynthesis genes in multiple strains of the Burkholderia cepacia complex, some isolates of the B. pseudomallei clade, and the plant pathogen B. glumae We then focused on B. lata ATCC 17760 to reveal the organization and function of genes involved in the production of dimethyl 4,9-dihydroxy-1,6-phenazinedicarboxylate. Using a combination of isogenic mutants and plasmids carrying different segments of the phz locus, we characterized three novel genes involved in the modification of the phenazine tricycle. Our functional studies revealed a connection between the presence and amount of phenazines and the dynamics of biofilm growth in flow cell and static experimental systems but at the same time failed to link the production of phenazines with the capacity of Burkholderia to kill fruit flies and rot onions.IMPORTANCE Although the production of phenazines in Burkholderia was first reported almost 70 years ago, the role these metabolites play in the biology of these economically important microorganisms remains poorly understood. Our results revealed that the phenazine biosynthetic pathway in Burkholderia has a complex evolutionary history, which likely involved horizontal gene transfers among several distantly related groups of organisms. The contribution of phenazines to the formation of biofilms suggests that Burkholderia, like fluorescent pseudomonads, may benefit from the unique redox-cycling properties of these versatile secondary metabolites.
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12
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Panter F, Bader CD, Müller R. The Sandarazols are Cryptic and Structurally Unique Plasmid-Encoded Toxins from a Rare Myxobacterium*. Angew Chem Int Ed Engl 2021; 60:8081-8088. [PMID: 33534143 PMCID: PMC8048970 DOI: 10.1002/anie.202014671] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Herein, we describe a new plasmid found in Sandaracinus sp. MSr10575 named pSa001 spanning 209.7 kbp that harbors a cryptic secondary metabolite biosynthesis gene cluster (BGC). Activation of this BGC by homologous-recombination-mediated exchange of the native promoter sequence against a vanillate inducible system led to the production and subsequent isolation and structure elucidation of novel secondary metabolites, the sandarazols A-G. The sandarazols contain intriguing structural features and very reactive functional groups such as an α-chlorinated ketone, an epoxyketone, and a (2R)-2-amino-3-(N,N-dimethylamino)-propionic acid building block. In-depth investigation of the underlying biosynthetic machinery led to a concise biosynthetic model for the new compound family, including several uncommon biosynthetic steps. The chlorinated congener sandarazol C shows an IC50 value of 0.5 μm against HCT 116 cells and a MIC of 14 μm against Mycobacterium smegmatis, which points at the sandarazols' potential function as defensive secondary metabolites or toxins.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
- Helmholtz International Lab for Anti-Infectives, Campus E8 166123SaarbrückenGermany
| | - Chantal D. Bader
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
| | - Rolf Müller
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
- Helmholtz International Lab for Anti-Infectives, Campus E8 166123SaarbrückenGermany
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13
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Panter F, Bader CD, Müller R. Die Sandarazole sind kryptische und strukturell einzigartige, Plasmid‐codierte Toxine aus einem seltenen Myxobakterium**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fabian Panter
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
- Helmholtz International Lab for Anti-Infectives, Campus E8 1 66123 Saarbrücken Deutschland
| | - Chantal D. Bader
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
| | - Rolf Müller
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
- Helmholtz International Lab for Anti-Infectives, Campus E8 1 66123 Saarbrücken Deutschland
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14
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Guo S, Wang Y, Bilal M, Hu H, Wang W, Zhang X. Microbial Synthesis of Antibacterial Phenazine-1,6-dicarboxylic Acid and the Role of PhzG in Pseudomonas chlororaphis GP72AN. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2373-2380. [PMID: 32013409 DOI: 10.1021/acs.jafc.9b07657] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pseudomonas chlororaphis have been demonstrated to be environmentally friendly biocontrol strains, and most of them can produce phenazine compounds. Phenazine-1,6-dicarboxylic acid (PDC), with a potential antibacterial activity, is generally found in Streptomyces but not in Pseudomonas. The present study aimed to explore the feasibility of PDC synthesis and the function of PhzG in Pseudomonas. A PDC producer was constructed by replacing phzG in P. chlororaphis with lphzG from Streptomyces lomondensis. Through gene deletion, common start codon changing, gene silence, and in vitro assay, our result revealed that the yield of PDC in P. chlororaphis is associated with the relative expression of phzG to phzA and phzB. In addition, it is found that PDC can be spontaneously synthesized without PhzG. This study provides an efficient way for PDC production and promotes a better understanding of PhzG function in PDC biosynthesis. Moreover, this study gives an alternative opportunity for developing new antibacterial biopesticides.
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Affiliation(s)
- Shuqi Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Yining Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
- National Experimental Teaching Center for Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
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15
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Whole Genome Sequence of Dermacoccus abyssi MT1.1 Isolated from the Challenger Deep of the Mariana Trench Reveals Phenazine Biosynthesis Locus and Environmental Adaptation Factors. Mar Drugs 2020; 18:md18030131. [PMID: 32106586 PMCID: PMC7143476 DOI: 10.3390/md18030131] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/21/2022] Open
Abstract
Dermacoccus abyssi strain MT1.1T is a piezotolerant actinobacterium that was isolated from Mariana Trench sediment collected at a depth of 10898 m. The organism was found to produce ten dermacozines (A‒J) that belonged to a new phenazine family and which displayed various biological activities such as radical scavenging and cytotoxicity. Here, we report on the isolation and identification of a new dermacozine compound, dermacozine M, the chemical structure of which was determined using 1D and 2D-NMR, and high resolution MS. A whole genome sequence of the strain contained six secondary metabolite-biosynthetic gene clusters (BGCs), including one responsible for the biosynthesis of a family of phenazine compounds. A pathway leading to the biosynthesis of dermacozines is proposed. Bioinformatic analyses of key stress-related genes provide an insight into how the organism adapted to the environmental conditions that prevail in the deep-sea.
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16
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Liu D, Yan R, Fu Y, Wang X, Zhang J, Xiang W. Antifungal, Plant Growth-Promoting, and Genomic Properties of an Endophytic Actinobacterium Streptomyces sp. NEAU-S7GS2. Front Microbiol 2019; 10:2077. [PMID: 31551997 PMCID: PMC6746918 DOI: 10.3389/fmicb.2019.02077] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 08/22/2019] [Indexed: 11/23/2022] Open
Abstract
Diseases caused by Sclerotinia sclerotiorum have caused severe losses of many economically important crops worldwide. Due to the long-term persistence of sclerotia in soil and the production of air-borne ascospores, synthetic fungicides play limited roles in controlling the diseases. The application of antagonistic microorganisms can effectively reduce the number of sclerotia and eventually eradicate S. sclerotiorum from soil, and therefore considerable interest has been focused on biological control. Streptomyces sp. NEAU-S7GS2 was isolated from the root of Glycine max and its rhizosphere soil. It showed significant inhibitory activity against the mycelial growth of S. sclerotiorum (99.1%) and completely inhibited sclerotia germination. Compared to the control, in the pot experiment the application of NEAU-S7GS2 not only demonstrated excellent potential to control sclerotinia stem rot of soybean with 77 and 38% decrease in disease incidence and disease index, respectively, but could promote the growth of soybean. The light microscopy and scanning electron microscopy showed that co-culture of NEAU-S7GS2 with S. sclerotiorum on potato dextrose agar could lead to contorted and fragmented mycelia of S. sclerotiorum, which was associated with the secretion of hydrolytic glucanase and cellulase and the production of active secondary metabolites by NEAU-S7GS2. The plant growth promoting activity of NEAU-S7GS2 was related to the solubilization of inorganic phosphate, and production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase and indole acetic acid (IAA). To further explore the plant growth promoting and antifungal mechanisms, the complete genome of strain NEAU-S7GS2 was sequenced. Several genes associated with ammonia assimilation, phosphate solubilization and IAA synthesis, together with genes encoding ACC deaminase, glucanase and α-amylase, were identified. AntiSMASH analysis led to the identification of four gene clusters responsible for the biosynthesis of siderophores including desferrioxamine B and enterobactin. Moreover, the biosynthetic gene clusters of lydicamycins, phenazines, and a glycosylated polyol macrolide showing 88% gene similarity to PM100117/PM100118 were identified. These results suggested that strain NEAU-S7GS2 may be a potential biocontrol agent and biofertilizer used in agriculture.
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Affiliation(s)
- Dongli Liu
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China
| | - Rui Yan
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China
| | - Yansong Fu
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China
| | - Xiangjing Wang
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China
| | - Ji Zhang
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China
| | - Wensheng Xiang
- Heilongjiang Provinical Key Laboratory of Agricultural Microbiology, Northeast Agricultural University, Harbin, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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17
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Lee HS, Kang JS, Choi BK, Lee HS, Lee YJ, Lee J, Shin HJ. Phenazine Derivatives with Anti-Inflammatory Activity from the Deep-Sea Sediment-Derived Yeast-Like Fungus Cystobasidium laryngis IV17-028. Mar Drugs 2019; 17:md17080482. [PMID: 31430989 PMCID: PMC6722648 DOI: 10.3390/md17080482] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 11/19/2022] Open
Abstract
Three new phenazine derivatives (1–3), along with known compounds (4–7) of saphenic acid derivatives, were isolated from a deep-sea sediment-derived yeast-like fungus Cystobasidium larynigs collected from the Indian Ocean. The structures of the new compounds (1–3) were determined by analysis of spectroscopic data, semi-synthesis and comparison of optical rotation values. All the isolated compounds (1–7), except for 2, showed nitric oxide (NO) production inhibitory effect against lipopolysaccharide (LPS)-induced murine macrophage RAW 264.7 cells without cytotoxicity at concentrations up to 30 μg/mL. This is the first report on the yeast-like fungus Cystobasidium laryngis producing phenazines and anti-inflammatory activity of 1–7 including saphenic acid (4).
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Affiliation(s)
- Hwa-Sun Lee
- Marine Natural Products Chemistry Laboratory, Korea Institute of Ocean Science Technology, 385 Haeyang-ro, Yeongdo-gu, Busan 49111, Korea
| | - Jong Soon Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudangi-ro, Ochang-eup, Cheongwon-gu, Cheongju 28116, Korea
| | - Byeoung-Kyu Choi
- Marine Natural Products Chemistry Laboratory, Korea Institute of Ocean Science Technology, 385 Haeyang-ro, Yeongdo-gu, Busan 49111, Korea
| | - Hyi-Seung Lee
- Marine Natural Products Chemistry Laboratory, Korea Institute of Ocean Science Technology, 385 Haeyang-ro, Yeongdo-gu, Busan 49111, Korea
| | - Yeon-Ju Lee
- Marine Natural Products Chemistry Laboratory, Korea Institute of Ocean Science Technology, 385 Haeyang-ro, Yeongdo-gu, Busan 49111, Korea
| | - Jihoon Lee
- Marine Natural Products Chemistry Laboratory, Korea Institute of Ocean Science Technology, 385 Haeyang-ro, Yeongdo-gu, Busan 49111, Korea
| | - Hee Jae Shin
- Marine Natural Products Chemistry Laboratory, Korea Institute of Ocean Science Technology, 385 Haeyang-ro, Yeongdo-gu, Busan 49111, Korea.
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18
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Bauman KD, Li J, Murata K, Mantovani SM, Dahesh S, Nizet V, Luhavaya H, Moore BS. Refactoring the Cryptic Streptophenazine Biosynthetic Gene Cluster Unites Phenazine, Polyketide, and Nonribosomal Peptide Biochemistry. Cell Chem Biol 2019; 26:724-736.e7. [PMID: 30853419 PMCID: PMC6525064 DOI: 10.1016/j.chembiol.2019.02.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/02/2019] [Accepted: 01/31/2019] [Indexed: 11/28/2022]
Abstract
The disconnect between the genomic prediction of secondary metabolite biosynthetic potential and the observed laboratory production profile of microorganisms is well documented. While heterologous expression of biosynthetic gene clusters (BGCs) is often seen as a potential solution to bridge this gap, it is not immune to many challenges including impaired regulation, the inability to recruit essential building blocks, and transcriptional and/or translational silence of the biosynthetic genes. Here we report the discovery, cloning, refactoring, and heterologous expression of a cryptic hybrid phenazine-type BGC (spz) from the marine actinomycete Streptomyces sp. CNB-091. Overexpression of the engineered spz pathway resulted in increased production and chemical diversity of phenazine natural products belonging to the streptophenazine family, including bioactive members containing an unprecedented N-formylglycine attachment. An atypical discrete adenylation enzyme in the spz cluster is required to introduce the formylglycine moiety and represents a phylogenetically distinct class of adenylation proteins.
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Affiliation(s)
- Katherine D Bauman
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Jie Li
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Kazuya Murata
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Simone M Mantovani
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Samira Dahesh
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA
| | - Victor Nizet
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA; Collaborative to Halt Antibiotic Resistant Microbes, University of California at San Diego, La Jolla, CA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA
| | - Hanna Luhavaya
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
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19
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Nofiani R, Philmus B, Nindita Y, Mahmud T. 3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis. MEDCHEMCOMM 2019; 10:1517-1530. [PMID: 31673313 DOI: 10.1039/c9md00162j] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 11/21/2022]
Abstract
The 3-ketoacyl-ACP synthase (KAS) III proteins are one of the most abundant enzymes in nature, as they are involved in the biosynthesis of fatty acids and natural products. KAS III enzymes catalyse a carbon-carbon bond formation reaction that involves the α-carbon of a thioester and the carbonyl carbon of another thioester. In addition to the typical KAS III enzymes involved in fatty acid and polyketide biosynthesis, there are proteins homologous to KAS III enzymes that catalyse reactions that are different from that of the traditional KAS III enzymes. Those include enzymes that are responsible for a head-to-head condensation reaction, the formation of acetoacetyl-CoA in mevalonate biosynthesis, tailoring processes via C-O bond formation or esterification, as well as amide formation. This review article highlights the diverse reactions catalysed by this class of enzymes and their role in natural product biosynthesis.
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Affiliation(s)
- Risa Nofiani
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA . .,Department of Chemistry , Universitas Tanjungpura , Pontianak , Indonesia
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Yosi Nindita
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
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20
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Shi YM, Brachmann AO, Westphalen MA, Neubacher N, Tobias NJ, Bode HB. Dual phenazine gene clusters enable diversification during biosynthesis. Nat Chem Biol 2019; 15:331-339. [PMID: 30886436 DOI: 10.1038/s41589-019-0246-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 02/13/2019] [Indexed: 11/10/2022]
Abstract
Biosynthetic gene clusters (BGCs) bridging genotype and phenotype continuously evolve through gene mutations and recombinations to generate chemical diversity. Phenazine BGCs are widespread in bacteria, and the biosynthetic mechanisms of the formation of the phenazine structural core have been illuminated in the last decade. However, little is known about the complex phenazine core-modification machinery. Here, we report the diversity-oriented modifications of the phenazine core through two distinct BGCs in the entomopathogenic bacterium Xenorhabdus szentirmaii, which lives in symbiosis with nematodes. A previously unidentified aldehyde intermediate, which can be modified by multiple enzymatic and non-enzymatic reactions, is a common intermediate bridging the pathways encoded by these BGCs. Evaluation of the antibiotic activity of the resulting phenazine derivatives suggests a highly effective strategy to convert Gram-positive specific phenazines into broad-spectrum antibiotics, which might help the bacteria-nematode complex to maintain its special environmental niche.
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Affiliation(s)
- Yi-Ming Shi
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Alexander O Brachmann
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany.,Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Margaretha A Westphalen
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Nick Neubacher
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Nicholas J Tobias
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany. .,Buchmann Institute for Molecular Life Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany.
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21
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Generation of a cluster-free Streptomyces albus chassis strains for improved heterologous expression of secondary metabolite clusters. Metab Eng 2018; 49:316-324. [DOI: 10.1016/j.ymben.2018.09.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/26/2018] [Accepted: 09/05/2018] [Indexed: 12/19/2022]
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22
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Coates RC, Bowen BP, Oberortner E, Thomashow L, Hadjithomas M, Zhao Z, Ke J, Silva L, Louie K, Wang G, Robinson D, Tarver A, Hamilton M, Lubbe A, Feltcher M, Dangl JL, Pati A, Weller D, Northen TR, Cheng JF, Mouncey NJ, Deutsch S, Yoshikuni Y. An integrated workflow for phenazine-modifying enzyme characterization. ACTA ACUST UNITED AC 2018; 45:567-577. [DOI: 10.1007/s10295-018-2025-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/09/2018] [Indexed: 02/04/2023]
Abstract
Abstract
Increasing availability of new genomes and putative biosynthetic gene clusters (BGCs) has extended the opportunity to access novel chemical diversity for agriculture, medicine, environmental and industrial purposes. However, functional characterization of BGCs through heterologous expression is limited because expression may require complex regulatory mechanisms, specific folding or activation. We developed an integrated workflow for BGC characterization that integrates pathway identification, modular design, DNA synthesis, assembly and characterization. This workflow was applied to characterize multiple phenazine-modifying enzymes. Phenazine pathways are useful for this workflow because all phenazines are derived from a core scaffold for modification by diverse modifying enzymes (PhzM, PhzS, PhzH, and PhzO) that produce characterized compounds. We expressed refactored synthetic modules of previously uncharacterized phenazine BGCs heterologously in Escherichia coli and were able to identify metabolic intermediates they produced, including a previously unidentified metabolite. These results demonstrate how this approach can accelerate functional characterization of BGCs.
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Affiliation(s)
- R Cameron Coates
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Benjamin P Bowen
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Ernst Oberortner
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Linda Thomashow
- 0000 0001 2157 6568 grid.30064.31 USDA Agricultural Research Service, Wheat Health, Genetics and Quality Washington State University Pullman WA USA
- 0000 0001 2157 6568 grid.30064.31 Department of Plant Pathology Washington State University Pullman WA USA
| | - Michalis Hadjithomas
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Zhiying Zhao
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Jing Ke
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Leslie Silva
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Katherine Louie
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Gaoyan Wang
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - David Robinson
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Angela Tarver
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Matthew Hamilton
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Andrea Lubbe
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Meghan Feltcher
- 0000000122483208 grid.10698.36 Department of Biology University of North Carolina at Chapel Hill Chapel Hill NC USA
| | - Jeffery L Dangl
- 0000000122483208 grid.10698.36 Department of Biology University of North Carolina at Chapel Hill Chapel Hill NC USA
- 0000000122483208 grid.10698.36 Howard Hughes Medical Institute University of North Carolina at Chapel Hill Chapel Hill NC USA
- 0000000122483208 grid.10698.36 Curriculum in Genetics and Molecular Biology University of North Carolina at Chapel Hill Chapel Hill NC USA
- 0000000122483208 grid.10698.36 Department of Microbiology and Immunology University of North Carolina at Chapel Hill Chapel Hill NC USA
- 0000000122483208 grid.10698.36 Carolina Center for Genome Sciences University of North Carolina at Chapel Hill Chapel Hill NC USA
| | - Amrita Pati
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - David Weller
- 0000 0001 2157 6568 grid.30064.31 USDA Agricultural Research Service, Wheat Health, Genetics and Quality Washington State University Pullman WA USA
- 0000 0001 2157 6568 grid.30064.31 Department of Plant Pathology Washington State University Pullman WA USA
| | - Trent R Northen
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Jan-Fang Cheng
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Nigel J Mouncey
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
| | - Samuel Deutsch
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
- 0000 0001 2231 4551 grid.184769.5 Biological Systems and Engineering Division Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Yasuo Yoshikuni
- 0000 0004 0449 479X grid.451309.a US DOE Joint Genome Institute Walnut Creek CA USA
- 0000 0001 2231 4551 grid.184769.5 Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA
- 0000 0001 2231 4551 grid.184769.5 Biological Systems and Engineering Division Lawrence Berkeley National Laboratory Berkeley CA USA
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23
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Guo S, Wang Y, Dai B, Wang W, Hu H, Huang X, Zhang X. PhzA, the shunt switch of phenazine-1,6-dicarboxylic acid biosynthesis in Pseudomonas chlororaphis HT66. Appl Microbiol Biotechnol 2017; 101:7165-7175. [PMID: 28871340 DOI: 10.1007/s00253-017-8474-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/30/2017] [Accepted: 08/03/2017] [Indexed: 11/29/2022]
Abstract
Natural phenazines are versatile secondary metabolites that are mainly produced by Pseudomonas and Streptomyces. All phenazine-type metabolites originate from two precursors: phenazine-1-carboxylic acid (PCA) in Pseudomonas or phenazine-1,6-dicarboxylic acid (PDC) in Streptomyces and other bacteria. Although the biosynthesis of PCA in Pseudomonas has been extensively studied, the origin of PDC still remains unclear. Comparing the phenazine biosynthesis operons of different species, we found that the phzA gene was restricted to Pseudomonas in which PCA is produced. By generating phzA-inactivated mutant, we found a new compound obviously accumulated; it was then isolated and identified as PDC. Protein sequence alignment showed that PhzA proteins from Pseudomonas form a separate group that is recognized by H73L and S77L mutations. Generating mutations of L73 into H73 and L77 into S77 resulted in a significant increase in PDC production. These findings suggest that phzA may act as a shunt switch of PDC biosynthesis in Pseudomonas and distinguish the pathway producing only PCA from the pathway forming PCA plus PDC. Using real-time PCR analysis, we suggested that the phzA, phzB, and phzG genes either directly or indirectly regulate the production of PDC, and phzA plays the most significant regulatory role. This is the first description of phzA in the biosynthesis of PDC, and the first-time substantial PDC was obtained in Pseudomonas. Therefore, this study not only provides valuable clues to better understand the biosynthesis of PCA and PDC in Pseudomonas but also introduces a method to produce PDC derivatives by genetically engineered strains.
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Affiliation(s)
- Shuqi Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yining Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bona Dai
- Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xianqing Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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24
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Losada AA, Cano-Prieto C, García-Salcedo R, Braña AF, Méndez C, Salas JA, Olano C. Caboxamycin biosynthesis pathway and identification of novel benzoxazoles produced by cross-talk in Streptomyces sp. NTK 937. Microb Biotechnol 2017; 10:873-885. [PMID: 28417606 PMCID: PMC5481532 DOI: 10.1111/1751-7915.12716] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/01/2017] [Accepted: 03/20/2017] [Indexed: 12/13/2022] Open
Abstract
Streptomyces sp. NTK937, producer of benzoxazole antibiotic caboxamycin, produces in addition a methyl ester derivative, O‐methylcaboxamycin. Caboxamycin cluster, comprising one regulatory and nine structural genes, has been delimited, and each gene has been individually inactivated to demonstrate its role in the biosynthetic process. The O‐methyltransferase potentially responsible for O‐methylcaboxamycin synthesis would reside outside this cluster. Five of the genes, cbxR, cbxA, cbxB, cbxD and cbxE, encoding a SARP transcriptional regulator, salicylate synthase, 3‐oxoacyl‐ACP‐synthase, ACP and amidohydrolase, respectively, have been found to be essential for caboxamycin biosynthesis. The remaining five structural genes were found to have paralogues distributed throughout the genome, capable of partaking in the process when their cluster homologue is inactivated. Two of such paralogues, cbxC’ and cbxI’, coding an AMP‐dependent synthetase‐ligase and an anthranilate synthase, respectively, have been identified. However, the other three genes might simultaneously have more than one paralogue, given that cbxF (DAHP synthase), cbxG (2,3‐dihydro‐2,3‐dihydroxybenzoate dehydrogenase) and cbxH (isochorismatase) have three, three and five putative paralogue genes, respectively, of similar function within the genome. As a result of genetic manipulation, a novel benzoxazole (3′‐hydroxycaboxamycin) has been identified in the salicylate synthase‐deficient mutant strain ΔcbxA. 3′‐hydroxycaboxamycin derives from the cross‐talk between the caboxamycin and enterobactin pathways.
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Affiliation(s)
- Armando A Losada
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Carolina Cano-Prieto
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Raúl García-Salcedo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, 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, 33006, 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, 33006, Oviedo, 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, 33006, Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
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25
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Li Z, Du L, Zhang W, Zhang X, Jiang Y, Liu K, Men P, Xu H, Fortman JL, Sherman DH, Yu B, Gao S, Li S. Complete elucidation of the late steps of bafilomycin biosynthesis in Streptomyces lohii. J Biol Chem 2017; 292:7095-7104. [PMID: 28292933 DOI: 10.1074/jbc.m116.751255] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/27/2017] [Indexed: 11/06/2022] Open
Abstract
Bafilomycins are an important subgroup of polyketides with diverse biological activities and possible applications as specific inhibitors of vacuolar H+-ATPase. However, the general toxicity and structural complexity of bafilomycins present formidable challenges to drug design via chemical modification, prompting interests in improving bafilomycin activities via biosynthetic approaches. Two bafilomycin biosynthetic gene clusters have been identified, but their post-polyketide synthase (PKS) tailoring steps for structural diversification and bioactivity improvement remain largely unknown. In this study, the post-PKS tailoring pathway from bafilomycin A1 (1)→C1 (2)→B1 (3) in the marine microorganism Streptomyces lohii was elucidated for the first time by in vivo gene inactivation and in vitro biochemical characterization. We found that fumarate is first adenylated by a novel fumarate adenylyltransferase Orf3. Then, the fumaryl transferase Orf2 is responsible for transferring the fumarate moiety from fumaryl-AMP to the 21-hydroxyl group of 1 to generate 2. Last, the ATP-dependent amide synthetase BafY catalyzes the condensation of 2 and 2-amino-3-hydroxycyclopent-2-enone (C5N) produced by the 5-aminolevulinic acid synthase BafZ and the acyl-CoA ligase BafX, giving rise to the final product 3. The elucidation of fumarate incorporation mechanism represents the first paradigm for biosynthesis of natural products containing the fumarate moiety. Moreover, the bafilomycin post-PKS tailoring pathway features an interesting cross-talk between primary and secondary metabolisms for natural product biosynthesis. Taken together, this work provides significant insights into bafilomycin biosynthesis to inform future pharmacological development of these compounds.
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Affiliation(s)
- Zhong Li
- From the Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101.,the University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Du
- From the Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101.,the University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhang
- From the Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101
| | - Xingwang Zhang
- From the Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101
| | - Yuanyuan Jiang
- From the Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101.,the University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Liu
- From the Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101
| | - Ping Men
- From the Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101
| | - Huifang Xu
- From the Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101
| | - Jeffrey L Fortman
- the Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, and
| | - David H Sherman
- the Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, and
| | - Bing Yu
- the State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Song Gao
- the State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Shengying Li
- From the Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101,
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26
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Abugrain ME, Brumsted CJ, Osborn AR, Philmus B, Mahmud T. A Highly Promiscuous ß-Ketoacyl-ACP Synthase (KAS) III-like Protein Is Involved in Pactamycin Biosynthesis. ACS Chem Biol 2017; 12:362-366. [PMID: 28060484 DOI: 10.1021/acschembio.6b01043] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
β-Ketoacyl-acyl carrier protein (β-Ketoacyl-ACP) synthase (KAS) III catalyzes the first step in fatty acid biosynthesis, involving a Claisen condensation of the acetyl-CoA starter unit with the first extender unit, malonyl-ACP, to form acetoacetyl-ACP. KAS III-like proteins have also been reported to catalyze acyltransferase reactions using coenzyme A esters or discrete ACP-bound substrates. Here, we report the in vivo and in vitro characterizations of a KAS III-like protein (PtmR), which directly transfers a 6-methylsalicylyl moiety from an iterative type I polyketide synthase to an aminocyclopentitol unit in pactamycin biosynthesis. PtmR is highly promiscuous, recognizing a wide array of S-acyl-N-acetylcysteamines as substrates to produce a suite of pactamycin derivatives with diverse alkyl and aromatic features. The results suggest that KAS III-like proteins may be used as versatile tools for modifications of complex natural products.
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Affiliation(s)
- Mostafa E. Abugrain
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97333, United States
| | - Corey J. Brumsted
- Department
of Chemistry, Oregon State University, Corvallis, Oregon 97333, United States
| | - Andrew R. Osborn
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97333, United States
| | - Benjamin Philmus
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97333, United States
| | - Taifo Mahmud
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97333, United States
- Department
of Chemistry, Oregon State University, Corvallis, Oregon 97333, United States
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27
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Isolation of phenazine 1,6-di-carboxylic acid from Pseudomonas aeruginosa strain HRW.1-S3 and its role in biofilm-mediated crude oil degradation and cytotoxicity against bacterial and cancer cells. Appl Microbiol Biotechnol 2015; 99:8653-65. [PMID: 26051670 DOI: 10.1007/s00253-015-6707-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/08/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
Abstract
Pseudomonas sp. has long been known for production of a wide range of secondary metabolites during late exponential and stationary phases of growth. Phenazine derivatives constitute a large group of secondary metabolites produced by microorganisms including Pseudomonas sp. Phenazine 1,6-di-carboxylic acid (PDC) is one of such metabolites and has been debated for its origin from Pseudomonas sp. The present study describes purification and characterization of PDC isolated from culture of a natural isolate of Pseudomonas sp. HRW.1-S3 while grown in presence of crude oil as sole carbon source. The isolated PDC was tested for its effect on biofilm formation by another environmental isolate of Pseudomonas sp. DSW.1-S4 which lacks the ability to produce any phenazine compound. PDC showed profound effect on both planktonic as well as biofilm mode of growth of DSW.1-S4 at concentrations between 5 and 20 μM. Interestingly, PDC showed substantial cytotoxicity against three cancer cell lines and against both Gram-positive and Gram-negative bacteria. Thus, the present study not only opens an avenue to understand interspecific cooperation between Pseudomonas species which may lead its applicability in bioremediation, but also it signifies the scope of future investigation on PDC for its therapeutic applications.
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28
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Cano-Prieto C, García-Salcedo R, Sánchez-Hidalgo M, Braña AF, Fiedler HP, Méndez C, Salas JA, Olano C. Genome Mining of Streptomyces sp. Tü 6176: Characterization of the Nataxazole Biosynthesis Pathway. Chembiochem 2015; 16:1461-73. [PMID: 25892546 DOI: 10.1002/cbic.201500153] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Indexed: 11/11/2022]
Abstract
Streptomyces sp. Tü 6176 produces the cytotoxic benzoxazole nataxazole. Bioinformatic analysis of the genome of this organism predicts the presence of 38 putative secondary-metabolite biosynthesis gene clusters, including those involved in the biosynthesis of AJI9561 and its derivative nataxazole, the antibiotic hygromycin B, and ionophores enterobactin and coelibactin. The nataxazole biosynthesis gene cluster was identified and characterized: it lacks the O-methyltransferase gene required to convert AJI9561 into nataxazole. This O-methyltransferase activity might act as a resistance mechanism, as AJI9561 shows antibiotic activity whereas nataxazole is inactive. Moreover, heterologous expression of the nataxazole biosynthesis gene cluster in S. lividans JT46 resulted in the production of AJI9561. Nataxazole biosynthesis requires the shikimate pathway to generate 3-hydroxyanthranilate and an iterative type I PKS to generate 6-methylsalicylate. Production of nataxazole was improved up to fourfold by disrupting one regulatory gene in the cluster. An additional benzoxazole, 5-hydroxynataxazole is produced by Streptomyces sp. Tü 6176. 5-Hydroxynataxazole derives from nataxazole by the activity of an as yet unidentified oxygenase; this implies cross-talk between the nataxazole biosynthesis pathway and an unknown pathway.
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Affiliation(s)
- Carolina Cano-Prieto
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería S/N, 33006 Oviedo (Spain)
| | - Raúl García-Salcedo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería S/N, 33006 Oviedo (Spain)
| | - Marina Sánchez-Hidalgo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería S/N, 33006 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, C/ Julian Clavería S/N, 33006 Oviedo (Spain)
| | - Hans-Peter Fiedler
- Mikrobiologisches Institut, Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen (Germany)
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería S/N, 33006 Oviedo (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, C/ Julian Clavería S/N, 33006 Oviedo (Spain)
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería S/N, 33006 Oviedo (Spain).
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29
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Wu C, van Wezel GP, Hae Choi Y. Identification of novel endophenaside antibiotics produced by Kitasatospora sp. MBT66. J Antibiot (Tokyo) 2015; 68:445-52. [DOI: 10.1038/ja.2015.14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/12/2015] [Accepted: 01/21/2015] [Indexed: 01/24/2023]
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30
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Blankenfeldt W, Parsons JF. The structural biology of phenazine biosynthesis. Curr Opin Struct Biol 2014; 29:26-33. [PMID: 25215885 DOI: 10.1016/j.sbi.2014.08.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/25/2014] [Indexed: 01/28/2023]
Abstract
The phenazines are a class of over 150 nitrogen-containing aromatic compounds of bacterial and archeal origin. Their redox properties not only explain their activity as broad-specificity antibiotics and virulence factors but also enable them to function as respiratory pigments, thus extending their importance to the primary metabolism of phenazine-producing species. Despite their discovery in the mid-19th century, the molecular mechanisms behind their biosynthesis have only been unraveled in the last decade. Here, we review the contribution of structural biology that has led to our current understanding of phenazine biosynthesis.
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Affiliation(s)
- Wulf Blankenfeldt
- Helmholtz Centre for Infection Research, Structure and Function of Proteins, Inhoffenstr. 7, 38124 Braunschweig, Germany.
| | - James F Parsons
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
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Abstract
The most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a DNA-binding domain. Among the >20 classes of one-component systems, the TetR family of regulators (TFRs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. However, TFRs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and many other aspects of prokaryotic physiology. There are several well-established model systems for understanding these important proteins, and structural studies have begun to unveil the mechanisms by which they bind DNA and recognize small-molecule ligands. The sequences for more than 200,000 TFRs are available in the public databases, and genomics studies are identifying their target genes. Three-dimensional structures have been solved for close to 200 TFRs. Comparison of these structures reveals a common overall architecture of nine conserved α helices. The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.
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32
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Xu N, Ahuja EG, Janning P, Mavrodi DV, Thomashow LS, Blankenfeldt W. Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1403-13. [PMID: 23897464 DOI: 10.1107/s0907444913008354] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 03/26/2013] [Indexed: 11/10/2022]
Abstract
Phenazines are redox-active secondary metabolites that many bacteria produce and secrete into the environment. They are broad-specificity antibiotics, but also act as virulence and survival factors in infectious diseases. Phenazines are derived from chorismic acid, but important details of their biosynthesis are still unclear. For example, three two-electron oxidations seem to be necessary in the final steps of the pathway, while only one oxidase, the FMN-dependent PhzG, is conserved in the phenazine-biosynthesis phz operon. Here, crystal structures of PhzG from Pseudomonas fluorescens 2-79 and from Burkholderia lata 383 in complex with excess FMN and with the phenazine-biosynthesis intermediates hexahydrophenazine-1,6-dicarboxylate and tetrahydrophenazine-1-carboxylate generated in situ are reported. Corroborated with biochemical data, these complexes demonstrate that PhzG is the terminal enzyme in phenazine biosynthesis and that its relaxed substrate specificity lets it participate in the generation of both phenazine-1,6-dicarboxylic acid (PDC) and phenazine-1-carboxylic acid (PCA). This suggests that competition between flavin-dependent oxidations through PhzG and spontaneous oxidative decarboxylations determines the ratio of PDC, PCA and unsubstituted phenazine as the products of phenazine biosynthesis. Further, the results indicate that PhzG synthesizes phenazines in their reduced form. These reduced molecules, and not the fully aromatized derivatives, are the likely end products in vivo, explaining why only one oxidase is required in the phenazine-biosynthesis pathway.
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Affiliation(s)
- Ningna Xu
- Lehrstuhl für Biochemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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